ASKEM_SKEMA_Milestone_7

ASKEM SKEMA Milestone 7 release. This includes:

• Code2FN
  • Added implicit conditional support for If statements.
  • Fixed issue with Binary operations that use the same variable as both operands.
  • Various Gromet formatting fixes such as removing extra new lines and consistent pathing format between different systems
  • Developed API endpoint and example clients for Code2FN pipeline
  • Developed script (single_file_ingester.py) to simplify Gromet generation for single files and code snippets
  • Defined set of primitive operators and created framework for primitive execution
  • Cleanup and rearranging of visitors in Code2FN Python to CAST and CAST to GroMEt steps.
• TextReading
  • version 1 of the scenario context engine into the text reading pipeline with support for location and temporal contexts, with the following highlights:
    • Detection of specific dates, times, date ranges, and time ranges
    • Detection of locations with different granularity levels: Abstract locations, countries, states/provinces, cities, organizations
    • An efficient algorithm to associate parameter extractions with the candidate scenario context detections based on the proximity of occurrence
• METAL
  • Improved the grounding mechanism to consider first relevant concepts of the DKG relevant to parameter extractions.
  • Extended support of metadata alignment to extractions of collections of documents of arbitrary length.
  • Updated the code to support metadata alignment on gromets with multiple modules
  • Created a version based on contextualized embeddings (using SciBert, but any other transformer model works as a drop in replacement) to do the metadata alignment.
• ISA
  • The conversion from MathML to graph representation has been preliminarily completed, including dealing with basic operations, parentheses, and arithmetic priority
  • The conversion from graph representation to adjacency matrix is completed.
  • The preliminary development of the structural alignment between equation graphs returns the matching ratio and the closest matched term/variable pairs between two equations.
  • Based on alignment results, a method is proposed to facilitate the identification of similarities and differences between models presented in two papers, or the investigation of code implementation issues
• MORAE
  • Target format of extraction changed from BiLayer to PetriNet in py-acset form
  • Developed code GroMEt to graph database representation to allow for structural and dataflow related queries to isolate and extract code roles.
  • Thin-thread pipeline to TA-2 developed and tested at the Hackathon/Evaluation
  • Basic integration into Terarium via REST API
• MOVIZ
  • Added support for GroMEt class features that were added in last release
  • Alterations to layout and visual design to better match hand-layout examples
  • Added labels over original hand-layout examples to better support debugging
  • Added interface for direct file GroMEt upload
  • MOVIZ demonstrated to run locally on non-visualization SKEMA team machines to aid debugging and exploration of GroMEt function networks.
  • MOVIZ demonstration on epidemiology model kernels.