turkunlp.bib

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@inproceedings{kupari-etal-2024-improving,
    title = "Improving {L}atin Dependency Parsing by Combining Treebanks and Predictions",
    author = "Kupari, Hanna-Mari and Henriksson, Erik and Laippala, Veronika and Kanerva, Jenna",
    booktitle = "Proceedings of the 4th International Conference on Natural Language Processing for Digital Humanities (NLP4DH'2024)",
    year = "2024",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2024.nlp4dh-1.21",
    doi = "10.18653/v1/2024.nlp4dh-1.21",
    pages = "216--228",
}

@inproceedings{myntti-etal-2024-intersecting,
    title = "Intersecting Register and Genre: Understanding the Contents of Web-Crawled Corpora",
    author = "Myntti, Amanda  and
      Repo, Liina  and
      Freyermuth, Elian  and
      Kanner, Antti  and
      Laippala, Veronika  and
      Henriksson, Erik",
    editor = {H{\"a}m{\"a}l{\"a}inen, Mika  and
      {\"O}hman, Emily  and
      Miyagawa, So  and
      Alnajjar, Khalid  and
      Bizzoni, Yuri},
    booktitle = "Proceedings of the 4th International Conference on Natural Language Processing for Digital Humanities",
    month = nov,
    year = "2024",
    address = "Miami, USA",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2024.nlp4dh-1.38",
    doi = "10.18653/v1/2024.nlp4dh-1.38",
    pages = "386--397",
}

@inproceedings{laato2024karelians,
   title = "Extracting social connections from {F}innish {K}arelian refugee interviews using {LLMs}",
   author = {Laato, Joonatan and Kanerva, Jenna and Loehr, John and Lummaa, Virpi and Ginter, Filip},
   booktitle={Proceedings of Fifth Conference on Computational Humanities Research (CHR'2024)},
   url={https://ceur-ws.org/Vol-3834/paper52.pdf}
   year={2024},
}


@inproceedings{eskelinen2024registerqa,
    title = "Building Question-Answer Data Using Web Register Identification",
    author = "Eskelinen, Anni  and
      Myntti, Amanda  and
      Henriksson, Erik  and
      Pyysalo, Sampo  and
      Laippala, Veronika",
    editor = "Calzolari, Nicoletta  and
      Kan, Min-Yen  and
      Hoste, Veronique  and
      Lenci, Alessandro  and
      Sakti, Sakriani  and
      Xue, Nianwen",
    booktitle = "Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024)",
    month = "may",
    year = "2024",
    address = "Torino, Italia",
    publisher = "ELRA and ICCL",
    url = "https://aclanthology.org/2024.lrec-main.234",
    pages = "2595--2611",
}

@article{kanerva2024semanticsearch,
    	author = {Jenna Kanerva and Hanna Kitti and Li-Hsin Chang and Teemu Vahtola and Mathias Creutz and Filip Ginter},
    	title = {Semantic Search as Extractive Paraphrase Span Detection},
    	journal = {Language Resources and Evaluation},
	year = {2024},
	url = {https://link.springer.com/article/10.1007/s10579-023-09715-7}
}

@inproceedings{chang2024asagchatgpt,
	title = {Automatic Short Answer Grading for Finnish with ChatGPT},
	author = {Chang, Li-Hsin and Ginter, Filip},
	booktitle = {Proceedings of the AAAI Conference on Artificial Intelligence},
	year = {2024},
	volume = {38},
	url = {https://ojs.aaai.org/index.php/AAAI/article/view/30363},
	doi = {10.1609/aaai.v38i21.30363},
	number = {21},
	month = {Mar.},
	pages = {23173-23181}
}

@article{skantsi2023analyzing,
  title={Analyzing the unrestricted web: The finnish corpus of online registers},
  author={Skantsi, Valtteri and Laippala, Veronika},
  journal={Nordic Journal of Linguistics},
  pages={1--31},
  publisher={Cambridge University Press},
	year = {2024},
	url = {https://www.cambridge.org/core/journals/nordic-journal-of-linguistics/article/analyzing-the-unrestricted-web-the-finnish-corpus-of-online-registers/BDCA0FE03ABD9087CC5652533880C8C0}
}

@inproceedings{muennighoff2023scaling,
      title={Scaling Data-Constrained Language Models},
      author={Niklas Muennighoff and Alexander M. Rush and Boaz Barak and Teven Le Scao and Aleksandra Piktus and Nouamane Tazi and Sampo Pyysalo and Thomas Wolf and Colin Raffel},
      year={2023},
      booktitle={NeurIPS},
}

@inproceedings{luukkonen-etal-2023-fingpt,
    title = "{F}in{GPT}: Large Generative Models for a Small Language",
    author = "Luukkonen, Risto  and
      Komulainen, Ville  and
      Luoma, Jouni  and
      Eskelinen, Anni  and
      Kanerva, Jenna  and
      Kupari, Hanna-Mari  and
      Ginter, Filip  and
      Laippala, Veronika  and
      Muennighoff, Niklas  and
      Piktus, Aleksandra  and
      Wang, Thomas  and
      Tazi, Nouamane  and
      Scao, Teven  and
      Wolf, Thomas  and
      Suominen, Osma  and
      Sairanen, Samuli  and
      Merioksa, Mikko  and
      Heinonen, Jyrki  and
      Vahtola, Aija  and
      Antao, Samuel  and
      Pyysalo, Sampo",
    editor = "Bouamor, Houda  and
      Pino, Juan  and
      Bali, Kalika",
    booktitle = "Proceedings of the 2023 Conference on Empirical Methods in Natural Language Processing",
    year = "2023",
    address = "Singapore",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2023.emnlp-main.164",
    doi = "10.18653/v1/2023.emnlp-main.164",
    pages = "2710--2726",
}



@article{repo2023foundingreg,
    	author = {Liina Repo and Brett Hashimoto and Veronika Laippala},
    	title = {In search of founding era registers: automatic modeling of registers from the corpus of Founding Era American English},
    	journal = {Digital Scholarship in the Humanities},
    	volume = {38},
    	number = {4},
    	pages = {1659-1677},
	year = {2023},
    	doi = {10.1093/llc/fqad049},
    	url = {https://doi.org/10.1093/llc/fqad049},
}

@article{ristila2023parltopics,
	author={Anna Ristil{\"a} and Kimmo Elo},
	title={Observing political and societal changes in {Finnish} parliamentary speech data, 1980–2010, with topic modelling},
	year={2023},
	journal={Parliaments, Estates and Representation},
	publisher={Routledge},
	doi = {10.1080/02606755.2023.2213550},
	url = {https://doi.org/10.1080/02606755.2023.2213550}
}

@inproceedings{eskelinen2023toxicity,
	title={Toxicity Detection in {Finnish} Using Machine Translation},
	author={Anni Eskelinen and Laura Silvala and Filip Ginter and Sampo Pyysalo and Veronika Laippala},
	booktitle={The 24rd Nordic Conference on Computational Linguistics (NoDaLiDa 2023)},
	year={2023},
	url={https://openreview.net/forum?id=X5DCw7mXz4}
}

@inproceedings{bassignana2023multicrossre,
      title={{Multi-CrossRE} A Multi-Lingual Multi-Domain Dataset for Relation Extraction}, 
      author={Elisa Bassignana and Filip Ginter and Sampo Pyysalo and Rob van der Goot and Barbara Plank},
      year={2023},
      booktitle={Proceedings of The 24th Nordic Conference on Computational Linguistics (NoDaLiDa' 2023)}
}

@inproceedings{bassignana2023silver,
      title={Silver Syntax Pre-training for Cross-Domain Relation Extraction}, 
      author={Elisa Bassignana and Filip Ginter and Sampo Pyysalo and Rob van der Goot and Barbara Plank},
      year={2023},
      booktitle={Findings of the Association for Computational Linguistics: ACL 2023},
      publisher={Association for Computational Linguistics}
}

@inproceedings{gehrmann-etal-2022-gemv2,
    title = "{GEM}v2: Multilingual {NLG} Benchmarking in a Single Line of Code",
    author = "Gehrmann, Sebastian and ManyCoauthors, Other and Kanerva, Jenna and Ginter, Filip and ManyCoauthors, Other and others",
    booktitle = "Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing: System Demonstrations",
    year = "2022",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2022.emnlp-demos.27",
    pages = "266--281"
}

@article{haris2023blockbuster,
  author={Haris, Muhammad Junaid and Upreti, Aanchal and Kurtaran, Melih and Ginter, Filip and Lafond, Sebastian and Azimi Rashti, Sepinoud},
  title={Identifying gender bias in blockbuster movies through the lens of machine learning},
  year={2023},
  journal={Humanities and social sciences communications},
}

@article{kanerva2023paraphrasejournal,
author={Jenna Kanerva and Filip Ginter and Li-Hsin Chang and Iiro Rastas and Valtteri Skantsi and Jemina Kilpel{\"a}inen and Hanna-Mari Kupari and Aurora Piirto and Jenna Saarni and Maija Sev{\'o}n and Otto Tarkka},
title={Towards Diverse and Contextually Anchored Paraphrase Modeling: A Dataset and Baselines for {Finnish}},
year={2023},
journal={Natural Language Engineering},
publisher={Cambridge University Press},
doi = {10.1017/S1351324923000086},
url = {https://doi.org/10.1017/S1351324923000086}
}

@inproceedings{ronnqvist-etal-2022-explaining,
    title = "Explaining Classes through Stable Word Attributions",
    author = {R{\"o}nnqvist, Samuel  and
      Kyr{\"o}l{\"a}inen, Aki-Juhani  and
      Myntti, Amanda  and
      Ginter, Filip  and
      Laippala, Veronika},
    booktitle = "Findings of the Association for Computational Linguistics: ACL 2022",
    month = "may",
    year = "2022",
    address = "Dublin, Ireland",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2022.findings-acl.85",
    doi = "10.18653/v1/2022.findings-acl.85",
    pages = "1063--1074",
    abstract = "Input saliency methods have recently become a popular tool for explaining predictions of deep learning models in NLP. Nevertheless, there has been little work investigating methods for aggregating prediction-level explanations to the class level, nor has a framework for evaluating such class explanations been established. We explore explanations based on XLM-R and the Integrated Gradients input attribution method, and propose 1) the Stable Attribution Class Explanation method (SACX) to extract keyword lists of classes in text classification tasks, and 2) a framework for the systematic evaluation of the keyword lists. We find that explanations of individual predictions are prone to noise, but that stable explanations can be effectively identified through repeated training and explanation. We evaluate on web register data and show that the class explanations are linguistically meaningful and distinguishing of the classes.",
}

@article{laippala2022corecorpus,
author={Veronika Laippala and Samuel R{\"o}nnqvist and Miika Oinonen and Aki-Juhani Kyr{\"o}l{\"a}inen and Anna Salmela and Douglas Biber and Jesse Egbert and Sampo Pyysalo},
title={Register identification from the unrestricted open Web using the Corpus of Online Registers of English},
year=2022,
journal={Language Resources and Evaluation},
doi={ https://doi.org/10.1007/s10579-022-09624-1}
}

@inproceedings{laippala-etal-2022-towards,
    title = "Towards better structured and less noisy Web data: Oscar with Register annotations",
    author = {Laippala, Veronika  and
      Salmela, Anna  and
      R{\"o}nnqvist, Samuel  and
      Aji, Alham Fikri  and
      Chang, Li-Hsin  and
      Dhifallah, Asma  and
      Goulart, Larissa  and
      Kortelainen, Henna  and
      P{\`a}mies, Marc  and
      Prina Dutra, Deise  and
      Skantsi, Valtteri  and
      Sutawika, Lintang  and
      Pyysalo, Sampo},
    booktitle = "Proceedings of the Eighth Workshop on Noisy User-generated Text (W-NUT 2022)",
    month = "oct",
    year = "2022",
    address = "Gyeongju, Republic of Korea",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2022.wnut-1.23",
    pages = "215--221",
    abstract = {Web-crawled datasets are known to be noisy, as they feature a wide range of language use covering both user-generated and professionally edited content as well as noise originating from the crawling process. This article presents one solution to reduce this noise by using automatic register (genre) identification -whether the texts are, e.g., forum discussions, lyrical or how-to pages. We apply the multilingual register identification model by R{\"o}nnqvist et al. (2021) and label the widely used Oscar dataset. Additionally, we evaluate the model against eight new languages, showing that the performance is comparable to previous findings on a restricted set of languages. Finally, we present and apply a machine learning method for further cleaning text files originating from Web crawls from remains of boilerplate and other elements not belonging to the main text of the Web page. The register labeled and cleaned dataset covers 351 million documents in 14 languages and is available at https://huggingface.co/datasets/TurkuNLP/register{\_}oscar.},
}

@inproceedings{zhang2022,
author = "Jinbin Zhang and Ryan, {Yann Ciar{\'a}n} and Iiro Rastas and Filip Ginter and Mikko Tolonen and Rohit Babbar",
title = "Detecting Sequential Genre Change in Eighteenth-Century Texts",
year = "2022",
publisher = "CEUR-WS.org",
pages = "243--255",
editor = "Karsdorp, Folgert and Lassche, Alie and Nielbo, Kristoffer",
booktitle = "Proceedings of the Computational Humanities Research Conference 2022",
url = "https://ceur-ws.org/Vol-3290/short_paper2630.pdf"
}

@article{Salmi_Kanerva_Kiiskinen_Ginter_2022, 
  author={Salmi, Hannu and Kanerva, Jenna and Kiiskinen, Harri and Ginter, Filip},
  title={Paimen, piika ja emäntä: Arvot ja ammatit suomalaisessa näytelmäelokuvassa 1907–2017},
  volume={35},
  url={https://journal.fi/lahikuva/article/view/125666},
  DOI={10.23994/lk.125666}, 
  number={4},
  journal={Lähikuva – audiovisuaalisen kulttuurin tieteellinen julkaisu}, 
  year={2022}, month={12}, pages={8–18}}

@article{paasikivi2022cholera,
author = {Sofia Paasikivi and Hannu Salmi and Aleksi Vesanto and Filip Ginter},
title = {Infectious Media: Cholera and the Circulation of Texts in the {Finnish} Press, 1860–1920},
journal = {Media History},
pages = {1-22},
year  = {2022},
publisher = {Routledge},
doi = {10.1080/13688804.2022.2054408},
URL = {https://doi.org/10.1080/13688804.2022.2054408},
}



@inproceedings{chang2022towards-automatic-short,
  title={Towards Automatic Short Answer Assessment for {Finnish} as a Paraphrase Retrieval},
  author={Chang, Li-Hsin and Kanerva, Jenna and Ginter, Filip},
  booktitle = {Proceedings of the 17th Workshop on Innovative Use of NLP for Building Educational Applications},
  year = {2022},
  publisher = {Association for Computational Linguistics},
  url = {https://aclanthology.org/2022.bea-1.30/}
}

@PhdThesis{FarrokhMehryaryPhD,
  Title                    = {Optimizing text mining methods for improving biomedical natural language processing},
  Author                   = {Farrokh Mehryary},
  School                   = {University of Turku},
  Year                     = {2022},
  Timestamp                = {2022-02-04},
  Month                    = {February},
  Address                  = {Turku, Finland},
  url = {https://urn.fi/URN:ISBN:978-951-29-8744-3},
  issn={2736-9684}
}

@inproceedings{ginter2022movie2year,
 title= {{Deep Learning} and Film History: {M}odel explanation techniques in the analysis of temporality in {Finnish} fiction film metadata},
 author = {Ginter, Filip and Kiiskinen, Harri and Kanerva, Jenna and Chang, Li-Hsin and Salmi, Hannu},
 booktitle = {Proceedings of the 6th Digital Humanities in the Nordic and Baltic Countries Conference (DHNB 2022)},
 year={2022}
 }

@inproceedings{rastas-2022-eccobert,
    title= {Explainable Publication Year Prediction of Eighteenth Century Texts with the {BERT} Model},
    author = {Rastas, Iiro and Ryan, Yann and Tiihonen, Iiro and Qaraei, Mohammadreza and Repo, Liina and Babbar, Rohit and M{\"a}kel{\"a}, Eetu and Tolonen, Mikko and Ginter, Filip},
    booktitle = {Proceedings of the 3rd International Workshop on Computational Approaches to Historical Language Change (LChange 2022)},
    year={2022}
}

@inproceedings{kanerva-2022-ood,
    title = "Out-of-Domain Evaluation of {Finnish} Dependency Parsing",
    author = {Kanerva, Jenna and Ginter, Filip},
    booktitle = "Proceedings of the 13th International Conference on Language Resources and Evaluation (LREC'22)",
    year = "2022",
    pages = "1114‑-1124",
    url = "http://www.lrec-conf.org/proceedings/lrec2022/pdf/2022.lrec-1.120.pdf"
}

@inproceedings{Robertson2022TallVocabL2Fi,
    title = {{TallVocabL2Fi}: {A}n Extensive Mapping of 15 {Finnish} {L}2 Learners’ Vocabulary},
    author = {Robertson, Frankie and Chang, Li-Hsin and Söyrinki, Sini},
    booktitle = "Proceedings of the 13th International Conference on Language Resources and Evaluation (LREC'22)",
    year = "2022",
    pages = "6377--6386",
    url = "http://www.lrec-conf.org/proceedings/lrec2022/pdf/2022.lrec-1.685.pdf"
}

@article{Laippala2021ExploringTR,
  title={Exploring the role of lexis and grammar for the stable identification of register in an unrestricted corpus of web documents},
  author={Veronika Laippala and Jesse Egbert and Douglas Biber and Aki-Juhani Kyr{\"o}l{\"a}inen},
  journal={Language Resources and Evaluation},
  year={2021},
  volume={55},
  pages={757 - 788}
}

@inproceedings{ronnqvist-etal-2021-multilingual,
    title = "Multilingual and Zero-Shot is Closing in on Monolingual Web Register Classification",
    author = {R{\"o}nnqvist, Samuel  and
      Skantsi, Valtteri  and
      Oinonen, Miika  and
      Laippala, Veronika},
    booktitle = "Proceedings of the 23rd Nordic Conference on Computational Linguistics (NoDaLiDa)",
    month = "may",
    year = "2021",
    address = "Reykjavik, Iceland (Online)",
    publisher = {Link{\"o}ping University Electronic Press, Sweden},
    url = "https://aclanthology.org/2021.nodalida-main.16",
    pages = "157--165",
    abstract = "This article studies register classification of documents from the unrestricted web, such as news articles or opinion blogs, in a multilingual setting, exploring both the benefit of training on multiple languages and the capabilities for zero-shot cross-lingual transfer. While the wide range of linguistic variation found on the web poses challenges for register classification, recent studies have shown that good levels of cross-lingual transfer from the extensive English CORE corpus to other languages can be achieved. In this study, we show that training on multiple languages 1) benefits languages with limited amounts of register-annotated data, 2) on average achieves performance on par with monolingual models, and 3) greatly improves upon previous zero-shot results in {Finnish}, French and Swedish. The best results are achieved with the multilingual XLM-R model. As data, we use the CORE corpus series featuring register annotated data from the unrestricted web.",
}

@article{hakala2019neural,
  title={Neural network and random forest models in protein function prediction},
  author={Hakala, Kai and Kaewphan, Suwisa and Bj{\"o}rne, Jari and Mehryary, Farrokh and Moen, Hans and Tolvanen, Martti and Salakoski, Tapio and Ginter, Filip},
  journal={IEEE/ACM Transactions on Computational Biology and Bioinformatics},     
  year={2020},  
  doi={10.1109/TCBB.2020.3044230}
}

@inproceedings{droganova-etal-2018-parse,
    title = {{Parse Me if You Can: Artificial Treebanks for Parsing Experiments on Elliptical Constructions}},
    author = {Droganova, Kira  and  Zeman, Daniel  and Kanerva, Jenna  and Ginter, Filip},
    booktitle = {Proceedings of the Eleventh International Conference on Language Resources and Evaluation ({LREC} 2018)},
     year = {2018},
    address = {Miyazaki, Japan},
    publisher = {European Language Resources Association (ELRA)},
    url = {https://aclanthology.org/L18-1290}
}

	
@article{kanerva2020dependency,
  title={Dependency parsing of biomedical text with {BERT}},
  author={Kanerva, Jenna and Ginter, Filip and Pyysalo, Sampo},
  journal={BMC Bioinformatics},
  volume={21},
  number={23},
  pages={1--12},
  year={2020},
  publisher={Springer},
  url={https://doi.org/10.1186/s12859-020-03905-8},
}

@inproceedings{laippala2020web,
  title={From Web Crawl to Clean Register-Annotated Corpora},
  author={Laippala, Veronika and R{\"o}nnqvist, Samuel and Hellstr{\"o}m, Saara and Luotolahti, Juhani and Repo, Liina and Salmela, Anna and Skantsi, Valtteri and Pyysalo, Sampo},
  booktitle={Proceedings of the 12th Web as Corpus Workshop},
  pages={14--22},
  year={2020}
}

@inproceedings{luoma2020broad,
  title={A broad-coverage corpus for {Finnish} named entity recognition},
  author={Luoma, Jouni and Oinonen, Miika and Pyyk{\"o}nen, Maria and Laippala, Veronika and Pyysalo, Sampo},
  booktitle={Proceedings of The 12th Language Resources and Evaluation Conference},
  pages={4615--4624},
  year={2020}
}

@article{moen2020assisting,
  title={Assisting nurses in care documentation: from automated sentence classification to coherent document structures with subject headings},
  author={Moen, Hans and Hakala, Kai and Peltonen, Laura-Maria and Matinolli, Hanna-Maria and Suhonen, Henry and Terho, Kirsi and Danielsson-Ojala, Riitta and Valta, Maija and Ginter, Filip and Salakoski, Tapio and others},
  journal={Journal of Biomedical Semantics},
  volume={11},
  number={1},
  pages={1--12},
  year={2020},
  publisher={Springer}
}

@article{paulin2020changing,
  title={Changing role of EMS--analyses of non-conveyed and conveyed patients in Finland},
  author={Paulin, Jani and Kurola, Jouni and Salanter{\"a}, Sanna and Moen, Hans and Guragain, Nischal and Koivisto, Mari and K{\"a}yhk{\"o}, Niina and Aaltonen, Venla and Iirola, Timo},
  journal={Scandinavian Journal of Trauma, Resuscitation and Emergency Medicine},
  volume={28},
  number={1},
  pages={1--14},
  year={2020},
  publisher={BioMed Central}
}

@article{peltonen2020exploring,
  title={Exploring Unsupervised Query Paraphrasing to Identify Relevant Search Phrases for a Literature Review},
  author={Peltonen, Laura-Maria and Tommila, Miretta and Moen, Hans},
  journal={Studies in Health Technology and Informatics},
  volume={272},
  pages={429--432},
  year={2020}
}

