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 …
of human cells has often been viewed as an insurmountable challenge. However, in the last …
Nonparametric identifiability of causal representations from unknown interventions
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 …
their causal relations from high-dimensional functions (“mixtures”) of the variables. Prior …
Learning linear causal representations from interventions under general nonlinear mixing
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 …
in a general setting, where the latent distribution is Gaussian but the mixing function is …
Learning nonparametric latent causal graphs with unknown interventions
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 …
and can be reconstructed from unknown interventions in the latent space. Our primary focus …
Multi-domain causal representation learning via weak distributional invariances
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 …
learning research. In particular, multi-domain datasets present a natural opportunity for …
Multi-view causal representation learning with partial observability
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 …
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
Inference of causal transcriptional regulatory networks (TRNs) from transcriptomic data
suffers notoriously from false positives. Approaches to control the false discovery rate (FDR) …
suffers notoriously from false positives. Approaches to control the false discovery rate (FDR) …
Identifying representations for intervention extrapolation
The premise of identifiable and causal representation learning is to improve the current
representation learning paradigm in terms of generalizability or robustness. Despite recent …
representation learning paradigm in terms of generalizability or robustness. Despite recent …
General identifiability and achievability for causal representation learning
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 …
latent causal model and a general transformation model that maps the latent data to the …
Causal representation learning from multiple distributions: A general setting
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 …
functions of the hidden causal variables (eg, the underlying concepts or objects). For the …