Toward the Identifiability of Comparative Deep Generative Models

Romain Lopez, Jan-Christian Huetter, Ehsan Hajiramezanali, Jonathan K Pritchard, Aviv Regev
Proceedings of the Third Conference on Causal Learning and Reasoning, PMLR 236:868-912, 2024.

Abstract

Deep Generative Models (DGMs) are versatile tools for learning data representations while adequately incorporating domain knowledge such as the specification of conditional probability distributions. Recently proposed DGMs tackle the important task of comparing data sets from different sources. One such example is the setting of contrastive analysis that focuses on describing patterns that are enriched in a target data set compared to a background data set. The practical deployment of those models often assumes that DGMs naturally infer interpretable and modular latent representations, which is known to be an issue in practice. Consequently, existing methods often rely on ad-hoc regularization schemes, although without any theoretical grounding. Here, we propose a theory of identifiability for comparative DGMs by extending recent advances in the field of non-linear independent component analysis. We show that, while these models lack identifiability across a general class of mixing functions, they surprisingly become identifiable when the mixing function is piece-wise affine (e.g., parameterized by a ReLU neural network). We also investigate the impact of model misspecification, and empirically show that previously proposed regularization techniques for fitting comparative DGMs help with identifiability when the number of latent variables is not known in advance. Finally, we introduce a novel methodology for fitting comparative DGMs that improves the treatment of multiple data sources via multi-objective optimization and that helps adjust the hyperparameter for the regularization in an interpretable manner, using constrained optimization. We empirically validate our theory and new methodology using simulated data as well as a recent data set of genetic perturbations in cells profiled via single-cell RNA sequencing.

Cite this Paper

BibTeX
@InProceedings{pmlr-v236-lopez24a, title = {Toward the Identifiability of Comparative Deep Generative Models}, author = {Lopez, Romain and Huetter, Jan-Christian and Hajiramezanali, Ehsan and Pritchard, Jonathan K and Regev, Aviv}, booktitle = {Proceedings of the Third Conference on Causal Learning and Reasoning}, pages = {868--912}, year = {2024}, editor = {Locatello, Francesco and Didelez, Vanessa}, volume = {236}, series = {Proceedings of Machine Learning Research}, month = {01--03 Apr}, publisher = {PMLR}, pdf = {https://proceedings.mlr.press/v236/lopez24a/lopez24a.pdf}, url = {https://proceedings.mlr.press/v236/lopez24a.html}, abstract = {Deep Generative Models (DGMs) are versatile tools for learning data representations while adequately incorporating domain knowledge such as the specification of conditional probability distributions. Recently proposed DGMs tackle the important task of comparing data sets from different sources. One such example is the setting of contrastive analysis that focuses on describing patterns that are enriched in a target data set compared to a background data set. The practical deployment of those models often assumes that DGMs naturally infer interpretable and modular latent representations, which is known to be an issue in practice. Consequently, existing methods often rely on ad-hoc regularization schemes, although without any theoretical grounding. Here, we propose a theory of identifiability for comparative DGMs by extending recent advances in the field of non-linear independent component analysis. We show that, while these models lack identifiability across a general class of mixing functions, they surprisingly become identifiable when the mixing function is piece-wise affine (e.g., parameterized by a ReLU neural network). We also investigate the impact of model misspecification, and empirically show that previously proposed regularization techniques for fitting comparative DGMs help with identifiability when the number of latent variables is not known in advance. Finally, we introduce a novel methodology for fitting comparative DGMs that improves the treatment of multiple data sources via multi-objective optimization and that helps adjust the hyperparameter for the regularization in an interpretable manner, using constrained optimization. We empirically validate our theory and new methodology using simulated data as well as a recent data set of genetic perturbations in cells profiled via single-cell RNA sequencing.} }
Endnote
%0 Conference Paper %T Toward the Identifiability of Comparative Deep Generative Models %A Romain Lopez %A Jan-Christian Huetter %A Ehsan Hajiramezanali %A Jonathan K Pritchard %A Aviv Regev %B Proceedings of the Third Conference on Causal Learning and Reasoning %C Proceedings of Machine Learning Research %D 2024 %E Francesco Locatello %E Vanessa Didelez %F pmlr-v236-lopez24a %I PMLR %P 868--912 %U https://proceedings.mlr.press/v236/lopez24a.html %V 236 %X Deep Generative Models (DGMs) are versatile tools for learning data representations while adequately incorporating domain knowledge such as the specification of conditional probability distributions. Recently proposed DGMs tackle the important task of comparing data sets from different sources. One such example is the setting of contrastive analysis that focuses on describing patterns that are enriched in a target data set compared to a background data set. The practical deployment of those models often assumes that DGMs naturally infer interpretable and modular latent representations, which is known to be an issue in practice. Consequently, existing methods often rely on ad-hoc regularization schemes, although without any theoretical grounding. Here, we propose a theory of identifiability for comparative DGMs by extending recent advances in the field of non-linear independent component analysis. We show that, while these models lack identifiability across a general class of mixing functions, they surprisingly become identifiable when the mixing function is piece-wise affine (e.g., parameterized by a ReLU neural network). We also investigate the impact of model misspecification, and empirically show that previously proposed regularization techniques for fitting comparative DGMs help with identifiability when the number of latent variables is not known in advance. Finally, we introduce a novel methodology for fitting comparative DGMs that improves the treatment of multiple data sources via multi-objective optimization and that helps adjust the hyperparameter for the regularization in an interpretable manner, using constrained optimization. We empirically validate our theory and new methodology using simulated data as well as a recent data set of genetic perturbations in cells profiled via single-cell RNA sequencing.
APA
Lopez, R., Huetter, J., Hajiramezanali, E., Pritchard, J.K. & Regev, A.. (2024). Toward the Identifiability of Comparative Deep Generative Models. Proceedings of the Third Conference on Causal Learning and Reasoning, in Proceedings of Machine Learning Research 236:868-912 Available from https://proceedings.mlr.press/v236/lopez24a.html.

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