@article{uronen2020towards,
  title={Towards automated detection of psychosocial risk factors with text mining},
  author={Uronen, L and Moen, H and Teperi, S and Martimo, KP and Hartiala, J and Salanter{\"a}, S},
  journal={Occupational Medicine},
  volume={70},
  number={3},
  pages={203--206},
  year={2020},
  publisher={Oxford University Press UK}
}

@article{salmi2020reuse,
author = { Hannu   Salmi  and  Petri   Paju  and  Heli   Rantala  and  Asko   Nivala  and  Aleksi   Vesanto  and  Filip   Ginter },
title = {The reuse of texts in {Finnish} newspapers and journals, 1771–1920: A digital humanities perspective},
journal = {Historical Methods: A Journal of Quantitative and Interdisciplinary History},
volume = {0},
number = {0},
pages = {1-15},
year  = {2020},
publisher = {Routledge},
doi = {10.1080/01615440.2020.1803166},
url = {https://doi.org/10.1080/01615440.2020.1803166}
}

@inproceedings{kanerva-etal-2020-turku,
    title = {{T}urku Enhanced Parser Pipeline: From Raw Text to Enhanced Graphs in the {IWPT} 2020 Shared Task},
    author = {Kanerva, Jenna  and Ginter, Filip  and Pyysalo, Sampo},
    booktitle = {Proceedings of the 16th International Conference on Parsing Technologies and the IWPT 2020 Shared Task on Parsing into Enhanced Universal Dependencies},
    month = {July},
    year = {2020},
    address = {Online},
    publisher = {Association for Computational Linguistics},
    url = {https://www.aclweb.org/anthology/2020.iwpt-1.17},
    pages = {162--173},
}

@article{kanerva2020lemmatizer,
  title={{Universal Lemmatizer}: A Sequence to Sequence Model for Lemmatizing {Universal Dependencies} Treebanks},
  author={Kanerva, Jenna and Ginter, Filip and Salakoski, Tapio},
  year={2020},
  journal={Natural Language Engineering},
  publisher={Cambridge University Press},
  DOI={10.1017/S1351324920000224},
  pages={1--30},
  url={http://dx.doi.org/10.1017/S1351324920000224}
  }
  
@article{moen2020supporting,
  title={Supporting the use of standardized nursing terminologies with automatic subject heading prediction: a comparison of sentence-level text classification methods},
  author={Moen, Hans and Hakala, Kai and Peltonen, Laura-Maria and Suhonen, Henry and Ginter, Filip and Salakoski, Tapio and Salanter{\"a}, Sanna},
  journal={Journal of the American Medical Informatics Association},
  volume={27},
  number={1},
  pages={81--88},
  year={2020},
  publisher={Oxford University Press}
}

@inproceedings{chang2021quantitative,
    title={Quantitative Evaluation of Alternative Translations in a Corpus of Highly Dissimilar {Finnish} Paraphrases},
    author={Chang, Li-Hsin and Pyysalo, Sampo and Kanerva, Jenna and Ginter, Filip},
    year={2021},
    booktitle={Proceedings for the First Workshop on Modelling Translation: Translatology in the Digital Age},
    url={https://www.aclweb.org/anthology/2021.motra-1.11.pdf}
}

@inproceedings{chang2021deep,
    title={Deep learning for sentence clustering in essay grading support},
    author={Chang, Li-Hsin and Rastas, Iiro and Pyysalo, Sampo and Ginter, Filip},
    year={2021},
    booktitle={Proceedings of the 14th International Conference on Educational Data Mining (EDM 2021)},
}

@inproceedings{chang2021towards,
    title={Towards Bilingually Competent Deep Language Modeling},
    author={Chang, Li-Hsin},
    year={2021},
    booktitle={Proceedings of the ESSLLI Student Session 2021},
}

@inproceedings{multilingualregisters2019,
    title={Toward Multilingual Identification of Online Registers},
    author={Laippala, Veronika and Kyllönen, Roosa and Egbert, Jesse and Biber, Douglas and Pyysalo, Sampo},
    year={2019},
    booktitle={Proceedings of the 22nd Nordic Conference on Computational Linguistics (NoDaLiDa’19)},
}

@inproceedings{baumgartner2019craft,
  title={{CRAFT} Shared Tasks 2019 Overview --- Integrated Structure, Semantics, and Coreference},
  author={Baumgartner, William and Bada, Michael and Pyysalo, Sampo and Ciosici, Manuel R. and Hailu, Negacy and Pielke-Lombardo, Harrison and Regan, Michael and Hunter, Lawrence},
  year={2019},
  booktitle={Proceedings of the BioNLP Open Shared Tasks 2019}
}

@inproceedings{hakala2019biomedical,
  title={Biomedical Named Entity Recognition with Multilingual {BERT}},
  author={Hakala, Kai and Pyysalo, Sampo},
  year={2019},
  booktitle={Proceedings of the BioNLP Open Shared Tasks 2019}
}

@inproceedings{thang2019neural,
  title={Neural Dependency Parsing of Biomedical Text: {TurkuNLP} entry in the {CRAFT} Structural Annotation Task},
  author={Ngo, Thang Minh and Kanerva, Jenna and Ginter, Filip and Pyysalo, Sampo},
  year={2019},
  booktitle={Proceedings of the BioNLP Open Shared Tasks 2019}
}

@article{zhou2019cafa,
  title={The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens},
  author={Zhou, Naihui and Jiang, Yuxiang and Bergquist, Timothy R and Lee, Alexandra J and Kacsoh, Balint Z and Crocker, Alex W and Lewis, Kimberley A and Georghiou, George and Nguyen, Huy N and Hamid, Md Nafiz and others},
  journal={Genome biology},
  volume={20},
  number={1},
  pages={1--23},
  year={2019},
  publisher={BioMed Central}
}

@inproceedings{moen2019nodalida,
    title={An Unsupervised Query Rewriting Approach Using N-gram Co-occurrence Statistics to Find Similar Phrases in Large Text Corpora},
    author={Moen, Hans and Peltonen, Laura-Maria and Suhonen, Henry and Matinolli, Hanna-Maria and Mieronkoski, Riitta and Telen, Kirsi and Terho, Kirsi and Salakoski, Tapio and Salanterä, Sanna},
    year={2019},
    booktitle={Proceedings of the 22nd Nordic Conference on Computational Linguistics (NoDaLiDa’19)},
}

@inproceedings{moen2019medinfo,
    title={Unsupervised Phrase-Level Query Rewriting for Assisting Search in Clinical Free Text},
    author={Moen, Hans and Peltonen, Laura-Maria and Suhonen, Henry and Koivumäki, Mikko and Salakoski, Tapio and Salanterä, Sanna},
    year={2019},
    booktitle={Proceedings of the 17th World Congress on Medical and Health Informatics (MedInfo’19)},
}

@article{vikstrom2018,
  title={Secondary use of electronic health records: Availability aspects in two Nordic countries},
  author={Vikström, Antti and Moen, Hans and Moosavi, Sanaz Rahimi and Salakoski, Tapio and Salanterä, Sanna},
  year={2018},
  journal={Health Information Management Journal}
}

@article{rantanen2019banks,
  title={Classifying Online Corporate Reputation with Machine Learning: A Study in the Banking Domain},
  author={Rantanen, Anette and Salminen, Joni and Ginter, Filip and Jansen, Bernard},
  year={2019},
  journal={Internet Research}
}

@inproceedings{kanerva2019newsgen,
  Title = {Template-free Data-to-Text Generation of {Finnish} Sports News},
  Author = {Jenna Kanerva and Samuel R{\"o}nnqvist and Riina Kekki and Tapio Salakoski and Filip Ginter},
  booktitle = {Proceedings of the 22nd Nordic Conference on Computational Linguistics (NoDaLiDa’19)},
  year={2019}
  }
  
@inproceedings{ronnqvist2019bert,
  Title = {Is Multilingual {BERT} Fluent in Language Generation?},
  Author = {Samuel R{\"o}nnqvist and Jenna Kanerva and Tapio Salakoski and Filip Ginter},
  booktitle = {Proceedings of the 1st NLPL Workshop on Deep Learning for Natural Language Processing},
  year={2019}
  }

@InProceedings{airola2012ranking,
  Title                    = {Machine Learning and Performance Estimation Methods for Ranking Problems},
  Author                   = {Airola, Antti},
  Booktitle                = {Proceedings of the Federated Computer Science Event},
  Year                     = {2012},
  Editor                   = {Tarkoma, Sasu and K\"{a}m\"{a}r\"{a}inen, Joni-Kristian and Pahikkala, Tapio},
  Pages                    = {8--14},
  Publisher                = {Unigrafia Oy},

  Owner                    = {ajairo},
  Timestamp                = {2012.11.06}
}

@PhdThesis{airola2011phd,
  Title                    = {Kernel-Based Ranking: Methods for Learning and Performance Estimation},
  Author                   = {Airola, Antti},
  School                   = {Turku Centre for Computer Science (TUCS)},
  Year                     = {2011},

  Owner                    = {ajairo},
  Timestamp                = {2012.11.06}
}

@InProceedings{airola2010permutation,
  Title                    = {Applying permutation tests for assessing the statistical significance of wrapper based feature selection},
  Author                   = {Airola, Antti and Pahikkala, Tapio and Boberg, Jorma and Salakoski, Tapio},
  Booktitle                = {Proceedings of The Ninth International Conference on Machine Learning and Applications (ICMLA'10)},
  Year                     = {2010},
  Editor                   = {Draghici, Sorin and Khoshgoftaar, Taghi M. and Palade, Vasile and Pedrycz, Witold and Wani, M. Arif and Zhu, Xingquan},
  Pages                    = {989--994},
  Publisher                = {IEEE},

  Url                      = {http://dx.doi.org/10.1109/ICMLA.2010.158}
}

@InProceedings{airola2010largescale,
  Title                    = {Large scale training methods for linear {RankRLS}},
  Author                   = {Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
  Booktitle                = {Proceedings of the {ECML/PKDD}-Workshop on Preference Learning {(PL-10)}},
  Year                     = {2010},
  Editor                   = {Eyke H{\"u}llermeier and Johannes F{\"u}rnkranz},

  Url                      = {www.ke.tu-darmstadt.de/events/PL-10/papers/11-Airola.pdf}
}

@InProceedings{airola2011improved,
  Title                    = {An Improved Training Algorithm for the Linear Ranking Support Vector Machine},
  Author                   = {Antti Airola and Tapio Pahikkala and Tapio Salakoski},
  Booktitle                = {Proceedings of the 21st International Conference on Artificial Neural Networks (ICANN 2011)},
  Year                     = {2011},
  Editor                   = {Timo Honkela and Wlodzislaw Duch and Mark A. Girolami and Samuel Kaski},
  Pages                    = {134-141},
  Publisher                = {Springer},
  Series                   = {Lecture Notes in Computer Science},
  Volume                   = {6791},

  Url                      = {http://dx.doi.org/10.1007/978-3-642-21735-7_17}
}

@Article{airola2011nystromcv,
  Title                    = {On learning and cross-validation with decomposed {N}ystr{\"o}m approximation of kernel matrix},
  Author                   = {Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
  Journal                  = {Neural Processing Letters},
  Year                     = {2011},

  Month                    = {February},
  Number                   = {1},
  Pages                    = {17--30},
  Volume                   = {33},

  Doi                      = {10.1007/s11063-010-9159-4},
  Url                      = {http://dx.doi.org/doi:10.1007/s11063-010-9159-4}
}

@Article{airola2011ranksvm,
  Title                    = {Training linear ranking {SVMs} in linearithmic time using red-black trees},
  Author                   = {Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
  Journal                  = {Pattern Recognition Letters},
  Year                     = {2011},

  Month                    = {July},
  Number                   = {9},
  Pages                    = {1328--1336},
  Volume                   = {32},

  Url                      = {http://dx.doi.org/doi:10.1016/j.patrec.2011.03.014}
}

@InCollection{airola2010comparison,
  Title                    = {A comparison of {AUC} estimators in small-sample studies},
  Author                   = {Airola, Antti and Pahikkala, Tapio and Waegeman, Willem and De Baets, Bernard and Salakoski, Tapio},
  Booktitle                = {JMLR Workshop and Conference Proceedings: Machine Learning in Systems Biology},
  Year                     = {2010},
  Editor                   = {D\v{z}eroski, Sa\v{s}o and Geurts, Pierre and Rousu, Juho},
  Pages                    = {3--13},

  File                     = {http://jmlr.csail.mit.edu/proceedings/papers/v8/airola10a/airola10a.pdf:PDF}
}

@InCollection{airola2009comparison,
  Title                    = {A comparison of {AUC} estimators in small-sample studies},
  Author                   = {Airola, Antti and Pahikkala, Tapio and Waegeman, Willem and De Baets, Bernard and Salakoski, Tapio},
  Booktitle                = {Proceedings of the Third International Workshop on Machine Learning in Systems Biology (MLSB'09)},
  Publisher                = {Helsinki University Printing House},
  Year                     = {2009},

  Address                  = {Helsinki, Finland},
  Editor                   = {D\v{z}eroski, Sa\v{s}o and Geurts, Pierre and Rousu, Juho},
  Pages                    = {15--23},

  File                     = {:http\://www.tucs.fi/publications/attachment.php?fname=inpAiPaWaDeSa09a.full.pdf:PDF}
}

@Article{airola2011experimental,
  Title                    = {An experimental comparison of cross-validation techniques for estimating the area under the {ROC} curve},
  Author                   = {Airola, Antti and Pahikkala, Tapio and Waegeman, Willem and De Baets, Bernard and Salakoski, Tapio},
  Journal                  = {Computational Statistics \& Data Analysis},
  Year                     = {2011},

  Month                    = {April},
  Number                   = {4},
  Pages                    = {1828--1844},
  Volume                   = {55},

  Doi                      = {10.1016/j.csda.2010.11.018 },
  Url                      = {http://dx.doi.org/10.1016/j.csda.2010.11.018 }
}

@InProceedings{airola08bionlp,
  Title                    = {A Graph Kernel for Protein-Protein Interaction Extraction},
  Author                   = {Airola, Antti and Pyysalo, Sampo and Bj{\"{o}}rne, Jari and Pahikkala, Tapio and Ginter, Filip and Salakoski, Tapio},
  Booktitle                = {Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing (BioNLP'08)},
  Year                     = {2008},
  Pages                    = {1--9},
  Publisher                = {Association for Computational Linguistics},

  File                     = {W08-0601.pdf:http\://aclweb.org/anthology-new/W/W08/W08-0601.pdf:PDF}
}

@Article{airola08allpathsbmc,
  Title                    = {All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning},
  Author                   = {Airola, Antti and Pyysalo, Sampo and Bj\"{o}rne, Jari and Pahikkala, Tapio and Ginter, Filip and Salakoski, Tapio },
  Journal                  = {BMC Bioinformatics},
  Year                     = {2008},
  Volume                   = {9 Suppl 11}
}

@Article{aittokallio2007inspiratory,
  Title                    = {Inspiratory Flow Shape Clustering: An Automated Method to Monitor Upper Airway Performance During Sleep},
  Author                   = {Tero Aittokallio and Jani S. Malminen and Tapio Pahikkala and Olli Polo and Olli Nevalainen},
  Journal                  = {Computer Methods and Programs in Biomedicine},
  Year                     = {2007},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {8--18},
  Volume                   = {85},

  Doi                      = {10.1016/j.cmpb.2006.09.012},
  Url                      = {http://dx.doi.org/10.1016/j.cmpb.2006.09.012}
}

@Article{aittokallio2003electrophoretic,
  Title                    = {Electrophoretic Signal Comparison Applied to mRNA Differential Display Analysis},
  Author                   = {Aittokallio, Tero and Pahikkala, Tapio and Ojala, Pekka and Nevalainen, Timo J. and Nevalainen, Olli},
  Journal                  = {BioTechniques},
  Year                     = {2003},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {116-122},
  Volume                   = {34}
}

@PhdThesis{bjorne2014biomedical,
  Title                    = {Biomedical Event Extraction with Machine Learning},
  Author                   = {Bj{\"o}rne, Jari},
  School                   = {TUCS Dissertations},
  Year                     = {2014}
}

@InProceedings{bjorne2013analyzing,
  Title                    = {Analyzing the {Japanese Toxicogenomics Project Dataset} with {SVM} and {RLS} Classifiers},
  Author                   = {Bj{\"o}rne, Jari and Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
  Booktitle                = {13th Annual International Conference on Critical Assessment of Massive Data Analysis (CAMDA 2013)},
  Year                     = {2013}
}

@InProceedings{bjorne2013uturku,
  Title                    = {{UTurku}: Drug Named Entity Recognition and Drug-Drug Interaction Extraction Using {SVM} Classification and Domain Knowledge},
  Author                   = {Bj{\"o}rne, Jari and Kaewphan, Suwisa and Salakoski, Tapio},
  Booktitle                = {Second Joint Conference on Lexical and Computational Semantics (*SEM), Volume 2: Proceedings of the Seventh International Workshop on Semantic Evaluation (SemEval 2013)},
  Year                     = {2013},
  Organization             = {Association for Computational Linguistics},
  Pages                    = {651--659}
}

@InProceedings{bjorne08how,
  Title                    = {How Complex are Complex Protein-protein Interactions?},
  Author                   = {Jari Bj{\"o}rne and Sampo Pyysalo and Filip Ginter and Tapio Salakoski},
  Booktitle                = {Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland},
  Year                     = {2008},
  Editor                   = {Tapio Salakoski and Dietrich Rebholz-Schuhmann and Sampo Pyysalo},
  Pages                    = {125--128},
  Publisher                = {Turku Centre for Computer Science (TUCS)},

  File                     = {smbmpaper_17.pdf:http\://mars.cs.utu.fi/smbm2008/files/smbm2008proceedings/smbmpaper_17.pdf:PDF}
}

@Article{bjornecancer,
  Title                    = {Cancer Progression Classification for Mutation Analysis},
  Author                   = {Bj{\"o}rne, Jari and Salakoski, Tapio},
  Journal                  = {The 14th Annual International Conference On Critical Assessment of Massive Data Analysis (CAMDA)},
  Year                     = {2015}
}

@InProceedings{bjorne2013tees,
  Title                    = {{TEES 2.1}: Automated annotation scheme learning in the BioNLP 2013 Shared Task},
  Author                   = {Bj{\"o}rne, Jari and Salakoski, Tapio},
  Booktitle                = {Proceedings of the BioNLP Shared Task 2013 Workshop},
  Year                     = {2013},
  Organization             = {Association for Computational Linguistics},
  Pages                    = {16--25}
}

@InProceedings{bjorne2011ddi,
  Title                    = {Drug-Drug Interaction Extraction from Biomedical Texts with SVM and RLS Classifiers},
  Author                   = {Bj\"{o}rne, Jari and Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
  Booktitle                = {Proceedings of the First Challenge task on Drug-Drug Interaction Extraction (DDIExtraction 2011)},
  Year                     = {2011},

  Address                  = {Huelva, Spain},
  Month                    = {August},
  Pages                    = {35--42},
  Publisher                = {CEUR Workshop Proceedings},

  Url                      = {http://ceur-ws.org/Vol-761/paper4.pdf}
}

@InProceedings{bjorne09learning,
  Title                    = {Learning to Extract Biological Event and Relation Graphs},
  Author                   = {Bj\"{o}rne, Jari and Ginter, Filip and Heimonen, Juho and Pyysalo, Sampo and Salakoski, Tapio},
  Booktitle                = {Proceedings of NODALIDA'09, Odense, Denmark},
  Year                     = {2009},
  Editor                   = {Jokinen, Kristiina and Bick, Eckhard},
  Pages                    = {18--25},

  File                     = {paper40.pdf:http\://dspace.utlib.ee/dspace/bitstream/10062/9547/1/paper40.pdf:PDF}
}

@Article{bjorne2010complex,
  Title                    = {Complex Event Extraction at {PubMed} Scale},
  Author                   = {Bj\"{o}rne, Jari and Ginter, Filip and Pyysalo, Sampo and Tsujii, Jun'ichi and Salakoski, Tapio},
  Journal                  = {Bioinformatics (ISMB'2010 proceedings volume)},
  Year                     = {2010},
  Pages                    = {i382--i390},
  Volume                   = {26},

  Owner                    = {ginter},
  Timestamp                = {2010.04.16},
  Url                      = {http://bioinformatics.oxfordjournals.org/cgi/content/full/btq180?ijkey=41vpyrHIQkfr2dP\&keytype=ref}
}

@InProceedings{bjorne2010scalingup,
  Title                    = {Scaling up Biomedical Event Extraction to the Entire {PubMed}},
  Author                   = {Bj\"{o}rne, Jari and Ginter, Filip and Pyysalo, Sampo and Tsujii, Jun'ichi and Salakoski, Tapio},
  Booktitle                = {Proceedings of the 2010 Workshop on Biomedical Natural Language Processing (BioNLP'10)},
  Year                     = {2010},
  Pages                    = {28--36},
  Publisher                = {ACL},

  File                     = {PDF:http\://aclweb.org/anthology-new/W/W10/W10-1904.pdf:PDF},
  Owner                    = {ginter},
  Timestamp                = {2010.05.21}
}

@Article{bjorne2010extractingcontext,
  Title                    = {Extracting Contextualized Complex Biological Events with Rich Graph-Based Feature Sets},
  Author                   = {Bj\"{o}rne, Jari and Heimonen, Juho and Ginter, Filip and Airola, Antti and Pahikkala, Tapio and Salakoski, Tapio},
  Journal                  = {Computational Intelligence},
  Year                     = {2011},
  Note                     = {Accepted in 2009},
  Number                   = {4},
  Pages                    = {541--557},
  Volume                   = {27},

  Doi                      = {10.1111/j.1467-8640.2011.00399.x},
  ISSN                     = {1467-8640},
  Keywords                 = {event extraction, BioNLP’09 Shared Task, machine learning, natural language processing, biomedical domain},
  Publisher                = {Blackwell Publishing Inc},
  Url                      = {http://dx.doi.org/10.1111/j.1467-8640.2011.00399.x}
}

@InProceedings{bjorne09sharedtask,
  Title                    = {Extracting Complex Biological Events with Rich Graph-Based Feature Sets},
  Author                   = {Bj\"{o}rne, Jari and Heimonen, Juho and Ginter, Filip and Airola,Antti and Pahikkala, Tapio and Salakoski, Tapio},
  Booktitle                = {Proceedings of the BioNLP'09 Shared Task on Event Extraction},
  Year                     = {2009},
  Pages                    = {10--18},

  File                     = {:http\://aclweb.org/anthology-new/W/W09/W09-1402.pdf:PDF}
}

@InProceedings{bjorne2011bionlpst,
  Title                    = {Generalizing Biomedical Event Extraction},
  Author                   = {Bj\"{o}rne, Jari and Salakoski, Tapio},
  Booktitle                = {Proceedings of BioNLP Shared Task 2011 Workshop},
  Year                     = {2011},

