Toward a foundation model of causal cell and tissue biology with a Perturbation Cell and Tissue Atlas

JE Rood, A Hupalowska, A Regev - Cell, 2024 - cell.com
Comprehensively charting the biologically causal circuits that govern the phenotypic space
of human cells has often been viewed as an insurmountable challenge. However, in the last …

Nonparametric identifiability of causal representations from unknown interventions

J von Kügelgen, M Besserve… - Advances in …, 2024 - proceedings.neurips.cc
We study causal representation learning, the task of inferring latent causal variables and
their causal relations from high-dimensional functions (“mixtures”) of the variables. Prior …

Learning linear causal representations from interventions under general nonlinear mixing

S Buchholz, G Rajendran… - Advances in …, 2024 - proceedings.neurips.cc
We study the problem of learning causal representations from unknown, latent interventions
in a general setting, where the latent distribution is Gaussian but the mixing function is …

Learning nonparametric latent causal graphs with unknown interventions

Y Jiang, B Aragam - Advances in Neural Information …, 2023 - proceedings.neurips.cc
We establish conditions under which latent causal graphs are nonparametrically identifiable
and can be reconstructed from unknown interventions in the latent space. Our primary focus …

Multi-domain causal representation learning via weak distributional invariances

K Ahuja, A Mansouri, Y Wang - International Conference on …, 2024 - proceedings.mlr.press
Causal representation learning has emerged as the center of action in causal machine
learning research. In particular, multi-domain datasets present a natural opportunity for …

Multi-view causal representation learning with partial observability

D Yao, D Xu, S Lachapelle, S Magliacane… - arxiv preprint arxiv …, 2023 - arxiv.org
We present a unified framework for studying the identifiability of representations learned
from simultaneously observed views, such as different data modalities. We allow a partially …

Transcriptome data are insufficient to control false discoveries in regulatory network inference

E Kernfeld, R Keener, P Cahan, A Battle - Cell systems, 2024 - cell.com
Inference of causal transcriptional regulatory networks (TRNs) from transcriptomic data
suffers notoriously from false positives. Approaches to control the false discovery rate (FDR) …

Identifying representations for intervention extrapolation

S Saengkyongam, E Rosenfeld, P Ravikumar… - arxiv preprint arxiv …, 2023 - arxiv.org
The premise of identifiable and causal representation learning is to improve the current
representation learning paradigm in terms of generalizability or robustness. Despite recent …

General identifiability and achievability for causal representation learning

B Varici, E Acartürk, K Shanmugam… - International …, 2024 - proceedings.mlr.press
This paper focuses on causal representation learning (CRL) under a general nonparametric
latent causal model and a general transformation model that maps the latent data to the …

Causal representation learning from multiple distributions: A general setting

K Zhang, S **e, I Ng, Y Zheng - arxiv preprint arxiv:2402.05052, 2024 - arxiv.org
In many problems, the measured variables (eg, image pixels) are just mathematical
functions of the hidden causal variables (eg, the underlying concepts or objects). For the …