Skip to content

Commit

Permalink
Fix doc issue
Browse files Browse the repository at this point in the history
  • Loading branch information
moinfar committed Nov 11, 2024
1 parent 542d51b commit bde28b0
Show file tree
Hide file tree
Showing 2 changed files with 41 additions and 1 deletion.
39 changes: 39 additions & 0 deletions docs/references.bib
Original file line number Diff line number Diff line change
Expand Up @@ -8,3 +8,42 @@ @article{Virshup_2023
title = {The scverse project provides a computational ecosystem for single-cell omics data analysis},
journal = {Nature Biotechnology}
}

@ARTICLE{Moinfar2024-cx,
doi = {10.1101/2024.11.06.622266},
url = {https://doi.org/10.1101/2024.11.06.622266},
title = "Unsupervised deep disentangled representation of single-cell omics",
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"
}
3 changes: 2 additions & 1 deletion docs/references.md
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
# References

If DRVI is helpful in your research, please consider citing the following paper:
If DRVI is helpful in your research, please consider citing {cite:p}`Moinfar2024-cx`.
For other references used in the documentation see below:

```{bibliography}
:cited:
Expand Down

0 comments on commit bde28b0

Please sign in to comment.