  Address                  = {Portland, Oregon, USA},
  Month                    = {June},
  Pages                    = {183--191},
  Publisher                = {Association for Computational Linguistics},

  Url                      = {http://www.aclweb.org/anthology/W11-1828}
}

@InProceedings{bjorne2011cafa,
  Title                    = {A Machine Learning Model and Evaluation of Text Mining for Protein Function Prediction},
  Author                   = {Bj\"{o}rne, Jari and Salakoski, Tapio},
  Booktitle                = {Automated Function Prediction Featuring a Critical Assessment of Function Annotations (AFP/CAFA) 2011},
  Year                     = {2011},

  Address                  = {Vienna, Austria},
  Month                    = {July},
  Pages                    = {7--8},
  Publisher                = {Automated Function Prediction -- an ISMB Special Interest Group},

  Url                      = {http://iddo-friedberg.net/afp-cafa-2011-booklet.pdf}
}

@InProceedings{bjorne2012epi,
  Title                    = {{PubMed}-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations},
  Author                   = {Bj\"{o}rne, Jari and Van Landeghem, Sofie and Pyysalo, Sampo and Ohta, Tomoko and Ginter, Filip and {Van de Peer}, Yves and Ananiadou, Sophia and Salakoski, Tapio},
  Booktitle                = {{BioNLP}: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing},
  Year                     = {2012},
  Pages                    = {82--90},
  Publisher                = {Association for Computational Linguistics},

  Owner                    = {ginter},
  Timestamp                = {2012.04.05}
}

@Article{bjorne2015tees,
  title={{TEES 2.2: Biomedical Event Extraction for Diverse Corpora}},
  author={Bj{\"o}rne, Jari and Salakoski, Tapio},
  journal={BMC bioinformatics},
  volume={16},
  number={16},
  pages={1},
  year={2015},
  publisher={BioMed Central}
}

@InProceedings{bjorne2017epe,
  Title                    = {EPE 2017: The {B}iomedical Event Extraction Downstream Application},
  Author                   = {Bj{\"o}rne, Jari and Ginter, Filip and Salakoski, Tapio},
  Booktitle                = {Proceedings of the 2017 Shared Task on Extrinsic Parser Evaluation (EPE 2017) at the Fourth International Conference on Dependency Linguistics (Depling 2017) and the 15th International Conference on Parsing Technologies (IWTP 2017)},
  Year                     = {2017},
  Pages                    = {17--24},
  Publisher                = {Association for Computational Linguistics},
  ISBN                     = {978-1-945626-74-6},
}

@Article{bohnet2013joint,
  Title                    = {Joint Morphological and Syntactic Analysis for Richly Inflected Languages},
  Author                   = {Bernd Bohnet and Joakim Nivre and Igor Boguslavsky and Rich{\'a}rd Farkas and Filip Ginter and Jan Haji{\v{c}}},
  Journal                  = {Transactions of the Association for Computational Linguistics},
  Year                     = {2013},
  Pages                    = {415--428},
  Volume                   = {1},

  Owner                    = {ginter},
  Timestamp                = {2013.09.21}
}

@InProceedings{demarneffe2014usd,
  Title                    = {Universal {S}tanford Dependencies: a Cross-Linguistic Typology},
  Author                   = {Marie-Catherine {de Marneffe} and Timothy Dozat and Natalia Silveira and Katri Haverinen and Filip Ginter and Joakim Nivre and Christopher D. Manning},
  Booktitle                = {Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC'14)},
  Year                     = {2014},
  Publisher                = {European Language Resources Association (ELRA)},

  ISBN                     = {978-2-9517408-8-4},
  Url                      = {http://www.lrec-conf.org/proceedings/lrec2014/pdf/1062_Paper.pdf}
}

@InProceedings{gieseke2012sqn,
  Title                    = {Sparse Quasi-Newton Optimization for Semi-Supervised Support Vector Machines},
  Author                   = {Gieseke, Fabian and Airola, Antti and Pahikkala, Tapio and Kramer, Oliver},
  Booktitle                = {Proceedings of the 1st International Conference on Pattern Recognition Applications and Methods (ICPRAM)},
  Year                     = {2012},
  Editor                   = {Latorre Carmona, Pedro and S{\'a}nchez, J. Salvador and Fred, Ana L. N.},
  Pages                    = {45-54},
  Publisher                = {SciTePress}
}

@InProceedings{gieseke2011speedy,
  Title                    = {Speedy Local Search for Semi-Supervised Regularized Least-Squares},
  Author                   = {Gieseke, Fabian and Kramer, Oliver and Airola, Antti and Pahikkala, Tapio},
  Booktitle                = {KI 2011: Advances in Artificial Intelligence},
  Year                     = {2011},
  Editor                   = {Bach, Joscha and Edelkamp, Stefan},
  Pages                    = {87--98},
  Publisher                = {Springer},
  Series                   = {Lecture Notes in Computer Science},
  Volume                   = {7006},

  Doi                      = {10.1007/978-3-642-24455-1_8},
  Location                 = {Berlin, Germany},
  Url                      = {http://dx.doi.org/10.1007/978-3-642-24455-1_8}
}

@Article{gieseke2012recurrent,
  Title                    = {Efficient recurrent local search strategies for semi- and unsupervised regularized least-squares classification},
  Author                   = {Gieseke, Fabian and Kramer, Oliver and Airola, Antti and Pahikkala, Tapio},
  Journal                  = {Evolutionary Intelligence},
  Year                     = {2012},
  Number                   = {3},
  Pages                    = {189--205},
  Volume                   = {5},

  Doi                      = {10.1007/s12065-012-0068-5},
  Url                      = {http://dx.doi.org/10.1007/s12065-012-0068-5}
}

@InProceedings{gieseke2009evolutionary,
  Title                    = {Fast evolutionary maximum margin clustering},
  Author                   = {Gieseke, Fabian and Pahikkala, Tapio and Kramer, Oliver},
  Booktitle                = {ICML '09: Proceedings of the 26th Annual International Conference on Machine Learning},
  Year                     = {2009},

  Address                  = {New York, NY, USA},
  Editor                   = {L\'{e}on Bottou and Michael Littman},
  Month                    = {June},
  Pages                    = {361--368},
  Publisher                = {ACM},
  Series                   = {ACM International Conference Proceeding Series},
  Volume                   = {382},

  Doi                      = {http://doi.acm.org/10.1145/1553374.1553421},
  File                     = {245.pdf:http\://www.cs.mcgill.ca/~icml2009/papers/245.pdf:PDF},
  ISBN                     = {978-1-60558-516-1},
  Location                 = {Montreal, Quebec, Canada},
  Url                      = {http://doi.acm.org/10.1145/1553374.1553421}
}

@PhdThesis{ginter07phd,
  Title                    = {Information Extraction in the Biomedical Domain: Methods and Resources},
  Author                   = {Ginter, Filip},
  School                   = {Turku Centre for Computer Science (TUCS)},
  Year                     = {2007}
}

@Article{ginter04disambiguation,
  Title                    = {New Techniques for Disambiguation in Natural Language and Their Application to Biological Text},
  Author                   = {Ginter, Filip and Boberg, Jorma and J{\"a}rvinen, Jouni and Salakoski, Tapio},
  Journal                  = {Journal of Machine Learning Research},
  Year                     = {2004},
  Pages                    = {605--621},
  Volume                   = {5},

  File                     = {ginter04a.pdf:http\://www.jmlr.org/papers/volume5/ginter04a/ginter04a.pdf:PDF},
  Publisher                = {MIT Press, Cambridge, Massachusetts}
}

@InProceedings{ginter06psearch,
  Title                    = {A Probabilistic Search for the Best Solution Among Partially Completed Candidates},
  Author                   = {Filip Ginter and Aleksandr Myll{\"{a}}ri and Tapio Salakoski},
  Booktitle                = {Proceedings of the HLT/NAACL'06 Workshop on Computationally Hard Problems and Joint Inference in Speech and Language Processing},
  Year                     = {2006},
  Editor                   = {McDonald, Ryan and Sutton, Charles and Daum{\'e}, Hal and McCallum, Andrew and Bilmes, Jeff and Pereira, Fernando},
  Pages                    = {33--40},
  Publisher                = {ACL},

  File                     = {W06-3605.pdf:http\://acl.ldc.upenn.edu/W/W06/W06-3605.pdf:PDF}
}

@InProceedings{ginter13ftb3,
  Title                    = {Building a Large Automatically Parsed Corpus of {Finnish}},
  Author                   = {Ginter, Filip and Nyblom, Jenna and Laippala, Veronika and Kohonen, Samuel and Haverinen, Katri and Vihjanen, Simo and Salakoski, Tapio},
  Booktitle                = {Proceedings of the 19th Nordic Conference on Computational Linguistics (NoDaLiDa'13)},
  Year                     = {2013},
  Pages                    = {291-300},

  File                     = {ecp1385026.pdf:http\://www.ep.liu.se/ecp/085/026/ecp1385026.pdf:PDF},
  Owner                    = {ginter},
  Timestamp                = {2013.03.14}
}

@InProceedings{ginter04extracting,
  Title                    = {Extracting Protein-Protein Interaction Sentences by Applying Rough Set Data Analysis},
  Author                   = {Ginter, Filip and Pahikkala, Tapio and Pyysalo, Sampo and Boberg, Jorma and J{\"a}rvinen, Jouni and Salakoski, Tapio},
  Booktitle                = {Proceedings of the Fourth International Conference on Rough Sets and Current Trends in Computing, Uppsala, Sweden},
  Year                     = {2004},
  Editor                   = {Tsumoto, Husaku and Slowinski, Roman and Komorowski, Jan and Grzymala-Busse, Jerzy W.},
  Month                    = {June},
  Pages                    = {780--785},
  Publisher                = {Springer, Heidelberg},
  Series                   = {Lecture Notes in Computer Science},
  Volume                   = {3066}
}

@InProceedings{ginter05ie,
  Title                    = {Information Extraction from Biomedical Text: {The} {BioText} Project},
  Author                   = {Ginter, Filip and Pahikkala, Tapio and Pyysalo, Sampo and Tsivtsivadze, Evgeni and Boberg, Jorma and J{\"a}rvinen, Jouni and Myll{\"a}ri, Aleksandr and Salakoski, Tapio},
  Booktitle                = {Proceedings of the Second Baltic Conference on Human Language Technologies HLT 05, Tallinn, Estonia},
  Year                     = {2005},
  Editor                   = {Langemets, Margit and Priit, Penjam},
  Month                    = {April},
  Pages                    = {131--136}
}

@TechReport{ginter06manual,
  Title                    = {{BioInfer} Relationship Annotation Manual},
  Author                   = {Ginter, Filip and Pyysalo, Sampo and Bj{\"{o}}rne, Jari and Heimonen, Juho and Salakoski, Tapio},
  Institution              = {Turku Centre for Computer Science (TUCS)},
  Year                     = {2007},
  Number                   = {TR 806}
}

@InProceedings{ginter04ontology,
  Title                    = {Ontology-Based Feature Transformations: {A} Data-Driven Approach},
  Author                   = {Ginter, Filip and Pyysalo, Sampo and Boberg, Jorma and J{\"a}rvinen, Jouni and Salakoski, Tapio},
  Booktitle                = {Proceedings of the 4th International Conference EsTAL 04, Alicante, Spain},
  Year                     = {2004},
  Editor                   = {Vicedo, Jose Luis and Mart\'{\i}nez-Barco, Patricio and Mu\~{n}oz, Rafael and Saiz Noeda, Maximiliano},
  Month                    = {October},
  Pages                    = {279--290},
  Publisher                = {Springer, Heidelberg},
  Series                   = {Lecture Notes in Computer Science},
  Volume                   = {3230},

  File                     = {ginter04ontology.pdf:http\://staff.cs.utu.fi/~ginter/fulltext/ginter04ontology.pdf:PDF}
}

@InProceedings{ginter06fslg,
  Title                    = {Regular Approximation of {Link Grammar}},
  Author                   = {Ginter, Filip and Pyysalo, Sampo and Boberg, Jorma and Salakoski, Tapio},
  Booktitle                = {Proceedings of the 5th International Conference on Natural Language Processing FinTAL 06, Turku, Finland},
  Year                     = {2006},
  Editor                   = {Salakoski, Tapio and Ginter, Filip and Pyysalo, Sampo and Pahikkala, Tapio},
  Pages                    = {564--575},
  Publisher                = {Springer, Heidelberg},
  Series                   = {Lecture Notes in Artificial Intelligence},
  Volume                   = {4139},

  File                     = {ginter06fslg.pdf:http\://staff.cs.utu.fi/~ginter/fulltext/ginter06fslg.pdf:PDF}
}

@InProceedings{ginter05docclas,
  Title                    = {Document Classification Using Semantic Networks with An Adaptive Similarity Measure},
  Author                   = {Ginter, Filip and Pyysalo, Sampo and Salakoski, Tapio},
  Booktitle                = {Proceedings of the International Conference on Recent Advances in Natural Language Processing RANLP 05, Borovets, Bulgaria},
  Year                     = {2005},
  Editor                   = {Angelova, Galia and Bontcheva, Kalina and Mitkov, Ruslan and Nicolov, Nicolas and Nikolov, Nikolai},
  Month                    = {September},
  Pages                    = {204--211},
  Publisher                = {Incoma, Bulgaria},

  File                     = {ginter05docclas.pdf:http\://staff.cs.utu.fi/~ginter/fulltext/ginter05docclas.pdf:PDF}
}

@InCollection{ginter06docclas,
  Title                    = {Document Classification Using Semantic Networks with An Adaptive Similarity Measure},
  Author                   = {Ginter, Filip and Pyysalo, Sampo and Salakoski, Tapio},
  Booktitle                = {Recent Advances in Natural Language Processing {IV}: {S}elected papers from {RANLP} 2005},
  Publisher                = {John Benjamins},
  Year                     = {2007},

  Address                  = {Amsterdam, The Netherlands},
  Editor                   = {Nicolov, Nicolas and Bontcheva, Kalina and Angelova, Galia and Mitkov, Ruslan},
  Pages                    = {137--146}
}

@InProceedings{ginter08combining,
  Title                    = {Combining {Hidden Markov Models} and Latent Semantic Analysis for Topic Segmentation and Labeling: {M}ethod and Clinical Application},
  Author                   = {Filip Ginter and Hanna Suominen and Sampo Pyysalo and Tapio Salakoski},
  Booktitle                = {Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland},
  Year                     = {2008},
  Editor                   = {Tapio Salakoski and Dietrich Rebholz-Schuhmann and Sampo Pyysalo},
  Pages                    = {37--44},
  Publisher                = {Turku Centre for Computer Science (TUCS)},

  File                     = {smbmpaper_14.pdf:http\://mars.cs.utu.fi/smbm2008/files/smbm2008proceedings/smbmpaper_14.pdf:PDF}
}

@Article{ginter09combiningjournal,
  Title                    = {Combining {Hidden Markov Models} and Latent Semantic Analysis for Topic Segmentation and Labeling: {M}ethod and Clinical Application},
  Author                   = {Filip Ginter and Hanna Suominen and Sampo Pyysalo and Tapio Salakoski},
  Journal                  = {International Journal of Medical Informatics, Special Issue on Mining of Clinical and Biomedical Text and Data},
  Year                     = {2009},
  Number                   = {12},
  Pages                    = {e1--e6},
  Volume                   = {78},

  Issue                    = {12},
  Publisher                = {Elsevier},
  Url                      = {http://dx.doi.org/10.1016/j.ijmedinf.2009.02.003}
}

@InProceedings{hakala2016syntactic,
  Title                    = {Syntactic analyses and named entity recognition for {PubMed} and {PubMed Central} —up-to-the-minute},
  Author                   = {Hakala, Kai and Kaewphan, Suwisa and Salakoski, Tapio and Ginter, Filip},
  Booktitle                = {Proceedings of the 2016 Workshop on Biomedical Natural Language Processing},
  Organization             = {Association for Computational Linguistics},
  Pages                    = {102--107},
  Year                     = {2016}
}

@InProceedings{hakala2015semeval,
  Title                    = {{UTU}: Adapting Biomedical Event Extraction System to Disorder Attribute Detection},
  Author                   = {Hakala, Kai},
  Booktitle                = {Proceedings of the 9th International Workshop on Semantic Evaluation (SemEval 2015)},
  Year                     = {2015},
  Pages                    = {375--379},
  Publisher                = {Association for Computational Linguistics},

  Owner                    = {ginter},
  Timestamp                = {2015.06.24},
  Url                      = {https://aclweb.org/anthology/S/S15/S15-2064.pdf}
}

@InProceedings{hakala2013hypothesis,
  Title                    = {Hypothesis Generation in Large-Scale Event Networks},
  Author                   = {Kai Hakala and Farrokh Mehryary and Suwisa Kaewphan and Filip Ginter},
  Booktitle                = {Proceedings of the 5th International Symposium on Languages in Biology and Medicine (LBM'13)},
  Year                     = {2013},
  Pages                    = {19--28},

  Owner                    = {ginter},
  Timestamp                = {2014.02.12}
}

@InProceedings{hakala2012cyevex,
  Title                    = {{CyEVEX}: Literature-scale network integration and visualization through Cytoscape},
  Author                   = {Hakala, Kai and Van Landeghem, Sofie and Kaewphan, Suwisa and Salakoski, Tapio and {Van de Peer}, Yves and Ginter, Filip},
  Booktitle                = {Proceedings of SMBM'12, Zurich, Switzerland},
  Year                     = {2012},
  Pages                    = {91--96},

  Owner                    = {ginter},
  Timestamp                = {2012.04.05}
}

@Article{hakala2015stextension,
  Title                    = {Application of the {EVEX} resource to event extraction and network construction: {Shared Task} entry and result analysis},
  Author                   = {Hakala, Kai and Van Landeghem, Sofie and Salakoski, Tapio and Van de Peer, Yves and Ginter, Filip},
  Journal                  = {BMC Bioinformatics},
  Year                     = {2015},
  Number                   = {Suppl 16},
  Pages                    = {S3},
  Volume                   = {16},

  Doi                      = {10.1186/1471-2105-16-S16-S3},
  ISSN                     = {1471-2105},
  Url                      = {http://www.biomedcentral.com/1471-2105/16/S16/S3}
}

@InProceedings{hakala2013st,
  Title                    = {{EVEX in ST'13}: Application of a large-scale text mining resource to event extraction and network construction},
  Author                   = {Hakala, Kai and Van Landeghem, Sofie and Salakoski, Tapio and Van de Peer, Yves and Ginter, Filip},
  Booktitle                = {Proceedings of the BioNLP Shared Task 2013 Workshop (BioNLP-ST'13)},
  Year                     = {2013},
  Pages                    = {26--34},

  File                     = {PDF:http\://aclweb.org/anthology-new/W/W13/W13-2004.pdf:PDF},
  Owner                    = {ginter},
  Timestamp                = {2013.06.06}
}

@Article{Jiang2016,
  author                   = "Jiang, Yuxiang and Oron, Ronnen Tal and Clark, T. Wyatt and Bankapur, R. Asma and D'Andrea, Daniel and Lepore, Rosalba and Funk, S. Christopher and Kahanda, Indika and Verspoor, M. Karin and Ben-Hur, Asa and Koo, Emily Da Chen and Penfold-Brown, Duncan and Shasha, Dennis and Youngs, Noah and Bonneau, Richard and Lin, Alexandra and Sahraeian, E. Sayed M. and Martelli, Luigi Pier and Profiti, Giuseppe and Casadio, Rita and Cao, Renzhi and Zhong, Zhaolong and Cheng, Jianlin and Altenhoff, Adrian and Skunca, Nives and Dessimoz, Christophe and Dogan, Tunca and Hakala, Kai and Kaewphan, Suwisa and Mehryary, Farrokh and Salakoski, Tapio and Ginter, Filip and Fang, Hai and Smithers, Ben and Oates, Matt and Gough, Julian and T{\"o}r{\"o}nen, Petri and Koskinen, Patrik and Holm, Liisa and Chen, Ching-Tai and Hsu, Wen-Lian and Bryson, Kevin and Cozzetto, Domenico and Minneci, Federico and Jones, T. David and Chapman, Samuel and BKC, Dukka and Khan, K. Ishita and Kihara, Daisuke and Ofer, Dan and Rappoport, Nadav and Stern, Amos and Cibrian-Uhalte, Elena and Denny, Paul and Foulger, E. Rebecca and Hieta, Reija and Legge, Duncan and Lovering, C. Ruth and Magrane, Michele and Melidoni, N. Anna and Mutowo-Meullenet, Prudence and Pichler, Klemens and Shypitsyna, Aleksandra and Li, Biao and Zakeri, Pooya and ElShal, Sarah and Tranchevent, L{\'e}on-Charles and Das, Sayoni and Dawson, L. Natalie and Lee, David and Lees, G. Jonathan and Sillitoe, Ian and Bhat, Prajwal and Nepusz, Tam{\'a}s and Romero, E. Alfonso and Sasidharan, Rajkumar and Yang, Haixuan and Paccanaro, Alberto and Gillis, Jesse and Sede{\~{n}}o-Cort{\'e}s, E. Adriana and Pavlidis, Paul and Feng, Shou and Cejuela, M. Juan and Goldberg, Tatyana and Hamp, Tobias and Richter, Lothar and Salamov, Asaf and Gabaldon, Toni and Marcet-Houben, Marina and Supek, Fran and Gong, Qingtian and Ning, Wei and Zhou, Yuanpeng and Tian, Weidong and Falda, Marco and Fontana, Paolo and Lavezzo, Enrico and Toppo, Stefano and Ferrari, Carlo and Giollo, Manuel and Piovesan, Damiano and Tosatto, C.E. Silvio and del Pozo, Angela and Fern{\'a}ndez, M. Jos{\'e} and Maietta, Paolo and Valencia, Alfonso and Tress, L. Michael and Benso, Alfredo and Di Carlo, Stefano and Politano, Gianfranco and Savino, Alessandro and Rehman, Ur Hafeez and Re, Matteo and Mesiti, Marco and Valentini, Giorgio and Bargsten, W. Joachim and van Dijk, J. Aalt D. and Gemovic, Branislava and Glisic, Sanja and Perovic, Vladmir and Veljkovic, Veljko and Veljkovic, Nevena and Almeida-e-Silva, C. Danillo and Vencio, N. Ricardo Z. and Sharan, Malvika and Vogel, J{\"o}rg and Kansakar, Lakesh and Zhang, Shanshan and Vucetic, Slobodan and Wang, Zheng and Sternberg, E. Michael J. and Wass, N. Mark and Huntley, P. Rachael and Martin, J. Maria and O'Donovan, Claire and Robinson, N. Peter and Moreau, Yves and Tramontano, Anna and Babbitt, C. Patricia and Brenner, E. Steven and Linial, Michal and Orengo, A. Christine and Rost, Burkhard and Greene, S. Casey and Mooney, D. Sean and Friedberg, Iddo and Radivojac, Predrag",
  title                    = "An expanded evaluation of protein function prediction methods shows an improvement in accuracy",
  journal                  = "Genome Biology",
  year                     = "2016",
  volume                   = "17",
  number                   = "1",
  pages                    = "1--19",
  issn                     = "1474-760X",
  doi                      = "10.1186/s13059-016-1037-6",
  url                      = "http://dx.doi.org/10.1186/s13059-016-1037-6"
}



