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 …

Causal machine learning for single-cell genomics

A Tejada-Lapuerta, P Bertin, S Bauer, H Aliee… - arXiv preprint arXiv …, 2023 - arxiv.org
Advances in single-cell omics allow for unprecedented insights into the transcription profiles
of individual cells. When combined with large-scale perturbation screens, through which …

Molecular causality in the advent of foundation models

S Lobentanzer, P Rodriguez-Mier, S Bauer… - Molecular Systems …, 2024 - embopress.org
Correlation is not causation: this simple and uncontroversial statement has far-reaching
implications. Defining and applying causality in biomedical research has posed significant …

Learning DAGs from data with few root causes

P Misiakos, C Wendler… - Advances in Neural …, 2024 - proceedings.neurips.cc
We present a novel perspective and algorithm for learning directed acyclic graphs (DAGs)
from data generated by a linear structural equation model (SEM). First, we show that a linear …

Causal Fourier analysis on directed acyclic graphs and posets

B Seifert, C Wendler, M Püschel - IEEE Transactions on Signal …, 2023 - ieeexplore.ieee.org
We present a novel form of Fourier analysis, and associated signal processing concepts, for
signals (or data) indexed by edge-weighted directed acyclic graphs (DAGs). This means that …

CausalTime: Realistically Generated Time-series for Benchmarking of Causal Discovery

Y Cheng, Z Wang, T Xiao, Q Zhong, J Suo… - arXiv preprint arXiv …, 2023 - arxiv.org
Time-series causal discovery (TSCD) is a fundamental problem of machine learning.
However, existing synthetic datasets cannot properly evaluate or predict the algorithms' …

The CausalBench challenge: A machine learning contest for gene network inference from single-cell perturbation data

M Chevalley, J Sackett-Sanders, Y Roohani… - arXiv preprint arXiv …, 2023 - arxiv.org
In drug discovery, mapping interactions between genes within cellular systems is a crucial
early step. This helps formulate hypotheses regarding molecular mechanisms that could …

Benchmarking bayesian causal discovery methods for downstream treatment effect estimation

CC Emezue, A Drouin, T Deleu, S Bauer… - arXiv preprint arXiv …, 2023 - arxiv.org
The practical utility of causality in decision-making is widely recognized, with causal
discovery and inference being inherently intertwined. Nevertheless, a notable gap exists in …

Assessing the overall and partial causal well-specification of nonlinear additive noise models

C Schultheiss, P Bühlmann - Journal of Machine Learning Research, 2024 - jmlr.org
We propose a method to detect model misspecifications in nonlinear causal additive and
potentially heteroscedastic noise models. We aim to identify predictor variables for which we …

Causality-oriented robustness: exploiting general additive interventions

X Shen, P Bühlmann, A Taeb - arXiv preprint arXiv:2307.10299, 2023 - arxiv.org
Since distribution shifts are common in real-world applications, there is a pressing need for
developing prediction models that are robust against such shifts. Existing frameworks, such …