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Fix doc issue
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moinfar committed Nov 11, 2024
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Expand Up @@ -16,33 +16,6 @@ @ARTICLE{Moinfar2024-cx
author = "Moinfar, Amir Ali and Theis, Fabian J",
journal = "bioRxiv",
pages = "2024.11.06.622266",
abstract = "Single-cell genomics allows for the unbiased exploration of
cellular heterogeneity. Representation learning methods summarize
high-dimensional single-cell data into a manageable latent space
in a typically nonlinear fashion, allowing cross-sample
integration or generative modeling. However, these methods often
produce entangled representations, limiting interpretability and
downstream analyses. Existing disentanglement methods instead
either require supervised information or impose sparsity and
linearity, which may not capture the complexity of biological
data. We, therefore, introduce Disentangled Representation
Variational Inference (DRVI), an unsupervised deep generative
model that learns nonlinear, disentangled representations of
single-cell omics. This is achieved by combining recently
introduced additive decoders with nonlinear pooling, for which we
theoretically prove disentanglement under reasonable assumptions.
We validate DRVI's disentanglement capabilities across diverse
relevant biological problems, from development to perturbational
studies and cell atlases, decomposing, for example, the Human Lung
Cell Atlas into meaningful, interpretable latent dimensions.
Moreover, we demonstrate that if applied to batch integration,
DRVI's integration quality does not suffer from the
disentanglement constraints and instead is on par with entangled
integration methods. With its disentangled latent space, DRVI is
inherently interpretable and facilitates the identification of
rare cell types, provides novel insights into cellular
heterogeneity beyond traditional cell types, and highlights
developmental stages.",
month = nov,
year = 2024,
language = "en"
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