@InCollection{haverinen13errors,
  Title                    = {A Dependency-based Analysis of Treebank Annotation Errors},
  Author                   = {Katri Haverinen and Filip Ginter and Veronika Laippala and Samuel Kohonen and Timo Viljanen and Jenna Nyblom and Tapio Salakoski},
  Booktitle                = {Computational Dependency Theory},
  Publisher                = {IOS Press},
  Year                     = {2013},
  Editor                   = {Gerdes, Kim and Haji{\v{c}}ov{\'a}, Eva and Wanner, Leo},

  Owner                    = {ginter},
  Timestamp                = {2013.09.24}
}

@InProceedings{haverinen11errors,
  Title                    = {A Dependency-based Analysis of Treebank Annotation Errors},
  Author                   = {Katri Haverinen and Filip Ginter and Veronika Laippala and Samuel Kohonen and Timo Viljanen and Jenna Nyblom and Tapio Salakoski},
  Booktitle                = {Proceedings of International Conference on Dependency Linguistics (Depling'11), Barcelona, Spain},
  Year                     = {2011},
  Pages                    = {115-124},

  File                     = {PDF:http\://depling.org/proceedingsDepling2011/papers/haverinenGinterLaippalaKohonenViljanenNyblomSalakoski.pdf:PDF},
  Owner                    = {ginter},
  Timestamp                = {2011.08.11}
}

@InProceedings{haverinen09parsing,
  Title                    = {Parsing Clinical {F}innish: Experiments with Rule-Based and Statistical Dependency Parsers},
  Author                   = {Haverinen, Katri and Ginter, Filip and Laippala, Veronika and Salakoski, Tapio},
  Booktitle                = {Proceedings of NODALIDA'09, Odense, Denmark},
  Year                     = {2009},
  Editor                   = {Jokinen, Kristiina and Bick, Eckhard},
  Pages                    = {65--72},

  File                     = {paper25.pdf:http\://dspace.utlib.ee/dspace/bitstream/10062/9728/1/paper25.pdf:PDF}
}

@InProceedings{haverinen2009wiki,
  Title                    = {Dependency Annotation of {W}ikipedia: First Steps towards a {F}innish Treebank},
  Author                   = {Haverinen, Katri and Ginter, Filip and Laippala, Veronika and Viljanen, Timo and Salakoski, Tapio},
  Booktitle                = {Proceedings of The Eighth International Workshop on Treebanks and Linguistic Theories (TLT8)},
  Year                     = {2009},
  Editor                   = {Passarotti, Marco and Przepi\'{o}rkowski, Adam and Raynaud, Sabina and van Eynde, Frank},
  Pages                    = {95--105},

  File                     = {PDF:http\://bionlp.utu.fi/sites/default/files/haverinen-et-al-2009.pdf:PDF},
  Owner                    = {ginter},
  Timestamp                = {2009.10.28}
}

@InProceedings{haverinen2010propbanking,
  Title                    = {Dependency-based {PropBanking} of Clinical {Finnish}},
  Author                   = {Haverinen, Katri and Ginter, Filip and Laippala, Veronika and Viljanen, Timo and Salakoski, Tapio},
  Booktitle                = {Proceedings of The Fourth Linguistic Annotation Workshop (LAW IV)},
  Year                     = {2010},
  Pages                    = {137--141},
  Publisher                = {ACL},

  File                     = {PDF:http\://aclweb.org/anthology-new/W/W10/W10-1819.pdf:PDF},
  Owner                    = {ginter},
  Timestamp                = {2010.05.21}
}

@InProceedings{haverinen08accurrate,
  Title                    = {Accurate Conversion of Dependency Parses: {T}argeting the {Stanford} Scheme},
  Author                   = {Katri Haverinen and Filip Ginter and Sampo Pyysalo and Tapio Salakoski},
  Booktitle                = {Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland},
  Year                     = {2008},
  Editor                   = {Tapio Salakoski and Dietrich Rebholz-Schuhmann and Sampo Pyysalo},
  Pages                    = {133--136},
  Publisher                = {Turku Centre for Computer Science (TUCS)},

  File                     = {smbmpaper_3.pdf:http\://mars.cs.utu.fi/smbm2008/files/smbm2008proceedings/smbmpaper_3.pdf:PDF}
}

@Article{haverinen2015propbank,
  Title                    = {The {F}innish {P}roposition {B}ank},
  Author                   = {Katri Haverinen and Jenna Kanerva and Samuel Kohonen and Anna Missil{\"a} and Stina Ojala and Timo Viljanen and Veronika Laippala and Filip Ginter},
  Journal                  = {Language Resources and Evaluation},
  Year                     = {2015},
  Number                   = {4},
  Pages                    = {907--926},
  Volume                   = {49},

  Doi                      = {10.1007/s10579-015-9310-y},
  Publisher                = {Springer Netherlands},
  Url                      = {http://dx.doi.org/10.1007/s10579-015-9310-y}
}

@InProceedings{haverinen13propbank,
  Title                    = {Towards a Dependency-based {PropBank} of General {Finnish}},
  Author                   = {Haverinen, Katri and Laippala, Veronika and Kohonen, Samuel and Missil{\"a}, Anna and Nyblom, Jenna and Ojala, Stina and Viljanen, Timo and Salakoski, Tapio and Ginter, Filip},
  Booktitle                = {Proceedings of the 19th Nordic Conference on Computational Linguistics (NoDaLiDa'13)},
  Year                     = {2013},
  Pages                    = {41--57},

  File                     = {ecp1385009.pdf:http\://www.ep.liu.se/ecp/085/009/ecp1385009.pdf:PDF},
  Owner                    = {ginter},
  Timestamp                = {2013.03.14}
}

@Article{haverinen2013tdt,
  Title                    = {Building the essential resources for {Finnish}: the {Turku Dependency Treebank}},
  Author                   = {Haverinen, Katri and Nyblom, Jenna and Viljanen, Timo and Laippala, Veronika and Kohonen, Samuel and Missil{\"a}, Anna and Ojala, Stina and Salakoski, Tapio and Ginter, Filip},
  Journal                  = {Language Resources and Evaluation},
  Year                     = {2014},
  Note                     = {Open access},
  Pages                    = {493-531},
  Volume                   = {48},

  Doi                      = {10.1007/s10579-013-9244-1},
  ISSN                     = {1574-020X},
  Issue                    = {3},
  Keywords                 = {Treebank; Finnish; Parsing; Morphology},
  Language                 = {English},
  Owner                    = {ginter},
  Publisher                = {Springer Netherlands},
  Timestamp                = {2013.08.15},
  Url                      = {http://dx.doi.org/10.1007/s10579-013-9244-1}
}

@InProceedings{haverinen2010treebankingfinnish,
  Title                    = {Treebanking {F}innish},
  Author                   = {Katri Haverinen and Timo Viljanen and Veronika Laippala and Samuel Kohonen and Filip Ginter and Tapio Salakoski},
  Booktitle                = {Proceedings of the Ninth International Workshop on Treebanks and Linguistic Theories (TLT9)},
  Year                     = {2010},
  Editor                   = {Dickinson, Markus and M\"{u}\"{u}risep, Kaili and Passarotti, Marco},
  Month                    = {December},
  Pages                    = {79--90},

  Owner                    = {ginter},
  Timestamp                = {2011.05.13},
  Url                      = {http://hdl.handle.net/10062/15936}
}

@InProceedings{heimonen2010reconstruction,
  Title                    = {Reconstruction of semantic relationships from their projections in biomolecular domain},
  Author                   = {Heimonen, Juho and Bj{\"o}rne, Jari and Salakoski, Tapio},
  Booktitle                = {Proceedings of the 2010 Workshop on Biomedical Natural Language Processing},
  Year                     = {2010},
  Organization             = {Association for Computational Linguistics},
  Pages                    = {108--116}
}

@InProceedings{heimonen08complex,
  Title                    = {Complex-to-Pairwise Mapping of Biological Relationships using a Semantic Network Representation},
  Author                   = {Juho Heimonen and Sampo Pyysalo and Filip Ginter and Tapio Salakoski},
  Booktitle                = {Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland},
  Year                     = {2008},
  Editor                   = {Tapio Salakoski and Dietrich Rebholz-Schuhmann and Sampo Pyysalo},
  Pages                    = {45--52},
  Publisher                = {Turku Centre for Computer Science (TUCS)},

  File                     = {smbmpaper_19.pdf:http\://mars.cs.utu.fi/smbm2008/files/smbm2008proceedings/smbmpaper_19.pdf:PDF}
}

@InProceedings{hiissa2006towards,
  Title                    = {Towards automated classification of intensive care nursing narratives},
  Author                   = {Marketta Hiissa and Tapio Pahikkala and Hanna Suominen and Tuija Lehtikunnas and Barbro Back and Eija Helena Karsten and Sanna Salanter{\"a} and Tapio Salakoski},
  Booktitle                = {Ubiquity: Technologies for Better Health in Aging Societies. Proceedings of MIE 2006, the 20th International Congress of the European Federation of Medical Informatics},
  Year                     = {2006},

  Address                  = {Amsterdam, the Netherlands},
  Editor                   = {Hasman, A and Haux, R and Van Der Lei, J and De Clercq E and Roger France, FH},
  Pages                    = {789--794},
  Publisher                = {IOS Press},
  Series                   = {Studies in Health Technology and Informatics},
  Volume                   = {124}
}

@Article{hiissa07,
  Title                    = {Towards automated classification of intensive care nursing narratives},
  Author                   = {Hiissa, Marketta and Pahikkala, Tapio and Suominen, Hanna and Lehtikunnas, Tuija and Back, Barbro and Karsten, Helena and Salanter{\"a}, Sanna and Salakoski, Tapio},
  Journal                  = {International Journal of Medical Informatics},
  Year                     = {2007},
  Pages                    = {S362--S368},
  Volume                   = {76S3},

  Doi                      = {http://dx.doi.org/10.1016/j.ijmedinf.2007.03.003}
}

@TechReport{hiissa06tr,
  Title                    = {Towards automated classification of intensive care nursing narratives},
  Author                   = {Hiissa, Marketta and Pahikkala, Tapio and Suominen, Hanna and Lehtikunnas, Tuija and Back, Barbro and Karsten, Helena and Salanter{\"a}, Sanna and Salakoski, Tapio},
  Institution              = {{TUCS}},
  Year                     = {2006},

  Address                  = {Turku Centre for Computer Science, Turku, Finland},

  Volume                   = {739}
}

@InProceedings{hiissa06sotetite,
  Title                    = {Kohti tehohoitoty{\"o}n narratiivien tehokkaampaa hy{\"o}dynt{\"a}mist{\"a} luonnollisen kielen k{\"a}sittelyn avulla (Towards more efficient use of intensive care narratives through natural language processing)},
  Author                   = {Hiissa, Marketta and Suominen, Hanna and Back, Barbro and Karsten, Helena and Salakoski, Tapio and Salanter{\"a}, Sanna},
  Booktitle                = {Sosiaali- ja terveydenhuollon tietotekniikan ja tiedonhallinnan tutkimusp{\"a}iv{\"a}t, Tutkimuspaperit 2006},
  Year                     = {2006},
  Editor                   = {H{\"a}yrinen, Kristiina},
  Pages                    = {17--23},
  Publisher                = {Valopaino Oy, Helsinki},
  Series                   = {Stakes, Ty{\"o}papereita 18/2006}
}

@InProceedings{kaewphan2014SemEval,
  Title                    = {{UTU}: Disease Mention Recognition and Normalization with {CRFs} and Vector Space Representations},
  Author                   = {Kaewphan, Suwisa and Hakala, Kai and Ginter, Filip},
  Booktitle                = {Proceedings of the 8th International Workshop on Semantic Evaluation (SemEval 2014)},
  Year                     = {2014},
  Pages                    = {807--811},
  Publisher                = {Association for Computational Linguistics and Dublin City University},

  Url                      = {http://www.aclweb.org/anthology/S/S14/S14-2143.pdf}
}

@InProceedings{kaewphan12nadph,
  Title                    = {Integrating Large-Scale Text Mining and Co-Expression Networks: Targeting {NADP(H)} Metabolism in E. coli with Event Extraction},
  Author                   = {Kaewphan, Suwisa and Kreula, Sanna and Van Landeghem, Sofie and {Van de Peer}, Yves and Jones, Patrik R. and Ginter, Filip},
  Booktitle                = {Proceedings of the Third Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM 2012)},
  Year                     = {2012},
  Pages                    = {8--15},

  Owner                    = {ginter},
  Timestamp                = {2012.04.05}
}
@article{10.1093/bioinformatics/btv570,
    author = {Kaewphan, Suwisa and Van Landeghem, Sofie and Ohta, Tomoko and Van de Peer, Yves and Ginter, Filip and Pyysalo, Sampo},
    title = "{Cell line name recognition in support of the identification of synthetic lethality in cancer from text}",
    journal = {Bioinformatics},
    volume = {32},
    number = {2},
    pages = {276-282},
    year = {2015},
    month = {10},
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btv570},
    url = {https://dx.doi.org/10.1093/bioinformatics/btv570},
    eprint = {http://oup.prod.sis.lan/bioinformatics/article-pdf/32/2/276/6690131/btv570.pdf},
}

@InProceedings{kanerva2014post,
  Title                    = {Post-hoc Manipulations of Vector Space Models with Application to {Semantic Role Labeling}},
  Author                   = {Kanerva, Jenna and Ginter, Filip},
  Booktitle                = {Proceedings of the 2nd Workshop on Continuous Vector Space Models and their Compositionality (CVSC) at EACL'14},
  Year                     = {2014},
  Pages                    = {1--10},

  Url                      = {https://aclweb.org/anthology/W/W14/W14-1501.pdf}
}

@InProceedings{kanerva2015semeval,
  Title                    = {{T}urku: Semantic Dependency Parsing as a Sequence Classification},
  Author                   = {Jenna Kanerva and Juhani Luotolahti and Filip Ginter},
  Booktitle                = {Proceedings of SemEval 2015},
  Year                     = {2015},
  Pages                    = {265--269},
  Publisher                = {Association for Computational Linguistics},

  Url                      = {https://aclweb.org/anthology/S/S15/S15-2161.pdf}
}

@InProceedings{kanerva2014SemEval,
  Title                    = {Turku: Broad-Coverage Semantic Parsing with Rich Features},
  Author                   = {Kanerva, Jenna and Luotolahti, Juhani and Ginter, Filip},
  Booktitle                = {Proceedings of the 8th International Workshop on Semantic Evaluation (SemEval 2014)},
  Year                     = {2014},
  Pages                    = {678--682},
  Publisher                = {Association for Computational Linguistics and Dublin City University},

  Url                      = {http://www.aclweb.org/anthology/S/S14/S14-2121.pdf}
}

@InProceedings{kanerva2014syn,
  Title                    = {Syntactic {N}-gram Collection from a Large-Scale Corpus of Internet {Finnish}},
  Author                   = {Kanerva, Jenna and Luotolahti, Matti and Laippala, Veronika and Ginter, Filip},
  Booktitle                = {Proceedings of the Sixth International Conference Baltic HLT 2014},
  Year                     = {2014},
  Pages                    = {184--191},
  Publisher                = {IOS Press},

  Doi                      = {10.3233/978-1-61499-442-8-184},
  Url                      = {http://ebooks.iospress.nl/volumearticle/38025}
}

@Article{kano2011ucompare,
  Title                    = {U-Compare bio-event meta-service: compatible BioNLP event extraction services},
  Author                   = {Kano, Yoshinobu and Bj\"{o}rne, Jari and Ginter, Filip and Salakoski, Tapio and Buyko, Ekaterina and Hahn, Udo and Cohen, Kevin and Verspoor, Karin and Roeder, Christophe and Hunter, Lawrence and Kilicoglu, Halil and Bergler, Sabine and Landeghem, Sofie and Parys, Thomas and {Van de Peer}, Yves and Miwa, Makoto and Ananiadou, Sophia and Neves, Mariana and Pascual-Montano, Alberto and Ozgur, Arzucan and Radev, Dragomir and Riedel, Sebastian and Saetre, Rune and Chun, Hong-Woo and Kim, Jin-Dong and Pyysalo, Sampo and Ohta, Tomoko and Tsujii, Jun'ichi},
  Journal                  = {BMC Bioinformatics},
  Year                     = {2011},
  Number                   = {1},
  Pages                    = {481},
  Volume                   = {12},

  Doi                      = {10.1186/1471-2105-12-481},
  ISSN                     = {1471-2105},
  Pubmedid                 = {22177292},
  Url                      = {http://www.biomedcentral.com/1471-2105/12/481}
}

@InProceedings{laippala08resource2,
  Title                    = {Resource-efficient construction of a full parser for {Finnish} nursing narratives},
  Author                   = {Laippala, Veronika and Ginter, Filip and Pyysalo, Sampo and Salakoski, Tapio},
  Booktitle                = {Proceedings of the First Louhi Conference on Text and Data Mining of Clinical Documents (Louhi'08), Turku, Finland},
  Year                     = {2008},
  Editor                   = {Karsten, Helena and Back, Barbro and Salakoski, Tapio and Salanter{\"a}, Sanna},
  Pages                    = {34--53},
  Publisher                = {Turku Centre for Computer Science (TUCS)}
}

@Article{laippala09parserjournal,
  Title                    = {Towards Automated Processing of Clinical {Finnish}: A Sublanguage Analysis and a Rule-Based Parser},
  Author                   = {Veronika Laippala and Filip Ginter and Sampo Pyysalo and Tapio Salakoski},
  Journal                  = {International Journal of Medical Informatics, Special Issue on Mining of Clinical and Biomedical Text and Data},
  Year                     = {2009},
  Number                   = {12},
  Pages                    = {e7--e12},
  Volume                   = {78},

  Publisher                = {Elsevier}
}

@Article{laippala2015syngrams,
  Title                    = {Syntactic {Ngrams} as Keystructures Reflecting Typical Syntactic Patterns of Corpora in {Finnish}},
  Author                   = {Veronika Laippala and Jenna Kanerva and Filip Ginter},
  Journal                  = {Procedia -- Social and Behavioral Sciences. Current Work in Corpus Linguistics: Working Traditionally-conceived Corpora and Beyon. Selected Papers from the 7th International Conference on Corpus Linguistics (CILC2015)},
  Year                     = {2015},
  Pages                    = {233--241},
  Volume                   = {198}
}

@InProceedings{laippala2015synngrams,
  Title                    = {Syntactic {N}-grams in the Classification of the {Finnish Internet Parsebank}: {D}etecting Translations and Informality},
  Author                   = {Laippala, Veronika and Kanerva, Jenna and Pyysalo, Sampo and Missil{\"a}, Anna and Salakoski, Tapio and Ginter, Filip},
  Booktitle                = {Proceedings of NoDaLiDa 2015},
  Year                     = {2015},
  Pages                    = {108--116},
  Publisher                = {NEALT},

  Url                      = {https://aclweb.org/anthology/W/W15/W15-1815.pdf}
}

@Article{laippala2014sp,
  Title                    = {Statistical parsing of varieties of clinical {Finnish}},
  Author                   = {Veronika Laippala and Timo Viljanen and Antti Airola and Jenna Kanerva and Sanna Salanter{\"a} and Tapio Salakoski and Filip Ginter},
  Journal                  = {Artificial Intelligence in Medicine},
  Year                     = {2014},
  Note                     = {Text Mining and Information Analysis of Health Documents },
  Number                   = {3},
  Pages                    = {131--136},
  Volume                   = {61},

  Doi                      = {10.1016/j.artmed.2014.02.002},
  ISSN                     = {0933-3657},
  Url                      = {http://dx.doi.org/10.1016/j.artmed.2014.02.002}
}

@InProceedings{laippala13statparsing,
  Title                    = {Statistical Parsing of Varieties of Clinical {Finnish}},
  Author                   = {Laippala, Veronika and Viljanen, Timo and Airola, Antti and Nyblom, Jenna and Salanter{\"a}, Sanna and Salakoski, Tapio and Ginter, Filip},
  Booktitle                = {Proceedings of the 4th International Louhi Workshop on Health Document Text Mining and Information Analysis (Louhi 2013)},
  Year                     = {2013},
  Editor                   = {Suominen, Hanna},

  File                     = {PDF:http\://www.nicta.com.au/__data/assets/pdf_file/0010/37657/louhi2013_submission_8.pdf:PDF},
  Owner                    = {ginter},
  Timestamp                = {2013.03.14}
}

@InProceedings{LLSuominenetal2009,
  Title                    = {Intensive care admission and discharge --- critical decision-making points},
  Author                   = {Lundgr{\'e}n-Laine, Helj{\"a} and Suominen, Hanna and Kontio, Elina and Salanter{\"a}, Sanna and Salakoski, Tapio},
  Booktitle                = {Connecting Health and Humans. Proceedings of NI2009, the 10th International Congress of Nursing Informatics},
  Year                     = {2009},

  Address                  = {Amsterdam, the Netherlands},
  Editor                   = {Saranto, K and Flatley Brennan, P and Park, H-A and Tallberg, M and Ensio, A},
  Pages                    = {358--361},
  Publisher                = {IOS Press},
  Series                   = {Studies in Health Technology and Informatics},
  Volume                   = {146}
}

@InProceedings{LundgrenLaine06,
  Title                    = {Tehohoidon elektroninen kirjaaminen -- kohti narratiivien automaattista luokittelua (Electronic intensive care documentation; towards automated classification of narratives)},
  Author                   = {Lundgren-Laine, Helj{\"a} and Hiissa, Marketta and Suominen, Hanna and Lehtikunnas, Tuija and Salanter{\"a}, Sanna},
  Booktitle                = {IX Kansallinen hoitotieteellinen konferenssi ''Viisas vaikuttaja''},
  Year                     = {2006},

  Address                  = {Turku, Finland},
  Pages                    = {98}
}

@InProceedings{luotolahti2015compression,
  Title                    = {Sentence Compression for Automatic Subtitling},
  Author                   = {Luotolahti, Juhani and Ginter, Filip},
  Booktitle                = {Proceedings of NoDaLiDa 2015},
  Year                     = {2015},
  Pages                    = {135--143},

  Url                      = {https://aclweb.org/anthology/W/W15/W15-1818.pdf}
}

@InProceedings{luotolahti2015parsebanks,
  Title                    = {Towards Universal Web Parsebanks},
  Author                   = {Luotolahti, Juhani and Kanerva, Jenna and Laippala, Veronika and Pyysalo, Sampo and Ginter, Filip},
  Booktitle                = {Proceedings of the International Conference on Dependency Linguistics (Depling'15)},
  Year                     = {2015},
  Pages                    = {211--220},
  Publisher                = {Uppsala University},

  Owner                    = {ginter},
  Timestamp                = {2015.06.24}
}

@InProceedings{luotolahti2015sets,
  Title                    = {{SETS:} Scalable and Efficient Tree Search in Dependency Graphs},
  Author                   = {Juhani Luotolahti and Jenna Kanerva and Sampo Pyysalo and Filip Ginter},
  Booktitle                = {Proceedings of the 2015 Conference of the North American Chapter of the Association for Computational Linguistics: Demonstrations},
  Year                     = {2015},
  Pages                    = {51--55},
  Publisher                = {Association for Computational Linguistics},

  Url                      = {https://aclweb.org/anthology/N/N15/N15-3011.pdf}
}

@Article{mehryary2016filtering,
  Title                    = {Filtering large-scale event collections using a combination of supervised and unsupervised learning for event trigger classification},
  Author                   = {Mehryary, Farrokh and Kaewphan, Suwisa and Hakala, Kai and Ginter, Filip},
  Journal                  = {Journal of Biomedical Semantics},
  Year                     = {2016},
  Number                   = {1},
  Pages                    = {1--13},
  Volume                   = {7},

  Doi                      = {10.1186/s13326-016-0070-4},
  ISSN                     = {2041-1480},
  Url                      = {http://dx.doi.org/10.1186/s13326-016-0070-4}
}

@InProceedings{mehryary2014clustering,
  Title                    = {Eliminating Incorrect Events from Large-Scale Event Networks by Trigger Word Clustering and Pruning},
  Author                   = {Farrokh Mehryary and Suwisa Kaewphan and Kai Hakala and Filip Ginter},
  Booktitle                = {Proceedings of SMBM'14},
  Year                     = {2014},
  Pages                    = {75--79},

  Url                      = {http://www.zora.uzh.ch/98982/}
}

@Article{moen2015care,
  Title                    = {Care episode retrieval: distributional semantic models for information retrieval in the clinical domain},
  Author                   = {Moen, Hans and Ginter, Filip and Marsi, Erwin and Peltonen, Laura-Maria and Salakoski, Tapio and Salanter{\"a}, Sanna},
  Journal                  = {BMC Medical Informatics and Decision Making},
  Year                     = {2015},
  Number                   = {Suppl 2},
  Pages                    = {S2},
  Volume                   = {15},

  Doi                      = {10.1186/1472-6947-15-S2-S2},
  ISSN                     = {1472-6947},
  Publisher                = {BioMed Central Ltd},
  Pubmedid                 = {26099735},
  Url                      = {http://www.biomedcentral.com/1472-6947/15/S2/S2}
}

@InProceedings{moen2014care,
  Title                    = {Care Episode Retrieval},
  Author                   = {Moen, Hans and Marsi, Erwin and Ginter, Filip and Murtola, Laura-Maria and Salakoski, Tapio and Salanter{\"{a}}, Sanna},
  Booktitle                = {Proceedings of the 5th International Workshop on Health Text Mining and Information Analysis (Louhi)},
  Year                     = {2014},
  Pages                    = {116--124},
  Publisher                = {Association for Computational Linguistics},

  Url                      = {http://www.aclweb.org/anthology/W14-1118}
}

@InProceedings{naula2010budgeted,
  Title                    = {Learning Multi-Label Predictors under Sparsity Budget},
  Author                   = {Naula, Pekka and Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio},
  Booktitle                = {Eleventh Scandinavian Conference on Artificial Intelligence, SCAI 2011},
  Year                     = {2011},
  Editor                   = {Kofod-Petersen, Anders and Heintz, Fredrik and Langseth, Helge},
  Month                    = {May},
  Pages                    = {30--39},
  Publisher                = {IOS Press},
  Series                   = {Frontiers in Artificial Intelligence and Applications},
  Volume                   = {227},

  ISBN                     = {978-1-60750-753-6}
}

@InProceedings{naula2011grlsmultitask,
  Title                    = {Greedy Regularized Least-Squares for Multi-Task Learning},
  Author                   = {Naula, Pekka and Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio},
  Booktitle                = {11th IEEE International Conference on Data Mining Workshops (ICDMW'11)},
  Year                     = {2011},
  Editor                   = {Spiliopoulou, Myra and Wang, Haixun and Cook, Diane and Pei, Jian and Wang, Wei and Za{\"i}ane, Osmar, and Wu, Xindong},
  Month                    = {December},
  Pages                    = {527--533},
  Publisher                = {IEEE Computer Society},

  Doi                      = {10.1109/ICDMW.2011.91}
}

@InProceedings{nivre2016udv1,
  Title                    = {{Universal Dependencies v1}: A Multilingual Treebank Collection},
  Author                   = {Joakim Nivre and Marie-Catherine de Marneffe and Filip Ginter and Yoav Goldberg and Jan Haji{\v{c}} and Christopher D. Manning and Ryan McDonald and Slav Petrov and Sampo Pyysalo and Natalia Silveira and Reut Tsarfaty and Daniel Zeman},
  Booktitle                = {Proceedings of Language Resources and Evaluation Conference (LREC'16)},
  Year                     = {2016},
  Owner                    = {ginter},
  Timestamp                = {2016.05.19}
}

@InProceedings{nyblom2013ccprop,
  Title                    = {Predicting conjunct propagation and other extended {Stanford Dependencies}},
  Author                   = {Nyblom, Jenna and Kohonen, Samuel and Haverinen, Katri and Salakoski, Tapio and Ginter, Filip},
  Booktitle                = {Proceedings of the International Conference on Dependency Linguistics (Depling 2013)},
  Year                     = {2013},
  Pages                    = {252--261},

  Owner                    = {ginter},
  Timestamp                = {2013.06.06}
}

@InProceedings{oepen2017epe,
  Title                    = {The 2017 {S}hared {T}ask on {E}xtrinsic {P}arser {E}valuation. {T}owards a Reusable Community Infrastructure},
  Author                   = {Oepen, Stephan and {\O}vrelid, Lilja and Bj{\"o}rne, Jari and Johansson, Richard and Lapponi, Emanuele and Ginter, Filip and Velldal, Erik},
  Booktitle                = {Proceedings of the 2017 Shared Task on Extrinsic Parser Evaluation (EPE 2017) at the Fourth International Conference on Dependency Linguistics (Depling 2017) and the 15th International Conference on Parsing Technologies (IWTP 2017)},
  Year                     = {2017},
  Pages                    = {1--16},
  Publisher                = {Association for Computational Linguistics},
  ISBN                     = {978-1-945626-74-6},
}

@InProceedings{okser2011fastgwas,
  Title                    = {Fast and Parallelized Greedy Forward Selection of Genetic Variants in Genome-Wide Association Studies},
  Author                   = {Okser, Sebastian and Pahikkala, Tapio and Airola, Antti and Aittokallio, Tero and Salakoski, Tapio},
  Booktitle                = {IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS'11)},
  Year                     = {2011},
  Editor                   = {Chen, Yidong and Huang, Yufei and Dougherty, Edward},
  Month                    = {December},
  Pages                    = {214--217},
  Publisher                = {IEEE Signal Processing Society},

  Doi                      = {10.1109/GENSiPS.2011.6169483}
}

@PhdThesis{pahikkala2008phdthesis,
  Title                    = {New Kernel Functions and Learning Methods for Text and Data Mining},
  Author                   = {Tapio Pahikkala},
  School                   = {Turku Centre for Computer Science (TUCS)},
  Year                     = {2008},

  Address                  = {Turku, Finland},
  Month                    = {June},

  Owner                    = {aatapa},
  Timestamp                = {2009.10.10}
}

@InProceedings{pahikkala2008lpocv,
  Title                    = {Exact and Efficient Leave-Pair-Out Cross-Validation for Ranking {RLS}},
  Author                   = {Pahikkala, Tapio and Airola, Antti and Boberg, Jorma and Salakoski, Tapio},
  Booktitle                = {Proceedings of the 2nd International and Interdisciplinary Conference on Adaptive Knowledge Representation and Reasoning (AKRR'08)},
  Year                     = {2008},
  Editor                   = {Timo Honkela and Matti P{\"o}ll{\"a} and Mari-Sanna Paukkeri and Olli Simula},
  Pages                    = {1--8},
  Publisher                = {Helsinki University of Technology},

  File                     = {attachment.php?fname=inpPaAiBoSa08a.pdf:http\://www.tucs.fi/publications/attachment.php?fname=inpPaAiBoSa08a.pdf:PDF}
}

@InProceedings{pahikkala2012shakingrls,
  Title                    = {Unsupervised Multi-Class Regularized Least-Squares Classification},
  Author                   = {Pahikkala, Tapio and Airola, Antti and Gieseke, Fabian and Kramer, Oliver},
  Booktitle                = {The 12th IEEE International Conference on Data Mining (ICDM 2012)},
  Year                     = {2012},
  Editor                   = {Zaki, Mohammed J. and Siebes, Arno and Yu, Jeffrey Xu and Goethals, Bart and Webb, Geoff and Wu, Xindong},
  Month                    = {December},
  Pages                    = {585--594},
  Publisher                = {IEEE Computer Society},

  Doi                      = {10.1109/ICDM.2012.71},
  Url                      = {http://staff.cs.utu.fi/~aatapa/publications/pdf/icdm2012preprint.pdf}
}

@InProceedings{pahikkala2010grankrls,
  Title                    = {Greedy {RankRLS}: a Linear Time Algorithm for Learning Sparse Ranking Models},
  Author                   = {Pahikkala, Tapio and Airola, Antti and Naula, Pekka and Salakoski, Tapio},
  Booktitle                = {SIGIR 2010 Workshop on Feature Generation and Selection for Information Retrieval},
  Year                     = {2010},
  Editor                   = {Gabrilovich, Evgeniy and Smola, Alexander J. and Tishby, Naftali},
  Pages                    = {11--18},
  Publisher                = {ACM}
}

@InProceedings{pahikkala2010greedyrls,
  Title                    = {Speeding up Greedy Forward Selection for Regularized Least-Squares},
  Author                   = {Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio},
  Booktitle                = {Proceedings of The Ninth International Conference on Machine Learning and Applications (ICMLA'10)},
  Year                     = {2010},
  Editor                   = {Draghici, Sorin and Khoshgoftaar, Taghi M. and Palade, Vasile and Pedrycz, Witold and Wani, M. Arif and Zhu, Xingquan},
  Month                    = {December},
  Pages                    = {325--330},
  Publisher                = {IEEE},

  Doi                      = {10.1109/ICMLA.2010.55},
  Url                      = {http://staff.cs.utu.fi/~aatapa/publications/inpPaAiSa10b.full.pdf}
}

@InProceedings{pahikkala2010fsrls,
  Title                    = {Feature Selection for Regularized Least-Squares: New Computational Short-Cuts and Fast Algorithmic Implementations},
  Author                   = {Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio},
  Booktitle                = {Proceedings of the Twentieth IEEE International Workshop on Machine Learning for Signal Processing (MLSP 2010)},
  Year                     = {2010},
  Editor                   = {Kaski, Samuel and Miller, David J. and Oja, Erkki and Honkela, Antti},
  Pages                    = {295--300},
  Publisher                = {IEEE},

  Doi                      = {10.1109/MLSP.2010.5589210},
  ISBN                     = {978-1-4244-7876-7},
  Location                 = {Kittil{\"a}, Finland},
  Url                      = {http://dx.doi.org/10.1109/MLSP.2010.5589210}
}

@InCollection{pahikkala2008aucmax,
  Title                    = {Efficient {AUC} Maximization with Regularized Least-Squares},
  Author                   = {Pahikkala, Tapio and Airola, Antti and Suominen, Hanna and Boberg, Jorma and Salakoski, Tapio},
  Booktitle                = {Proceedings of the 10th Scandinavian Conference on Artificial Intelligence (SCAI 2008)},
  Publisher                = {IOS Press},
  Year                     = {2008},

  Address                  = {Amsterdam, Netherlands},
  Editor                   = {Anders Holst and Per Kreuger and Peter Funk},
  Pages                    = {12--19},
  Series                   = {Frontiers in Artificial Intelligence and Applications},
  Volume                   = {173},

  File                     = {attachment.php?fname=inpPaAiSuBoSa08a.pdf:http\://www.tucs.fi/publications/attachment.php?fname=inpPaAiSuBoSa08a.pdf:PDF}
}

@InProceedings{pahikkala2011parallelonline,
  Title                    = {A parallel online regularized least-squares machine learning algorithm for future multi-core processors},
  Author                   = {Pahikkala, Tapio and Airola, Antti and Xu, Thomas Canhao and Liljeberg, Pasi and Tenhunen, Hannu and Salakoski, Tapio},
  Booktitle                = {Proceedings of the 1st International Conference on Pervasive and Embedded Computing and Communication Systems (PECCS 2011)},
  Year                     = {2011},
  Editor                   = {Benavente-Peces, C{\'e}sar and Filipe, Joaquim},
  Month                    = {March},
  Pages                    = {590--599},
  Publisher                = {SciTePress},

  ISBN                     = {978-989-8425-48-5},
  Location                 = {Algarve, Portugal}
}

@Article{pahikkala2012parallelizedonline,
  Title                    = {Parallelized Online Regularized Least-Squares for Adaptive Embedded Systems},
  Author                   = {Pahikkala, Tapio and Airola, Antti and Xu, Thomas Canhao and Liljeberg, Pasi and Tenhunen, Hannu and Salakoski, Tapio},
  Journal                  = {International Journal of Embedded and Real-Time Communication Systems},
  Year                     = {2012},

  Month                    = {April},
  Number                   = {2},
  Pages                    = {73--91},
  Volume                   = {3},

  Doi                      = {10.4018/jertcs.2012040104},
  ISSN                     = {1947-3176},
  Publisher                = {IGI Global}
}

@InProceedings{pahikkala06ltbayes,
  Title                    = {Incorporating External Information in Bayesian Classifiers via Linear Feature Transformations},
  Author                   = {Tapio Pahikkala and Jorma Boberg and Aleksandr Myll\"{a}ri and Tapio Salakoski},
  Booktitle                = {Proceedings of the 5th International Conference on Natural Language Processing FinTAL 06, Turku, Finland},
  Year                     = {2006},
  Editor                   = {Salakoski, Tapio and Ginter, Filip and Pyysalo, Sampo and Pahikkala, Tapio},
  Pages                    = {399--410},
  Publisher                = {Springer, Heidelberg},
  Series                   = {Lecture Notes in Artificial Intelligence},
  Volume                   = {4139},

  File                     = {:http\://tucs.fi/publications/attachment.php?fname=inpPaBoMySa06a.pdf:PDF}
}

@InProceedings{pahikkala06rls,
  Title                    = {Fast n-Fold Cross-Validation for Regularized Least-Squares},
  Author                   = {Tapio Pahikkala and Jorma Boberg and Tapio Salakoski},
  Booktitle                = {Proceedings of the Ninth Scandinavian Conference on Artificial Intelligence (SCAI 2006)},
  Year                     = {2006},

  Address                  = {Espoo, Finland},
  Editor                   = {Timo Honkela and Tapani Raiko and Jukka Kortela and Harri Valpola},
  Pages                    = {83-90},
  Publisher                = {Otamedia Oy},

  File                     = {:http\://www.tucs.fi/publications/attachment.php?fname=inpPaBoSa06a.pdf:PDF},
  Location                 = {Espoo, Finland}
}

@Article{pahikkala05contextual,
  Title                    = {Contextual Weighting for Support Vector Machines in Literature Mining: {An} Application to Gene Versus Protein Name Disambiguation},
  Author                   = {Pahikkala, Tapio and Ginter, Filip and Boberg, Jorma and J{\"a}rvinen, Jouni and Salakoski, Tapio},
  Journal                  = {BMC Bioinformatics},
  Year                     = {2005},
  Number                   = {1},
  Pages                    = {157},
  Volume                   = {6},

  Doi                      = {http://dx.doi.org/doi:10.1186/1471-2105-6-157},
  File                     = {157:http\://www.biomedcentral.com/1471-2105/6/157:PDF}
}

@Article{pahikkala2012wrappergwas,
  Title                    = {Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations},
  Author                   = {Pahikkala, Tapio and Okser, Sebastian and Airola, Antti and Salakoski, Tapio and Aittokallio, Tero},
  Journal                  = {Algorithms for Molecular Biology},
  Year                     = {2012},
  Number                   = {1},
  Pages                    = {11},
  Volume                   = {7},

  Doi                      = {10.1186/1748-7188-7-11},
  ISSN                     = {1748-7188},
  Url                      = {http://www.almob.org/content/7/1/11}
}

@Article{pahikkala2009matrix,
  Title                    = {Matrix representations, linear transformations, and kernels for disambiguation in natural language},
  Author                   = {Pahikkala, Tapio and Pyysalo, Sampo and Boberg, Jorma and J\"{a}rvinen, Jouni and Salakoski, Tapio},
  Journal                  = {Machine Learning},
  Year                     = {2009},
  Number                   = {2},
  Pages                    = {133--158},
  Volume                   = {74},

  Address                  = {Hingham, MA, USA},
  Doi                      = {http://dx.doi.org/10.1007/s10994-008-5082-6},
  File                     = {attachment.php?fname=jPaPyBoJaSa08a.pdf:http\://www.tucs.fi/publications/attachment.php?fname=jPaPyBoJaSa08a.pdf:PDF},
  ISSN                     = {0885-6125},
  Publisher                = {Kluwer Academic Publishers},
  Url                      = {http://dx.doi.org/10.1007/s10994-008-5082-6}
}

@InProceedings{pahikkala05improving,
  Title                    = {Improving the performance of Bayesian and support vector classifiers in word sense disambiguation using positional information},
  Author                   = {Tapio Pahikkala and Sampo Pyysalo and Jorma Boberg and Aleksandr Myll{\"a}ri and Tapio Salakoski},
  Booktitle                = {Proceedings of the International and Interdisciplinary Conference on Adaptive Knowledge Representation and Reasoning},
  Year                     = {2005},

  Address                  = {Espoo, Finland},
  Editor                   = {Timo Honkela and Ville K{\"o}n{\"o}nen and Matti P{\"o}ll{\"a} and Olli Simula},
  Pages                    = {90--97},
  Publisher                = {Helsinki University of Technology},

  File                     = {:http\://www.tucs.fi/publications/attachment.php?fname=inpPaPyBoMySa05a.pdf:PDF}
}

@InProceedings{pahikkala05kernels,
  Title                    = {Kernels Incorporating Word Positional Information in Natural Language Disambiguation Tasks},
  Author                   = {Pahikkala, Tapio and Pyysalo, Sampo and Ginter, Filip and Boberg, Jorma and J{\"a}rvinen, Jouni and Salakoski, Tapio},
  Booktitle                = {Proceedings of the Eighteenth International Florida Artificial Intelligence Research Society Conference},
  Year                     = {2005},

  Address                  = {Menlo Park, Ca.},
  Editor                   = {Russell, Ingrid and Markov, Zdravko},
  Month                    = {May},
  Note                     = {Copyright AAAI Press, http://www.aaai.org/},
  Pages                    = {442--447},
  Publisher                = {AAAI Press},

  File                     = {attachment.php?fname=inpPaPyGiBoJaSa05a.pdf:http\://www.tucs.fi/publications/attachment.php?fname=inpPaPyGiBoJaSa05a.pdf:PDF},
  Location                 = {Clearwater Beach, Florida}
}

@Article{pahikkala2012efficientcv,
  Title                    = {Efficient cross-validation for kernelized least-squares regression with sparse basis expansions},
  Author                   = {Pahikkala, Tapio and Suominen, Hanna and Boberg, Jorma},
  Journal                  = {Machine Learning},
  Year                     = {2012},

  Month                    = {June},
  Number                   = {3},
  Pages                    = {381-407},
  Volume                   = {87},

  Affiliation              = {Department of Information Technology and Turku Centre for Computer Science, University of Turku, 20014 Turku, Finland},
  Doi                      = {10.1007/s10994-012-5287-6},
  File                     = {PDF:http\://staff.cs.utu.fi/~aatapa/publications/CV_postprint.pdf:PDF},
  ISSN                     = {0885-6125},
  Publisher                = {Springer Netherlands},
  Url                      = {http://dx.doi.org/10.1007/s10994-012-5287-6}
}

@InProceedings{pahikkala07mlg,
  Title                    = {Transductive Ranking via Pairwise Regularized Least-Squares},
  Author                   = {Pahikkala, Tapio and Suominen, Hanna and Boberg, Jorma and Salakoski, Tapio},
  Booktitle                = {The 5th International Workshop on Mining and Learning with Graphs (MLG'07)},
  Year                     = {2007},
  Editor                   = {Frasconi, P and Kersting, K and Tsuda, K},
  Pages                    = {175--178},

  File                     = {:http\://www.tucs.fi/publications/attachment.php?fname=inpPaSuBoSa07a.pdf:PDF},
  Location                 = {Florence, Italy}
}

@InProceedings{pahikkala2009holdout,
  Title                    = {Efficient Hold-Out for Subset of Regressors},
  Author                   = {Tapio Pahikkala and Hanna Suominen and Jorma Boberg and Tapio Salakoski},
  Booktitle                = {{Proceedings of the 9th International Conference on Adaptive and Natural Computing Algorithms (ICANNGA'09)}},
  Year                     = {2009},

  Address                  = {Berlin, Germany},
  Editor                   = {Mikko Kolehmainen and Pekka Toivanen and Bartlomiej Beliczynski},
  Pages                    = {350--359},
  Publisher                = {Springer},
  Series                   = {Lecture Notes in Computer Science},
  Volume                   = {5495},

  Doi                      = {DOI:10.1007/978-3-642-04921-7_36},
  File                     = {attachment.php?fname=inpPaSuBoSa09a.full.pdf:http\://www.tucs.fi/publications/attachment.php?fname=inpPaSuBoSa09a.full.pdf:PDF},
  Url                      = {http://dx.doi.org/DOI:10.1007/978-3-642-04921-7_36}
}

@InProceedings{pahikkala2007rankrls,
  Title                    = {Learning to Rank with Pairwise Regularized Least-Squares},
  Author                   = {Tapio Pahikkala and Evgeni Tsivtsivadze and Antti Airola and Jorma Boberg and Tapio Salakoski},
  Booktitle                = {SIGIR 2007 Workshop on Learning to Rank for Information Retrieval},
  Year                     = {2007},
  Editor                   = {Joachims, Thorsten and Li, Hang and Liu, Tie-Yan and Zhai, ChengXiang},
  Pages                    = {27-33},

  File                     = {:http\://www.tucs.fi/publications/attachment.php?fname=inpPaTsAiBoSa07a.pdf:PDF}
}

@Article{pahikkala2009preferences,
  Title                    = {An Efficient Algorithm for Learning to Rank from Preference Graphs},
  Author                   = {Tapio Pahikkala and Evgeni Tsivtsivadze and Antti Airola and Jouni J{\"a}rvinen and Jorma Boberg},
  Journal                  = {Machine Learning},
  Year                     = {2009},
  Number                   = {1},
  Pages                    = {129--165},
  Volume                   = {75},

  Doi                      = {http://dx.doi.org/10.1007/s10994-008-5097-z},
  File                     = {attachment.php?fname=jPaTsAiJaBo09a.pdf:http\://www.tucs.fi/publications/attachment.php?fname=jPaTsAiJaBo09a.full.pdf:PDF},
  Url                      = {http://dx.doi.org/10.1007/s10994-008-5097-z}
}

@InProceedings{pahikkala2008npref,
  Title                    = {Regularized Least-Squares for Learning Non-Transitive Preferences between Strategies},
  Author                   = {Tapio Pahikkala and Evgeni Tsivtsivadze and Antti Airola and Tapio Salakoski},
  Booktitle                = {Proceedings of the 13th Finnish Artificial Intelligence Conference and Nokia Workshop on Machine Consciousness},
  Year                     = {2008},
  Editor                   = {Tapani Raiko and Pentti Haikonen and Jaakko V{\"a}yrynen},
  Pages                    = {94--98},
  Publisher                = {Finnish Artificial Intelligence Society},
  Series                   = {Publications of the Finnish Artificial Intelligence Society},
  Volume                   = {24}
}

@InProceedings{pahikkala2006graph,
  Title                    = {Graph Kernels versus Graph Representations: a Case Study in Parse Ranking},
  Author                   = {Tapio Pahikkala and Evgeni Tsivtsivadze and Jorma Boberg and Tapio Salakoski},
  Booktitle                = {Proceedings of the ECML/PKDD'06 workshop on Mining and Learning with Graphs (MLG'06)},
  Year                     = {2006},

  Address                  = {Berlin, Germany},
  Editor                   = {Thomas G{\"a}rtner and Gemma C. Garriga and Thorsten Meinl},

  File                     = {:http\://www.tucs.fi/publications/attachment.php?fname=inpPaTsBoSa06a.pdf:PDF},
  Location                 = {Berlin, Germany}
}

@InProceedings{pahikkala2010conditional,
  Title                    = {Conditional Ranking on Relational Data},
  Author                   = {Pahikkala, Tapio and Waegeman, Willem and Airola, Antti and Salakoski, Tapio and De Baets, Bernard},
  Booktitle                = {Machine Learning and Knowledge Discovery in Databases, European Conference, ECML PKDD 2010, Barcelona, Spain, September 20-24, 2010, Proceedings, Part II},
  Year                     = {2010},
  Editor                   = {Jos{\'e} L. Balc{\'a}zar and Francesco Bonchi and Aristides Gionis and Mich{\`e}le Sebag},
  Pages                    = {499-514},
  Publisher                = {Springer},
  Series                   = {Lecture Notes in Computer Science},
  Volume                   = {6322},

  Doi                      = {10.1007/978-3-642-15883-4_32},
  Url                      = {http://dx.doi.org/10.1007/978-3-642-15883-4_32}
}

@InProceedings{pahikkala2009beyond,
  Title                    = {From Ranking to Intransitive Preference Learning: Rock-Paper-Scissors and beyond},
  Author                   = {Tapio Pahikkala and Willem Waegeman and Evgeni Tsivtsivadze and Bernard De Baets and Tapio Salakoski},
  Booktitle                = {Proceedings of the {ECML/PKDD}-Workshop on Preference Learning {(PL-09)}},
  Year                     = {2009},
  Editor                   = {Eyke H{\"u}llermeier and Johannes F{\"u}rnkranz},
  Pages                    = {84--100}
}

@InProceedings{pahikkala2009benelearn,
  Title                    = {Learning Intransitive Reciprocal Relations with Regularized Least-Squares},
  Author                   = {Tapio Pahikkala and Willem Waegeman and Evgeni Tsivtsivadze and Bernard De Baets and Tapio Salakoski},
  Booktitle                = {{Proceedings of the 18th Annual Belgian-Dutch Conference on Machine Learning (Benelearn 09)}},
  Year                     = {2009},
  Editor                   = {van Zaanen, Menno and Stehouwer, Herman and van Erp, Marieke},
  Pages                    = {13--20}
}

@Article{pahikkala2010reciprocalkm,
  Title                    = {Learning Intransitive Reciprocal Relations with Kernel Methods},
  Author                   = {Tapio Pahikkala and Willem Waegeman and Evgeni Tsivtsivadze and Tapio Salakoski and Bernard De Baets},
  Journal                  = {European Journal of Operational Research},
  Year                     = {2010},
  Number                   = {3},
  Pages                    = {676--685},
  Volume                   = {206},

  Doi                      = {http://dx.doi.org/10.1016/j.ejor.2010.03.018},
  Url                      = {http://dx.doi.org/10.1016/j.ejor.2010.03.018}
}

@Article{pyysalo08comparative,
  Title                    = {Comparative Analysis of Five Protein-protein Interaction Corpora},
  Author                   = {Pyysalo, Sampo and Airola, Antti and Heimonen, Juho and Bj{\"{o}}rne, Jari and Ginter, Filip and Salakoski, Tapio},
  Journal                  = {BMC Bioinformatics, special issue},
  Year                     = {2008},
  Number                   = {Suppl 3},
  Pages                    = {S6},
  Volume                   = {9},

  File                     = {S6:http\://www.biomedcentral.com/1471-2105/9/S3/S6:PDF}
}

@InProceedings{pyysalo06lexical,
  Title                    = {Lexical Adaptation of {Link Grammar} to the Biomedical Sublanguage: a Comparative Evaluation of Three Approaches},
  Author                   = {Sampo Pyysalo and Sophie Aubin and Adeline Nazarenko and Tapio Salakoski},
  Booktitle                = {Proceedings of the Second International Symposium on Semantic Mining in Biomedicine (SMBM'06)},
  Year                     = {2006},
  Pages                    = {60--67}
}

@Article{pyysalo06lexicalBMC,
  Title                    = {Lexical Adaptation of {Link Grammar} to the Biomedical Sublanguage: a Comparative Evaluation of Three Approaches},
  Author                   = {Sampo Pyysalo and Sophie Aubin and Adeline Nazarenko and Tapio Salakoski},
  Journal                  = {BMC Bioinformatics},
  Year                     = {2006},
  Pages                    = {S2},
  Volume                   = {7(Suppl 3)}
}

@InProceedings{pyysalo2015restful,
  Title                    = {Sharing annotations better: {RESTful Open Annotation}},
  Author                   = {Sampo Pyysalo and Jorge Campos and Cejuela, Juan Miguel and Filip Ginter and Kai Hakala and Chen Li and Pontus Stenetorp and Jensen, Lars Juhl},
  Booktitle                = {Proceedings of ACL'15: Demonstrations},
  Year                     = {2015},
  Owner                    = {ginter},
  Timestamp                = {2015.06.24}
}

@Article{pyysalo06corpus,
  Title                    = {{BioInfer}: {A} Corpus for Information Extraction in the Biomedical Domain},
  Author                   = {Sampo Pyysalo and Filip Ginter and Juho Heimonen and Jari Bj{\"{o}}rne and Jorma Boberg and Jouni J{\"{a}}rvinen and Tapio Salakoski},
  Journal                  = {BMC Bioinformatics},
  Year                     = {2007},
  Pages                    = {50},
  Volume                   = {8},

  File                     = {50:http\://www.biomedcentral.com/1471-2105/8/50:PDF}
}

@InProceedings{pyysalo07unification,
  Title                    = {On the unification of syntactic annotations under the Stanford dependency scheme: A case study on {BioInfer} and {GENIA}},
  Author                   = {Pyysalo, Sampo and Ginter, Filip and Laippala, Veronika and Haverinen, Katri and Heimonen, Juho and Salakoski, Tapio},
  Booktitle                = {ACL'07 workshop on Biological, translational, and clinical language processing (BioNLP'07)},
  Year                     = {2007},

  Address                  = {Prague, Czech Republic},
  Pages                    = {25--32},
  Publisher                = {Association for Computational Linguistics},

  File                     = {W07-1004.pdf:http\://aclweb.org/anthology-new/W/W07/W07-1004.pdf:PDF}
}

@InProceedings{pyysalo2013dist,
  Title                    = {Distributional Semantic Resources for Biomedical Text Mining},
  Author                   = {Sampo Pyysalo and Filip Ginter and Hans Moen and Tapio Salakoski and Sophia Ananiadou},
  Booktitle                = {Proceedings of the 5th International Symposium on Languages in Biology and Medicine},
  Year                     = {2013},
  Pages                    = {39--44},

  Owner                    = {ginter},
  Timestamp                = {2014.02.12}
}

@Article{pyysalo06evaluation,
  Title                    = {Evaluation of Two Dependency Parsers on Biomedical Corpus Targeted at Protein-Protein Interactions},
  Author                   = {Pyysalo, Sampo and Ginter, Filip and Pahikkala, Tapio and Boberg, Jorma and J{\"a}rvinen, Jouni and Salakoski, Tapio},
  Journal                  = {Recent Advances in Natural Language Processing for Biomedical Applications, special issue of the International Journal of Medical Informatics},
  Year                     = {2006},
  Number                   = {6},
  Pages                    = {430--442},
  Volume                   = {75},

  Editor                   = {Robert Baud and Nigel Collier and Adeline Nazarenko and Patrick Ruch},
  Publisher                = {Elsevier}
}

@InProceedings{pyysalo04analysis,
  Title                    = {Analysis of {Link Grammar} on Biomedical Dependency Corpus Targeted at Protein-Protein Interactions},
  Author                   = {Pyysalo, Sampo and Ginter, Filip and Pahikkala, Tapio and Koivula, Jeppe and Boberg, Jorma and J{\"a}rvinen, Jouni and Salakoski, Tapio},
  Booktitle                = {Proceedings of Joint Workshop on Natural Language Processing in Biomedicine and its Applications JNLPBA 04, Geneva, Switzerland},
  Year                     = {2004},
  Editor                   = {Collier, Nigel and Ruch, Patrick and Nazarenko, Adeline},
  Month                    = {August},
  Pages                    = {15--21}
}

@InProceedings{pyysalo2015udfinnish,
  Title                    = {Universal {D}ependencies for {F}innish},
  Author                   = {Pyysalo, Sampo and Kanerva, Jenna and Missil{\"a}, Anna and Laippala, Veronika and Ginter, Filip},
  Booktitle                = {Proceedings of NoDaLiDa 2015},
  Year                     = {2015},
  Pages                    = {163--172},
  Publisher                = {NEALT},

  Url                      = {https://aclweb.org/anthology/W/W15/W15-1821.pdf}
}

@InProceedings{pyysalo08why,
  Title                    = {Why Biomedical Relation Extraction Results are Incomparable and What to do about it},
  Author                   = {Pyysalo, Sampo and S{\ae}tre, Rune and Tsujii, Jun'ichi and Salakoski, Tapio},
  Booktitle                = {Proceedings of the Third International Symposium on Semantic Mining in Biomedicine},
  Year                     = {2008},
  Editor                   = {Tapio Salakoski and Dietrich Rebholz-Schuhmann and Sampo Pyysalo},
  Pages                    = {149--152},
  Publisher                = {Turku Centre for Computer Science (TUCS)}
}

@Article{radivojac2013large,
  Title                    = {A large-scale evaluation of computational protein function prediction},
  Author                   = {Radivojac, Predrag and Clark, Wyatt T and Oron, Tal Ronnen and Schnoes, Alexandra M and Wittkop, Tobias and Sokolov, Artem and Graim, Kiley and Funk, Christopher and Verspoor, Karin and Ben-Hur, Asa and others},
  Journal                  = {Nature methods},
  Year                     = {2013},
  Number                   = {3},
  Pages                    = {221--227},
  Volume                   = {10},

  Publisher                = {Nature Publishing Group}
}

@InProceedings{stock2012monadic,
  Title                    = {Learning Monadic and Dyadic Relations: Three Case Studies in Systems Biology},
  Author                   = {Stock, Michiel and Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio and De Baets, Bernard and Waegeman, Willem},
  Booktitle                = {Proceedings of the ECML/PKDD 2012 Workshop on Learning and Discovery in Symbolic Systems Biology},
  Year                     = {2012},
  Editor                   = {Oliver Ray and Katsumi Inoue},
  Month                    = {September},
  Pages                    = {74--84}
}

@InProceedings{suominen07tktp,
  Title                    = {Kieliteknologian menetelmien soveltaminen potilasdokumentaation hy{\"o}dynt{\"a}miseen (Applying human language technology to utilization of patient documentation)},
  Author                   = {Suominen, Hanna},
  Booktitle                = {Tietojenk{\"a}sittelytieteen p{\"a}iv{\"a}t 2007},
  Year                     = {2007},
  Editor                   = {Koskinen, M and Jauhiainen, E},
  Pages                    = {46--50},
  Publisher                = {Jyv{\"a}skyl{\"a}n yliopistopaino, Jyv{\"a}skyl{\"a}},
  Series                   = {Tietojenk{\"a}sittelytieteiden julkaisuja. Tutkimuksia TU-25}
}

@InProceedings{suominen08challenge,
  Title                    = {Machine Learning to Automate the Assignment of Diagnosis Codes to Free-text Radiology Reports: a Method Description},
  Author                   = {Suominen, Hanna and Ginter, Filip and Pyysalo, Sampo and Airola, Antti and Pahikkala, Tapio and Salanter{\"{a}}, Sanna and Salakoski, Tapio},
  Booktitle                = {Proceedings of the ICML/UAI workshop on Machine Learning in health care applications},
  Year                     = {2008},
  Editor                   = {M Hauskrecht and D Schuurmans and D Szepesvari}
}

@InProceedings{suominen06ethics,
  Title                    = {Theoretical considerations of ethics in text mining of nursing documents},
  Author                   = {Suominen, Hanna and Lehtikunnas, Tuija and Back, Barbro and Karsten, Helena and Salakoski, Tapio and Salanter{\"a}, Sanna},
  Booktitle                = {Consumer-Centered Computer-Supported Care for Healthy People, Proceedings of NI2006, The 9th International Congress on Nursing Informatics},
  Year                     = {2006},
  Editor                   = {Park, HA and Murray, P and Delaney, C},
  Pages                    = {353--364},
  Publisher                = {IOS Press, Amsterdam, Netherlands},
  Series                   = {Studies in Health Technology and Informatics},
  Volume                   = {122}
}

@Article{suominen07ethicsjournal,
  Title                    = {Applying language technology to nursing documents: pros and cons with a focus on ethics},
  Author                   = {Suominen, Hanna and Lehtikunnas, Tuija and Back, Barbro and Karsten, Helena and Salakoski, Tapio and Salanter{\"a}, Sanna},
  Journal                  = {International Journal of Medical Informatics},
  Year                     = {2007},
  Pages                    = {S293--S301},
  Volume                   = {76S2}
}

@InProceedings{SuominenetalNI2009,
  Title                    = {Evaluating pain in intensive care},
  Author                   = {Suominen, Hanna and Lundgr{\'e}n-Laine, Helj{\"a} and Salakoski, Tapio and Salanter{\"a}, Sanna},
  Booktitle                = {Connecting Health and Humans. Proceedings of NI2009, the 10th International Congress of Nursing Informatics},
  Year                     = {2009},

  Address                  = {Amsterdam, the Netherlands},
  Editor                   = {Saranto, K and Flatley Brennan, P and Park, H-A and Tallberg, M and Ensio, A},
  Pages                    = {191-196},
  Publisher                = {IOS Press},
  Series                   = {Studies in Health Technology and Informatics},
  Volume                   = {146}
}

@InProceedings{suominen09informationflow,
  Title                    = {Information flow in intensive care narratives},
  Author                   = {Suominen, Hanna and Lundgr{\'e}n-Laine, Helj{\"a} and Salanter{\"a}, Sanna and Karsten, Helena and Salakoski, Tapio},
  Booktitle                = {Proceedings of IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBM 2009},
  Year                     = {2009},
  Pages                    = {325--330},

  File                     = {PDF:http\://bionlp.utu.fi/sites/default/files/suominenetal2009flow.pdf:PDF},
  Owner                    = {ginter},
  Timestamp                = {2010.06.11}
}

@InProceedings{suominen08laakaripaivat,
  Title                    = {Tehohoidon elektroniset potilasasiakirjat -- hy{\"o}dynt{\"a}m{\"a}t{\"o}n voimavara (Electronic intensive care patient records; an untapped resource])},
  Author                   = {Suominen, Hanna and Lundgren-Laine, Helj{\"a} and Pertti{\"a}, Juha and Salakoski, Tapio and Salanter{\"a}, Sanna},
  Booktitle                = {The Finnish Medical Convention 2008},
  Year                     = {2008},

  Address                  = {Helsinki, Finland}
}

@InProceedings{suominen2006ranking,
  Title                    = {Relevance ranking of intensive care nursing narratives},
  Author                   = {Hanna Suominen and Tapio Pahikkala and Marketta Hiissa and Tuija Lehtikunnas and Barbro Back and Eija Helena Karsten and Sanna Salanter{\"a} and Tapio Salakoski},
  Booktitle                = {Knowledge-Based {\&} Intelligent Information {\&} Engineering Systems. Proceedings of the 10th International Conference, KES 2006, Part I},
  Year                     = {2006},

  Address                  = {Berlin / Heidelberg, Germany},
  Editor                   = {Gabrys, B and Howlett, RJ and and Jain, LC},
  Pages                    = {720--727},
  Publisher                = { Springer},
  Series                   = {Lecture Notes in Computer Science},
  Volume                   = {4251}
}

@TechReport{suominen06tr,
  Title                    = {Relevance Ranking of Intensive Care Nursing Narratives},
  Author                   = {Suominen, Hanna and Pahikkala, Tapio and Hiissa, Marketta and Lehtikunnas, Tuija and Back, Barbro and Karsten, Helena and Salanter{\"{a}}, Sanna and Salakoski, Tapio},
  Institution              = {{TUCS}},
  Year                     = {2006},

  Address                  = {Turku Centre for Computer Science, Turku, Finland},

  Volume                   = {740}
}

@InProceedings{SuominenetalAKRR,
  Title                    = {Critical points in assessing learning performance via cross-validation},
  Author                   = {Suominen, Hanna and Pahikkala, Tapio and Salakoski, Tapio},
  Booktitle                = {Proceedings of the 2nd International and Interdiciplinary Conference on Adaptive Knowledge Representation and Reasoning (AKRR 2008)},
  Year                     = {2008},

  Address                  = {Espoo, Finland},
  Editor                   = {Honkela, T and P{\"o}ll{\"a}, M and Paukkeri, MS and Simula O},
  Pages                    = {9--22},
  Publisher                = {Multiprint}
}

@InProceedings{suominen08segposter,
  Title                    = {Automated text segmentation and topic labeling of clinical narratives},
  Author                   = {Suominen, Hanna and Pyysalo, Sampo and Ginter, Filip and Salakoski, Tapio},
  Booktitle                = {Proceedings of the First Louhi Conference on Text and Data Mining of Clinical Documents (Louhi'08), Turku, Finland},
  Year                     = {2008},
  Editor                   = {Karsten, Helena and Back, Barbro and Salakoski, Tapio and Salanter{\"{a}}, Sanna},
  Pages                    = {99--103},
  Publisher                = {Turku Centre for Computer Science (TUCS)},
  Series                   = {TUCS General Publications},
  Volume                   = {52}
}

@InCollection{suominen08measures,
  Title                    = { Performance Evaluation Measures for Text Mining},
  Author                   = {Suominen, Hanna and Pyysalo, Sampo and Hiissa, Marketta and Ginter, Filip and Liu, Shuhua and Marghescu, Dorina and Pahikkala, Tapio and Back, Barbro and Karsten, Helena and Salakoski, Tapio},
  Booktitle                = {Handbook of Research on Text and Web Mining Technologies},
  Publisher                = {IGI Global},
  Year                     = {2008},

  Address                  = {Hershey, Pennsylvania, USA},
  Editor                   = {M Song and Y-FB Wu},
  Pages                    = {724--747}
}

@InProceedings{SuominenetalSPIRE,
  Title                    = {Information retrieval and personal health records: user needs and domain tailoring},
  Author                   = {Suominen, Hanna and Salakoski, Tapio},
  Booktitle                = {SPIRE 2009 Workshop on Task-based Information Access},
  Year                     = {2009},
  Note                     = {In Press}
}

@InProceedings{suominen05,
  Title                    = {Natural language processing for nursing documentation},
  Author                   = {Suominen, Hanna J and Lehtikunnas, Tuija and Hiissa, Marketta and Back, Barbro and Karsten, Helena and Salakoski, Tapio and Salanter{\"a}, Sanna},
  Booktitle                = {Proceedings of the 2nd International Conference on Computational Intelligence in Medicine and Healthcare (CIMED 2005)},
  Year                     = {2005},

  Address                  = {Costa da Caparica, Portugal},
  Editor                   = {JM Fonseca},
  Pages                    = {147--154}
}

@InProceedings{tiedemann2015WMT,
  Title                    = {Morphological Segmentation and {OPUS} for {Finnish-English} Machine Translation},
  Author                   = {Tiedemann, J\"{o}rg and Ginter, Filip and Kanerva, Jenna},
  Booktitle                = {Proceedings of the Tenth Workshop on Statistical Machine Translation},
  Year                     = {2015},

  Address                  = {Lisbon, Portugal},
  Pages                    = {177--183},
  Publisher                = {Association for Computational Linguistics},

  Url                      = {http://aclweb.org/anthology/W15-3021}
}

@InProceedings{tsivtsivadze2007prot,
  Title                    = {Locality Kernels for Protein Classification},
  Author                   = {Evgeni Tsivtsivadze and Jorma Boberg and Tapio Salakoski},
  Booktitle                = {Algorithms in Bioinformatics, 7th International Workshop, WABI 2007, Philadelphia, PA, USA, September 8-9, 2007, Proceedings},
  Year                     = {2007},
  Editor                   = {Raffaele Giancarlo and Sridhar Hannenhalli},
  Pages                    = {2-11},
  Publisher                = {Springer},
  Series                   = {Lecture Notes in Computer Science},
  Volume                   = {4645}
}

@InProceedings{tsivtsivadze2008coreg,
  Title                    = {Learning Preferences with Co-Regularized Least Squares},
  Author                   = {Evgeni Tsivtsivadze and Fabian Gieseke and Tapio Pahikkala and Jorma Boberg and Tapio Salakoski},
  Booktitle                = {{ECML/PKDD-Workshop on Preference Learning (PL-08)}},
  Year                     = {2008},
  Editor                   = {Eyke H{\"u}llermeier and Johannes F{\"u}rnkranz},
  Pages                    = {55--62},

  Owner                    = {aatapa},
  Timestamp                = {2009.10.10}
}

@InProceedings{tsivtsivadze08sparse,
  Title                    = {A Sparse Regularized Least-Squares Preference Learning Algorithm},
  Author                   = {Evgeni Tsivtsivadze and Tapio Pahikkala and Antti Airola and Jorma Boberg and Tapio Salakoski},
  Booktitle                = {Proceedings of the 10th Scandinavian Conference on Artificial Intelligence (SCAI 2008)},
  Year                     = {2008},
  Editor                   = {Anders Holst and Per Kreuger and Peter Funk},
  Pages                    = {76--83},
  Publisher                = {IOS Press},
  Volume                   = {173},

  File                     = {attachment.php?fname=inpTsPaAiBoSa08a.pdf:http\://www.tucs.fi/publications/attachment.php?fname=inpTsPaAiBoSa08a.pdf:PDF}
}

@InProceedings{tsivtsivadze2006locality,
  Title                    = {Locality-Convolution Kernel and Its Application to Dependency Parse Ranking},
  Author                   = {Evgeni Tsivtsivadze and Tapio Pahikkala and Jorma Boberg and Tapio Salakoski},
  Booktitle                = {Proceedings of the The 19th International Conference on Industrial, Engineering {\&} Other Applications of Applied Intelligent Systems},
  Year                     = {2006},

  Address                  = {Berlin},
  Editor                   = {Moonis Ali and Richard Dapoigny},
  Pages                    = {610--618},
  Publisher                = {Springer},
  Series                   = {Lecture Notes in Artificial Intelligence},
  Volume                   = {4031}
}

@InCollection{tsivtsivadze2008kft,
  Title                    = {Kernel Methods for Text Analysis},
  Author                   = {Evgeni Tsivtsivadze and Tapio Pahikkala and Jorma Boberg and Tapio Salakoski},
  Booktitle                = {Advances of Computational Intelligence in Industrial Systems},
  Publisher                = {Springer},
  Year                     = {2008},
  Editor                   = {Ying Liu and Aixin Sun and Han Tong Loh and Wen Feng Lu and Ee-Peng Lim},
  Pages                    = {81--97},
  Series                   = {Studies in Computational Intelligence},
  Volume                   = {116}
}

@Article{tsivtsivadze2009localityjournal,
  Title                    = {Locality Kernels for Sequential Data and Their Applications to Parse Ranking},
  Author                   = {Evgeni Tsivtsivadze and Tapio Pahikkala and Jorma Boberg and Tapio Salakoski},
  Journal                  = {Applied Intelligence},
  Year                     = {2009},
  Number                   = {1},
  Pages                    = {81--88},
  Volume                   = {31}
}

@InCollection{tsivtsivadze2010coreg,
  Title                    = {Co-Regularized Least-Squares for Label Ranking},
  Author                   = {Evgeni Tsivtsivadze and Tapio Pahikkala and Jorma Boberg and Tapio Salakoski and Tom Heskes},
  Booktitle                = {Preference Learning},
  Publisher                = {Springer},
  Year                     = {2010},

  Address                  = {Berlin Heidelberg},
  Chapter                  = {6},
  Edition                  = {1st},
  Editor                   = {Johannes F{\"u}rnkranz and Eyke H{\"u}llermeier},
  Pages                    = {107--123},

  Doi                      = {10.1007/978-3-642-14125-6_6},
  ISBN                     = {978-3-642-14124-9},
  Url                      = {http://dx.doi.org/10.1007/978-3-642-14125-6_6}
}

@InProceedings{tsivtsivadze2005ranking,
  Title                    = {Regularized Least-Squares for Parse Ranking},
  Author                   = {Evgeni Tsivtsivadze and Tapio Pahikkala and Sampo Pyysalo and Jorma Boberg and Aleksandr Myll\"{a}ri and Tapio Salakoski},
  Booktitle                = {Proceedings of the 6th International Symposium on Intelligent Data Analysis},
  Year                     = {2005},

  Address                  = {Berlin},
  Editor                   = {A. Fazel Famili and Joost N. Kok and Jos{\'e} Manuel Pe{\~n}a and Arno Siebes and A. J. Feelders},
  Month                    = {September},
  Pages                    = {464--474},
  Publisher                = {Springer},
  Series                   = {Lecture Notes in Computer Science},
  Volume                   = {3646},

  Location                 = {Madrid, Spain}
}

@Article{vahamaa2007dd,
  Title                    = {Computer-assisted identification of multi-trace electrophoretic patterns in differential display experiments},
  Author                   = {Heidi V{\"a}h{\"a}maa and Pekka Ojala and Tapio Pahikkala and Olli S. Nevalainen and Riitta Lahesmaa and Tero Aittokallio},
  Journal                  = {Electrophoresis},
  Year                     = {2007},
  Number                   = {6},
  Pages                    = {879--893},
  Volume                   = {28},

  Doi                      = {doi:10.1002/elps.200600424},
  Url                      = {http://dx.doi.org/doi:10.1002/elps.200600424}
}

@Article{vanlandeghem13evex2,
  Title                    = {Large-scale event extraction from literature with multi-level gene normalization},
  Author                   = {Van Landeghem, Sofie and Bj{\"o}rne, Jari and Wei, Chih-Hsuan and Hakala, Kai and Pyysalo, Sampo and Ananiadou, Sophia and Kao, Hung-Yu and Lu, Zhiyong and Salakoski, Tapio and Van de Peer, Yves and Ginter, Filip},
  Journal                  = {PLoS ONE},
  Year                     = {2013},
  Number                   = {4},
  Pages                    = {e55814},
  Volume                   = {8},

  Doi                      = {10.1371/journal.pone.0055814},
  Owner                    = {ginter},
  Timestamp                = {2013.03.14}
}

@InProceedings{vanlandeghem2011evex,
  Title                    = {{EVEX}: A {PubMed}-Scale Resource for Homology-Based Generalization of Text Mining Predictions},
  Author                   = {Van Landeghem, Sofie and Ginter, Filip and Van de Peer, Yves and Salakoski, Tapio},
  Booktitle                = {Proceedings of BioNLP'11 Workshop},
  Year                     = {2011},
  Pages                    = {28--37},
  Publisher                = {Association for Computational Linguistics},

  File                     = {PDF:http\://aclweb.org/anthology-new/W/W11/W11-0204.pdf:PDF},
  Owner                    = {ginter},
  Timestamp                = {2011.05.13}
}

@Article{vanlandeghem12evexweb,
  Title                    = {Exploring Biomolecular Literature with {EVEX}: Connecting Genes through Events, Homology and Indirect Associations},
  Author                   = {Van Landeghem, Sofie and Hakala, Kai and R\"{o}nnqvist, Samuel and Salakoski, Tapio and Van de Peer, Yves and Ginter, Filip},
  Journal                  = {Advances in Bioinformatics, special issue Literature-Mining Solutions for Life Science Research},
  Year                     = {2012},

  Owner                    = {ginter},
  Timestamp                = {2012.04.05}
}

@InProceedings{vanlandeghem2013eval,
  Title                    = {Evaluating large-scale text mining applications beyond the traditional numeric performance measures},
  Author                   = {Van Landeghem, Sofie and Kaewphan, Suwisa and Ginter, Filip and Van de Peer, Yves},
  Booktitle                = {Proceedings of the 2013 Workshop on Biomedical Natural Language Processing (BioNLP'13)},
  Year                     = {2013},
  Pages                    = {63--71},

  File                     = {PDF:http\://aclweb.org/anthology-new/W/W13/W13-1908.pdf:PDF},
  Owner                    = {ginter},
  Timestamp                = {2013.06.06}
}

@InProceedings{waegeman2011learningvalued,
  Title                    = {Learning Valued Relations from Data},
  Author                   = {Waegeman, Willem and Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio and De Baets, Bernard},
  Booktitle                = {Eurofuse 2011},
  Year                     = {2012},
  Editor                   = {Melo-Pinto, Pedro and Couto, Pedro and Ser\^{o}dio, Carlos and Fodor, J\'{a}nos and De Baets, Bernard},
  Pages                    = {257--268},
  Publisher                = {Springer},
  Series                   = {Advances in Intelligent and Soft Computing},
  Volume                   = {107},

  Doi                      = {10.1007/978-3-642-24001-0_24},
  Url                      = {http://dx.doi.org/10.1007/978-3-642-24001-0_24}
}

@InProceedings{waegeman2012objectretrieval,
  Title                    = {Conditional Ranking Algorithms for Efficient Object Retrieval and Object Querying on Relational Data},
  Author                   = {Waegeman, Willem and Stock, Michiel and De Baets, Bernard and Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio},
  Booktitle                = {Proceedings of the 12th Dutch-Belgian Information Retrieval Workshop (DIR 2012)},
  Year                     = {2012},
  Editor                   = {Demeester, Thomas and Deleu, Johannes and Mertens, Laurent and Plaetinck, Dieter and De Moor, An and Hoang, Thong and Wauters, Tim and Develder, Chris and Vermeulen, Brecht and Demeester, Piet},
  Pages                    = {59-60},
  Publisher                = {Ghent University}
}

@InProceedings{xu2012blunoc,
  Title                    = {Implementation and Analysis of Block Dense Matrix Decomposition on Network-on-Chips},
  Author                   = {Xu, Thomas Canhao and Pahikkala, Tapio and Airola, Antti and Liljeberg, Pasi and Plosila, Juha and Salakoski, Tapio and Tenhunen, Hannu},
  Booktitle                = {The 14th IEEE International Conference on High Performance Computing and Communications (HPCC-2012)},
  Year                     = {2012},
  Editor                   = {Min, Geyong and Hu, Jia and Liu, Lei (Chris) and Yang, Laurence T. and Seelam, Seetharami and Lefevre, Laurent},
  Month                    = {June},
  Pages                    = {516--523},
  Publisher                = {IEEE Computer Society},

  Doi                      = {10.1109/HPCC.2012.76}
}

@Proceedings{Louhi,
  Title                    = {Proceedings of the First Conference on Text and Data Mining of Clinical Documents (Louhi'08)},
  Year                     = {2008},

  Address                  = {Turku, Finland},
  Editor                   = {Karsten, Helena and Back, Barbro and Salakoski, Tapio and Salanter{\"a}, Sanna and Suominen, Hanna},
  Publisher                = {Turku Centre for Computer Science},
  Series                   = {TUCS General Publication},
  Volume                   = {52}
}

@Proceedings{pahikkala2010step,
  Title                    = {Proceedings of the 14th Finnish Artificial Intelligence Conference, STeP 2010},
  Year                     = {2010},

  Address                  = {Espoo, Finland},
  Editor                   = {Pahikkala, Tapio and V{\"a}yrynen, Jaakko and Kortela, Jukka and Airola, Antti},
  Number                   = {25},
  Publisher                = {Aalto--Print},
  Series                   = {Publications of the Finnish Artificial Intelligence Society}
}

@Proceedings{salakoski06fintal,
  Title                    = {Proceedings of the Fifth International Conference on Natural Language Processing FinTAL 06, Turku, Finland},
  Year                     = {2006},
  Editor                   = {Salakoski, Tapio and Ginter, Filip and Pyysalo, Sampo and Pahikkala, Tapio},
  Publisher                = {Springer, Heidelberg},
  Series                   = {Lecture Notes in Artificial Intelligence},
  Volume                   = {4139}
}

@Proceedings{tarkoma2012ytp,
  Title                    = {The Federated Computer Science Event},
  Year                     = {2012},

  Address                  = {Helsinki, Finland},
  Editor                   = {Tarkoma, Sasu and K{\"a}m{\"a}r{\"a}inen, Joni-Kristian and Pahikkala, Tapio},
  Publisher                = {Unigrafia Oy},

  Url                      = {http://www.cs.helsinki.fi/u/starkoma/ytp/YTP-Proceedings-2012.pdf}
}

@InProceedings{mehryary2016bionlpst,
  Title                    = {Deep Learning with Minimal Training Data: {TurkuNLP} Entry in the {BioNLP Shared Task} 2016},
  Author                   = {Mehryary, Farrokh and Bj\"{o}rne, Jari and Pyysalo, Sampo and Salakoski, Tapio and Ginter, Filip},
  Booktitle                = {Proceedings of the 4th BioNLP Shared Task Workshop},
  Year                     = {2016},
  Pages                    = {73--81},
  Publisher                = {Association for Computational Linguistics},
}

@InProceedings{bjorne2016SemEval,
   author    = {Bj\"{o}rne, Jari  and  Salakoski, Tapio},
   title     = {{UTU at SemEval-2016 Task 10: Binary Classification for Expression Detection (BCED)}},
   booktitle = {{Proceedings of the 10th International Workshop on Semantic Evaluation (SemEval-2016)}},
   year      = {2016},
   publisher = {Association for Computational Linguistics},
   pages     = {925--930},
   url       = {http://www.aclweb.org/anthology/S16-1142}
}

@article{moen2016aiim,
  title     = {Comparison of automatic summarisation methods for clinical free text notes},
  year      = {2016},
  author    = {Hans Moen and Laura{-}Maria Peltonen and Juho Heimonen and Antti Airola and Tapio Pahikkala and Tapio Salakoski and Sanna Salanter{\"{a}}},
  journal   = {Artificial Intelligence in Medicine},
  volume    = {67},
  pages     = {25--37},
  url       = {http://dx.doi.org/10.1016/j.artmed.2016.01.003},
  doi       = {10.1016/j.artmed.2016.01.003}
}



@article{laippala16emoticons,
  Title                    = {Dependency profiles as a tool for big data analysis of linguistic constructions: A case study of emoticons},
  Author                   = {Laippala, Veronika and Kyröläinen, Aki-Juhani and Kanerva, Jenna and Luotolahti, Juhani and Ginter, Filip},
  Year                     = {2017},
  Journal                  = {Journal of Estonian and Finno-Ugric Linguistics.
Grammar in Use: Approaches to Baltic Finnic.},
  volume                   = {8},
  pages                    = {127--153}
}


@InProceedings{tiedemann-EtAl:2016:WMT,
  author    = {Tiedemann, J\"{o}rg  and  Cap, Fabienne  and  Kanerva, Jenna  and  Ginter, Filip  and  Stymne, Sara  and  \"{O}stling, Robert  and  Weller-Di Marco, Marion},
  title     = {Phrase-Based SMT for {F}innish with More Data, Better Models and Alternative Alignment and Translation Tools},
  booktitle = {Proceedings of the First Conference on Machine Translation},
  month     = {August},
  year      = {2016},
  address   = {Berlin, Germany},
  publisher = {Association for Computational Linguistics},
  pages     = {391--398},
  url       = {http://www.aclweb.org/anthology/W/W16/W16-2326.pdf}
}

@InProceedings{luotolahti-kanerva-ginter:2016:WMT,
  author    = {Luotolahti, Juhani  and  Kanerva, Jenna  and  Ginter, Filip},
  title     = {Cross-Lingual Pronoun Prediction with Deep Recurrent Neural Networks},
  booktitle = {Proceedings of the First Conference on Machine Translation},
  month     = {August},
  year      = {2016},
  address   = {Berlin, Germany},
  publisher = {Association for Computational Linguistics},
  pages     = {596--601},
  url       = {http://www.aclweb.org/anthology/W/W16/W16-2353.pdf}
}



@article{Lehti2016,
author = {Lehti, Lotta and Isos{\"{a}}vi, Johanna and Laippala, Veronika and Luotolahti, Matti},
journal = {WiderScreen},
number = {1–2},
title = {Linguistic analysis of online conflicts: {A} case study of flaming in {S}mokahontas comment thread in {Y}ou{T}ube},
year = {2016}
}



@inbook{huumo2016empirical,
author = {Huumo, Tuomas and Kyr{\"o}l{\"a}inen, Aki-Juhani and Kanerva, Jenna and Luotolahti, Juhani and Salakoski, Tapio and Ginter, Filip and Laippala, Veronika},
booktitle = {Empirical approaches to cognitive linguistics: {A}nalysing real-life data},
year={2017},
editor = {Luodonpää-Manni, Milla and Penttilä, Esa and Viimaranta, Johanna},
location = {Newcastle Upon Tyne},
publisher = {Cambridge Scholars Publishing},
title = {Distributional semantics of the partitive {A} argument construction in {F}innish}
}

@misc{laippala2016textlink,
author = {Laippala, Veronika and Kyr{\"o}l{\"a}inen, Aki-Juhani and Komppa, Johanna and Vilkuna, Maria and Kalliokoski, Jyrki and Ginter, Filip},
booktitle = {Conference handbook: {T}ext{L}ink – {S}tructuring discourse in multilingual {E}urope. {S}econd {A}ction {C}onference},
editor = {Degand, Liesbeth and D{\'e}r, Csilla and Furk{\'o}, P{\'e}ter and Webber, Bonnie},
location = {Debrecen},
pages = {70–73},
publisher = {Debrecen University Press},
title = {Sentence-initial discourse relational devices in the {F}innish {I}nternet},
year = {2016}
}


@InProceedings{luotolahti2017depsearch,
  author    = {Luotolahti, Juhani and Kanerva, Jenna and Ginter, Filip},
  title     = {Dep\_search: Efficient Search Tool for Large Dependency Parsebanks},
  booktitle = {Proceedings of the 21st Nordic Conference on Computational Linguistics (NoDaLiDa)},
  year      = {2017},
  address   = {Gothenburg, Sweden},
  publisher = {Link{\"o}ping University Electronic Press},
  url = {http://www.aclweb.org/anthology/W17-0233}
}

@InProceedings{vesanto2017asystem,
  author    = {Vesanto, Aleksi and Nivala, Asko and Salakoski, Tapio and Salmi, Hannu and Ginter, Filip},
  title     = {A System for Identifying and Exploring Text Repetition in Large Historical Document Corpora},
  booktitle = {Proceedings of the 21st Nordic Conference on Computational Linguistics (NoDaLiDa)},
  year      = {2017},
  address   = {Gothenburg, Sweden},
  publisher = {Link{\"o}ping University Electronic Press},
}

@InProceedings{vesanto2017applying,
  author    = {Vesanto, Aleksi and Nivala, Asko and Rantala, Heli and Salakoski, Tapio and Salmi, Hannu and Ginter, Filip},
  title     = {Applying {BLAST} to Text Reuse Detection in {F}innish Newspapers and Journals, 1771--1910},
  booktitle = {Proceedings of the NoDaLiDa Historical Text Processing Workshop},
  year      = {2017},
  address   = {Gothenburg, Sweden},
  publisher = {Link{\"o}ping University Electronic Press},
}

@InProceedings{laippala2017creating,
  author    = {Laippala, Veronika and Luotolahti, Juhani and Kyr{\"o}l{\"a}inen, Aki-Juhani and Salakoski, Tapio and Ginter, Filip},
  title     = {Creating register sub-corpora for the {Finnish Internet Parsebank}},
  booktitle = {Proceedings of the 21st Nordic Conference on Computational Linguistics (NoDaLiDa)},
  year      = {2017},
  address   = {Gothenburg, Sweden},
  publisher = {Link{\"o}ping University Electronic Press},
}

@inproceedings{conll2017kanerva,
    author = {Kanerva, Jenna and Luotolahti, Juhani and Ginter, Filip},
  title     = {{TurkuNLP}: Delexicalized Pre-training of Word Embeddings for Dependency Parsing},
  booktitle = {{Proceedings of the CoNLL 2017 Shared Task: Multilingual Parsing from Raw Text to Universal Dependencies}},
  publisher = {Association for Computational Linguistics},
  location  = {Vancouver, Canada},
  year      = {2017}
}

@inproceedings{hakala2017twitter,
  title = {Ensemble of Convolutional Neural Networks for Medicine Intake Recognition in Twitter},
  author = {Kai Hakala and Farrokh Mehryary and Hans Moen and Suwisa Kaewphan and Tapio Salakoski and Filip Ginter},
  booktitle = {Proceedings of the 2nd Social Media Mining for Health Research and Applications Workshop},
  publisher = {CEUR Workshop Proceedings},
  year      = {2017}
}

@InProceedings{mehryary2017bb3,
  Title                    = {End-to-End System for Bacteria Habitat Extraction},
  Author                   = {Mehryary, Farrokh and Hakala, Kai and Kaewphan, Suwisa and Bj\"orne, Jari and Salakoski, Tapio and Ginter, Filip},
  Booktitle                = {Proceedings of the 2017 Workshop on Biomedical Natural Language Processing},
  Organization             = {Association for Computational Linguistics},
  Year                     = {2017}
}

@inproceedings{kaewphan2017turkunlp,
  title = {TurkuNLP Entry for Interactive Bio-ID Assignment},
  author = {Suwisa Kaewphan and Farrokh Mehryary and Kai Hakala and Tapio Salakoski and Filip Ginter},
  booktitle = {Proceedings of the BioCreative VI Workshop},
  publisher = {BioCreative VI Workshop Proceedings},
  year      = {2018}
}

@InProceedings{moen2017pain,
  Title                    = {Detecting mentions of pain and acute confusion in {Finnish} clinical text},
  Author                   = {Moen, Hans and Hakala, Kai and Mehryary, Farrokh and Peltonen, Laura-Maria and Salakoski, Tapio and Ginter, Filip and Salanter\"a, Sanna},
  Booktitle                = {Proceedings of the 2017 Workshop on Biomedical Natural Language Processing},
  Organization             = {Association for Computational Linguistics},
  Year                     = {2017}
}

@inproceedings{udst:overview,
    author = {Zeman, Daniel and Popel, Martin and Straka, Milan and Haji{\v{c}}, Jan and Nivre, Joakim and Ginter, Filip and Luotolahti, Juhani and Pyysalo, Sampo and Petrov, Slav and Potthast, Martin and Tyers, Francis and Badmaeva, Elena and G{\"{o}}k{\i}rmak, Memduh and Nedoluzhko, Anna and Cinkov{\'{a}}, Silvie and Haji{\v{c}} jr., Jan and Hlav{\'{a}}{\v{c}}ov{\'{a}}, Jaroslava and Kettnerov{\'{a}}, V{\'{a}}clava and Ure{\v{s}}ov{\'{a}}, Zde{\v{n}}ka and Kanerva, Jenna and Ojala, Stina and Missil{\"{a}}, Anna and Manning, Christopher and Schuster, Sebastian and Reddy, Siva and Taji, Dima and Habash, Nizar and Leung, Herman and de Marneffe, Marie-Catherine and Sanguinetti, Manuela and Simi, Maria and Kanayama, Hiroshi and de Paiva, Valeria and Droganova, Kira and Mart{\'{\i}}nez Alonso, H{\v{e}}ctor and Uszkoreit, Hans and Macketanz, Vivien and Burchardt, Aljoscha and Harris, Kim and Marheinecke, Katrin and Rehm, Georg and Kayadelen, Tolga and Attia, Mohammed and Elkahky, Ali and Yu, Zhuoran and Pitler, Emily and Lertpradit, Saran and Mandl, Michael and Kirchner, Jesse and Fernandez Alcalde, Hector and Strnadova, Jana and Banerjee, Esha and Manurung, Ruli and Stella, Antonio and Shimada, Atsuko and Kwak, Sookyoung and Mendon{\c{c}}a, Gustavo and Lando, Tatiana and Nitisaroj, Rattima and Li, Josie},
  title     = {{CoNLL 2017 Shared Task: Multilingual Parsing from Raw Text to Universal Dependencies}},
  booktitle = {{Proceedings of the CoNLL 2017 Shared Task: Multilingual Parsing from Raw Text to Universal Dependencies}},
  publisher = {Association for Computational Linguistics},
  location  = {Vancouver, Canada},
  year      = {2017}
}

@InProceedings{kanerva2017fully,
  title = {Fully Delexicalized Contexts for Syntax-Based Word Embeddings},
  author = {Kanerva, Jenna and Pyysalo, Sampo and Ginter, Filip},
  booktitle = {Proceedings of the International Conference on Dependency Linguistics (Depling'17)},
  year = {2017},
  url = {http://www.aclweb.org/anthology/W17-6511}
}

@InProceedings{marneffe2017assessing,
  title = {Assessing the Annotation Consistency of the {U}niversal {D}ependencies Corpora},
  author = {de Marneffe, Marie-Catherine and Grioni, Matias and Kanerva, Jenna and Ginter, Filip},
  booktitle = {Proceedings of the International Conference on Dependency Linguistics (Depling'17)},
  year = {2017},
  url = {http://aclweb.org/anthology/W17-6514}
}


@InProceedings{luotolahti-kanerva-ginter:2017:DiscoMT,
  author    = {Luotolahti, Juhani  and  Kanerva, Jenna  and  Ginter, Filip},
  title     = {Cross-Lingual Pronoun Prediction with Deep Recurrent Neural Networks v2.0},
  booktitle = {Proceedings of the Third Workshop on Discourse in Machine Translation},
  month     = {September},
  year      = {2017},
  address   = {Copenhagen, Denmark},
  publisher = {Association for Computational Linguistics},
  pages     = {63--66},
  url       = {http://aclweb.org/anthology/W17-4808}
}

@article{Laippala-discours2017,
  author = {Laippala, Veronika},
  journal = {Discours},
  number = {20},
  title = {Variation in the Marking of Text Organization in French Research Articles: From Short and Specific to Extended and Vague},
  year = {2017}
}


@InCollection{Laippala-wikicorpus2017,
  Title                    = {Corpus WikiDisc: Ressource pour la caractérisation des discussions en ligne},
  Author                   = {Ho-Dac, Lydia-Mai and Laippala, Veronika},
  Booktitle                = {Corpus de communication médiée par les réseaux. Construction, structuration, analyse},
  Year                     = {2017},
  Editor                   = {Ciara R. Wigham and Gudrun Ledegen},
  Publisher                = {L'Harmattan},
  Address                  = {Paris},
  Pages                    = {107--123}
}

@InProceedings{Laippala-wikiconf2016,
  title = {French Wikipedia Talk Pages: Profiling and Conflict Detection},
  author = {Ho-Dac, Lydia-Mai and Laippala, Veronika and Poudat, Celine and Tanguy, Ludovic},
  booktitle = {Proceedings of the 4th Conference on CMC and Social Media Corpora for the Humanities, Slovenia, 27-28.9.2016},
  year = {2016}
}

@InProceedings{mehryary2017chemprot,
  Title = {Combining Support Vector Machines and {LSTM} Networks for Chemical-Protein Relation Extraction}, 
  Author = {Mehryary, Farrokh and Bj\"orne, Jari and Salakoski, Tapio and Ginter, Filip}, 
  Booktitle = {Proceedings of the BioCreative VI Workshop},
  Pages = {175--179},
  Year = {2017}
}

@article{kyrolainen2017autoencoder,
	author = {Aki-Juhani Kyr{\"o}l{\"a}inen and Juhani Luotolahti and Filip Ginter},
	title = {An autoencoder-based neural network model for selectional preference: evidence from pseudo-disambiguation and cloze tasks},
	journal = {Eesti ja soome-ugri keeleteaduse ajakiri. Journal of Estonian and Finno-Ugric Linguistics},
	volume = {8},
	number = {2},
	year = {2017},
	issn = {2228-1339},	
  url = {http://jeful.ut.ee/index.php/JEFUL/article/view/jeful.2017.8.2.04}
}

@InCollection{Laippala-wikiconf2017,
  Title                    = {Exploring Wikipedia Talk Pages for Conflict Detection},
  Author                   = {Ho-Dac, Lydia-Mai and Laippala, Veronika and Celine Poudat and Ludovic Tanguy},
  Booktitle                = {Investigating Computer-Mediated Communication: Corpus-Based Approaches to Language in the Digital World},
  Year                     = {2017},
  Editor                   = {Darja Fiser and Michael Beisswenger},
  Publisher                = {Llubljana University Press},
  Address                  = {Ljubljana},
  Pages                    = {146--168}
}

@Article{Majewska2017,
  author="Majewska, Olga
  and Vuli{\'{c}}, Ivan
  and McCarthy, Diana
  and Huang, Yan
  and Murakami, Akira
  and Laippala, Veronika
  and Korhonen, Anna",
title="Investigating the cross-lingual translatability of VerbNet-style classification",
journal="Language Resources and Evaluation",
year="2017"
}

@Article{tidskrift2018,
  author={Salmi, Hannu and Nivala, Asko and Rantala, Heli and Sippola, Reetta and Vesanto, Aleksi and Ginter, Filip},
  title={{\AA}teranv{\"a}ndningen av text i den finska tidningspressen 1771--1853},
  journal={Historisk Tidskrift F{\"o}r Finland},
  pages={46--76},
  number={1},
  volume={103},
  year={2018}
}

@InProceedings{W18-2311,
  author = 	{Bj{\"o}rne, Jari and Salakoski, Tapio},
  title = 	{Biomedical Event Extraction Using Convolutional Neural Networks and Dependency Parsing},
  booktitle = 	{Proceedings of the BioNLP 2018 workshop},
  year = 	{2018},
  publisher = 	{Association for Computational Linguistics},
  pages = 	{98--108},
  location = 	{Melbourne, Australia},
  url = 	{http://aclweb.org/anthology/W18-2311}
}

@Article{johansson2018charlie,
  author={Johansson, Marjut and Kyr{\"o}l{\"a}inen, Aki-Juhani and Ginter, Filip and Lehti, Lotta and Krizs{\'a}n, Attila and Laippala, Veronika},
  title={Opening up \#jesuisCharlie Anatomy of a Twitter discussion with mixed methods},
  journal={Journal of Pragmatics},
  year={2018}
}

@article{10.7717/peerj.4806,
 title = {Finding novel relationships with integrated gene-gene association network analysis of \textit{Synechocystis sp.} PCC 6803 using species-independent text-mining},
 author = {Kreula, Sanna M. and Kaewphan, Suwisa and Ginter, Filip and Jones, Patrik R.},
 year = 2018,
 month = {may},
 keywords = {Cyanobacteria, Synechocystis sp. PCC 6803, Network analysis, Text-mining, Systems biology, Metabolism},
 volume = 6,
 pages = {e4806},
 journal = {PeerJ},
 issn = {2167-8359},
 url = {https://doi.org/10.7717/peerj.4806},
 doi = {10.7717/peerj.4806}
}  

@inproceedings{udst:turkunlp,
author = {Jenna Kanerva and Filip Ginter and Niko Miekka and Akseli Leino and Tapio Salakoski},
title = {Turku Neural Parser Pipeline: An End-to-End System for the CoNLL 2018 Shared Task},
booktitle = {Proceedings of the CoNLL 2018 Shared Task: Multilingual Parsing from Raw Text to Universal Dependencies},
publisher = "Association for Computational Linguistics",
location = "Brussels, Belgium",
year={2018},
url={http://www.aclweb.org/anthology/K18-2013}
}

@inproceedings{nivre2018ench,
author = {Joakim Nivre and Paola Marongiu and Filip Ginter and Jenna Kanerva and Simonetta Montemagni and Sebastian Schuster and Maria Simi},
title = {Enhancing {U}niversal {D}ependency Treebanks: A Case Study},
booktitle = {Proceedings of the 2018 Workshop on Universal Dependencies (UDW 2018)},
publisher = "Association for Computational Linguistics",
location = "Brussels, Belgium",
year={2018},
url={http://www.aclweb.org/anthology/W18-6012}
}

@inproceedings{droganova2018mind,
author = {Kira Droganova and Filip Ginter and Jenna Kanerva and Daniel Zeman},
title = {Mind the Gap: Data Enrichment in Dependency Parsing of Elliptical Constructions},
booktitle = {Proceedings of the 2018 Workshop on Universal Dependencies (UDW 2018)},
publisher = "Association for Computational Linguistics",
location = "Brussels, Belgium",
year={2018},
url={http://aclweb.org/anthology/W18-6006}
}

@inproceedings{zeman2018stoverview,
  title={{CoNLL 2018 Shared Task}: Multilingual Parsing from Raw Text to {Universal Dependencies}},
  author={Zeman, Daniel and Haji{\v{c}}, Jan and Popel, Martin and Potthast, Martin and Straka, Milan and Ginter, Filip and Nivre, Joakim and Petrov, Slav},
  Booktitle = {Proceedings of the CoNLL 2018 Shared Task, EMNLP'18},
  Year = {2018},
  url={http://www.aclweb.org/anthology/K18-2001}
  }

@InProceedings{jj2018hass,
  Title = {Neural Network Hate Deletion: Developing a Machine Learning Model to Eliminate Hate from Online Comments}, 
  Author = {Salminen, Joni and Luotolahti, Juhani and Almerekhi, Hind and Jansen, Bernard J. and Jung, Soon-Gyo}, 
  Booktitle = {Proceedings of the INSCI'2018 },
  year={2018}
}

@article{10.1093/database/bay096,
    author = {Kaewphan, Suwisa and Salakoski, Tapio and Ginter, Filip and Miekka, Niko and Hakala, Kai},
    title = "{Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling}",
    journal = {Database},
    volume = {2018},
    year = {2018},
    month = {09},
    issn = {1758-0463},
    doi = {10.1093/database/bay096},
    url = {https://dx.doi.org/10.1093/database/bay096},
    eprint = {http://oup.prod.sis.lan/database/article-pdf/doi/10.1093/database/bay096/27329393/bay096.pdf},
}

@Article{sarker2018twitter,
  author={Sarker, Abeed and Belousov Maksim and Friedrichs Jasper and Hakala, Kai and Kiritchenko Svetlana and Mehryary, Farrokh and Han, Sifei and Tran, Tung and Rios, Anthony and Kavuluru, Ramakanth and de Bruijn, Berry and Ginter, Filip and Mahata, Debanjan and Mohammad, Saif M. and Nenadic, Goran and Gonzalez-Hernandez, Graciela},
  title={{Data and systems for medication-related text classification and concept normalization from Twitter: insights from the Social Media Mining for Health (SMM4H)-2017 shared task}},
  journal={Journal of the American Medical Informatics Association},
  year={2018}
}

@Article{jasanatcllt,
	author={Laippala, Veronika and Kyröläinen, Aki-Juhani and Kanerva, Jenna and Ginter, Filip},
	title={Dependency profiles in the large-scale analysis of discourse connectives},
        journal={Corpus linguistics and linguistic theory},
	year={2018},
	note={in print}
}

@InProceedings{moen2018headings,
  Title                    = {Evaluation of a Prototype System that Automatically Assigns Subject Headings to Nursing Narratives Using Recurrent Neural Network},
  Author                   = {Hans Moen and Kai Hakala and Laura-Maria Peltonen and Henry Suhonen and Petri Loukasm{\"a}ki and Tapio Salakoski and Filip Ginter and Sanna Salanter{\"a}},
  Booktitle                = {Proceedings of the Ninth International Workshop on Health Text Mining and Information Analysis (Louhi)},
  Year                     = {2018},
  Publisher                = {Association for Computational Linguistics}
}

@InProceedings{moen2018improving,
  author = 	{Moen, Hans and Peltonen, Laura-Maria and Koivum{\"a}ki, Mikko and Suhonen, Henry and Salakoski, Tapio and Ginter, Filip and Salanter{\"a}, Sanna},
  title = 	{Improving Layman Readability of Clinical Narratives with Unsupervised Synonym Replacement},
  booktitle = 	{Building Continents of Knowledge in Oceans of Data: The Future of Co-Created eHealth - Proceedings of {MIE} 2018, Medical Informatics Europe},
  series = 	{Studies in Health Technology and Informatics},
  year = 	{2018},
  publisher = 	{{IOS} Press},
  pages = 	{725--729},
  location = 	{Gothenburg, Sweden},
  url = 	{https://doi.org/10.3233/978-1-61499-852-5-725}
}

@Article{mehryary2018oxfordDB,
author = {Mehryary, Farrokh and Bj{\"{o}}rne, Jari and Salakoski, Tapio and Ginter, Filip},
title = {Potent pairing: ensemble of long short-term memory networks and support vector machine for chemical-protein relation extraction},
journal = {Database},
volume = {2018},
number = {},
pages = {bay120},
year = {2018},
doi = {10.1093/database/bay120},
URL = {http://dx.doi.org/10.1093/database/bay120},
eprint = {/oup/backfile/content_public/journal/database/2018/10.1093_database_bay120/2/bay120.pdf}
}

@inproceedings{salminen2018neural,
  title={Neural Network Hate Deletion: Developing a Machine Learning Model to Eliminate Hate from Online Comments},
  author={Salminen, Joni and Luotolahti, Juhani and Almerekhi, Hind and Jansen, Bernard J and Jung, Soon-gyo},
  booktitle={International Conference on Internet Science},
  pages={25--39},
  year={2018},
  organization={Springer}
}

@inproceedings{nivre2020udv2,
  title={{Universal Dependencies v2}: An Evergrowing Multilingual Treebank Collection },
  author={Nivre, Joakim and de Marneffe, Marie-Catherine and Ginter, Filip and Haji\v{c}, Jan and Manning, Christopher D. and Pyysalo, Sampo and Schuster, Sebastian},
  year={2020},
  booktitle={Proceedings of 12th Conference on Language Resources and Evaluation LREC'2020}
  }

@inproceedings{tiedemann2020fiskmo,
  title={The {FISKM{\"O} Project}: Resources and Tools for {Finnish-Swedish} Machine Translation and Cross-Linguistic Research},
  author={Tiedemann,J{\"o}rg and Nieminen, Tommi and Aulamo, Mikko and Kanerva, Jenna and Leino, Akseli and Ginter, Filip and Papula, Niko},
  year={2020},
  booktitle={Proceedings of 12th Conference on Language Resources and Evaluation LREC'2020}
  }

@inproceedings{mehryary2020pairs,
  title={Entity-Pair Embeddings for Improving Relation Extraction in the Biomedical Domain},
  author={Mehryary, Farrokh and Moen, Hans and Salakoski, Tapio and Ginter, Filip},
  year={2020},
  booktitle={Proceedings of the 28th European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning ESANN'2020}
  }

@inproceedings{pyysalo2021wikiberts,
  title={{WikiBERT} Models: {Deep} Transfer Learning for Many Languages},
  author={Sampo Pyysalo and Jenna Kanerva and Antti Virtanen and Filip Ginter},
  booktitle={Proceedings of the 23rd Nordic Conference on Computational Linguistics (NoDaLiDa 2021)},
  year={2021},
  url={https://www.aclweb.org/anthology/2021.nodalida-main.1.pdf}
}

@inproceedings{pyysalo2021finegrained,
  title={Fine-grained Named Entity Annotation for {Finnish}},
  author={Jouni Luoma and Li-Hsin Chang and Filip Ginter and Sampo Pyysalo},
  booktitle={Proceedings of the 23rd Nordic Conference on Computational Linguistics (NoDaLiDa 2021)},
  year={2021},
  url={https://www.aclweb.org/anthology/2021.nodalida-main.14.pdf}
}

@inproceedings{kanerva20201paraphrase,
  title={Finnish Paraphrase Corpus},
  author={Jenna Kanerva and Filip Ginter and Li-Hsin Chang and Iiro Rastas and Valtteri Skantsi and Jemina Kilpel{\"a}inen and Hanna-Mari Kupari and Jenna Saarni and Maija Sev{\'o}n and Otto Tarkka},
  booktitle={Proceedings of the 23rd Nordic Conference on Computational Linguistics (NoDaLiDa 2021)},
  year={2021},
  url={https://www.aclweb.org/anthology/2021.nodalida-main.29.pdf}
}

@article{topaz2021improve,
  title={How to Improve Information Technology to Support Healthcare to Address the COVID-19 Pandemic: an International Survey with Health Informatics Experts},
  author={Topaz, Max and Peltonen, Laura-Maria and Mitchell, James and Alhuwail, Dari and Barakati, Seyedeh-Samin and Lewis, Adrienne and Moen, Hans and Veeranki, Sai Pavan Kumar and Block, Lori and Risling, Tracie and others},
  journal={Yearbook of Medical Informatics},
  year={2021},
  publisher={Georg Thieme Verlag KG}
}

@inproceedings{moen2021screen,
  title={Towards Automated Screening of Literature on Artificial Intelligence in Nursing},
  author={Moen, Hans and Alhuwail, Dari and Björne, Jari and Block, Lori and Celin, Sven and Jeon, Eunjoo and Kreiner, Karl and Mitchell, James and O\v{z}egovi\'{c}, Gabriela and Ronquillo, Charlene Esteban and Sequeira, Lydia and Tayaben, Jude and Topaz, Maxim and Veeranki, Sai Pavan Kumar and Peltonen, Laura-Maria},
  booktitle={MEDINFO 2021: One World, One Health},
  year={2021},
  publisher={{IOS} Press}
}

@inproceedings{reunamo2021explain,
  title={Text Classification Model Explainability for Keyword Extraction -- Towards Keyword-based Summarization of Nursing Care Episodes},
  author={Reunamo, Akseli and Peltonen, Laura-Maria and Mustonen, Reetta and Saari, Minttu and Salakoski, Tapio and Salanterä, Sanna and Moen, Hans},
  booktitle={MEDINFO 2021: One World, One Health},
  year={2021},
  publisher={{IOS} Press}
}

@article{santalahti2021gps,
  title={How GPs can Recognize Persistent Frequent Attenders at {Finnish} Primary Health Care Using Electronic Patient Records},
  author={Santalahti, Anne and Luutonen, Sinikka and Vahlberg, Tero and Moen, Hans and Salanter{\"a}, Sanna and Rautava, P{\"a}ivi},
  journal={Journal of Primary Care \& Community Health},
  volume={12},
  pages={21501327211024417},
  year={2021},
  publisher={SAGE Publications Sage CA: Los Angeles, CA}
}

@article{von2021artificial,
  title={Artificial Intelligence-based technologies in nursing: A scoping literature review of the evidence},
  author={Von Gerich, Hanna and Moen, Hans and Block, Lorraine J and Chu, Charlene H and DeForest, Haley and Hobensack, Mollie and Michalowski, Martin and Mitchell, James and Nibber, Raji and Olalia, Mary Anne and Pruinelli, Lisiane and Ronquillo, Charlene E and Topaz, Maxim and Peltonen, Laura-Maria},
  journal={International Journal of Nursing Studies},
  pages={104153},
  year={2021},
  publisher={Elsevier}
}

@inproceedings{repo2021zeroshot,
  title={Beyond the English web: Zero-shot cross-lingual and lightweight monolingual classification of registers},
  author={Repo, Liina and Skantsi, Valtteri and R{\"o}nnqvist, Samuel and Hellstr{\"o}m, Saara and Oinonen, Miika and Salmela, Anna and Biber, Douglas and Egbert, Jesse and Pyysalo, Sampo and Laippala, Veronika},
  booktitle={Proceedings of the 16th Conference of the European Chapter of the Association for Computational Linguistics: Student Research Workshop},
  year={2021},
  url={https://aclanthology.org/2021.eacl-srw.24.pdf}
}

@ARTICLE{Szklarczyk2023-jm,
  title     = "The {STRING} database in 2023: protein-protein association
               networks and functional enrichment analyses for any sequenced
               genome of interest",
  author    = "Szklarczyk, Damian and Kirsch, Rebecca and Koutrouli, Mikaela
               and Nastou, Katerina and Mehryary, Farrokh and Hachilif, Radja
               and Gable, Annika L and Fang, Tao and Doncheva, Nadezhda T and
               Pyysalo, Sampo and Bork, Peer and Jensen, Lars J and von Mering,
               Christian",
  journal   = "Nucleic Acids Res.",
  publisher = "Oxford University Press (OUP)",
  volume    =  51,
  number    = "D1",
  pages     = "D638--D646",
  year      =  2023,
  copyright = "https://creativecommons.org/licenses/by/4.0/",
  language  = "en"
}

@article{10.1093/database/baad080,
    author = {Miranda-Escalada, Antonio and Mehryary, Farrokh and Luoma, Jouni and Estrada-Zavala, Darryl and Gasco, Luis and Pyysalo, Sampo and Valencia, Alfonso and Krallinger, Martin},
    title = "{Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical–protein relations}",
    journal = {Database},
    volume = {2023},
    pages = {baad080},
    year = {2023},
    month = {11},
    issn = {1758-0463},
    doi = {10.1093/database/baad080},
    url = {https://doi.org/10.1093/database/baad080},
    eprint = {https://academic.oup.com/database/article-pdf/doi/10.1093/database/baad080/53895851/baad080.pdf},
}

@inproceedings{Miranda2021OverviewOD,
  title={Overview of DrugProt BioCreative VII track: quality evaluation and large scale text mining of drug- gene/protein relations},
  author={Antonio Miranda and Farrokh Mehryary and Jouni Luoma and Sampo Pyysalo and Alfonso Valencia and Martin Krallinger},
  booktitle={Proceedings of the BioCreative VII Challenge Evaluation Workshop},
  ISBN={978-0-578-32368-8},  
  year={2021},
  url={https://biocreative.bioinformatics.udel.edu/media/store/files/2021/Track1_pos_1_BC7_overview.pdf}
}