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Biomarker discovery from high-throughput transcriptomic data is crucial for advancing precision medicine. However, existing methods often neglect gene-gene regulatory relationships and lack stability across datasets, leading to conflation…

Quantitative Methods · Quantitative Biology 2025-11-18 Chaowang Lan , Jingxin Wu , Yulong Yuan , Chuxun Liu , Huangyi Kang , Caihua Liu

Reconstructing accurate causal models of dynamic systems from time-series of sensor data is a key problem in many real-world scenarios. In this paper, we present an overview based on our experience about practical challenges that the causal…

Robotics · Computer Science 2023-01-11 Luca Castri , Sariah Mghames , Nicola Bellotto

Unraveling the causal relationships among the execution of process activities is a crucial element in predicting the consequences of process interventions and making informed decisions regarding process improvements. Process discovery…

Artificial Intelligence · Computer Science 2025-01-15 Fabiana Fournier , Lior Limonad , Inna Skarbovsky , Yuval David

Discovering causal relations among observed variables in a given data set is a major objective in studies of statistics and artificial intelligence. Recently, some techniques to discover a unique causal model have been explored based on…

Machine Learning · Statistics 2014-01-23 Takanori Inazumi , Takashi Washio , Shohei Shimizu , Joe Suzuki , Akihiro Yamamoto , Yoshinobu Kawahara

We introduce a causal modeling framework that captures the input-output behavior of predictive models (e.g., machine learning models). The framework enables us to identify features that directly cause the predictions, which has broad…

Machine Learning · Computer Science 2025-05-20 Yizuo Chen , Amit Bhatia

Climate models are essential to understand and project climate change, yet long-standing biases and uncertainties in their projections remain. This is largely associated with the representation of subgrid-scale processes, particularly…

Causal discovery for dynamical systems poses a major challenge in fields where active interventions are infeasible. Most methods used to investigate these systems and their associated benchmarks are tailored to deterministic,…

Machine Learning · Computer Science 2025-10-13 Benjamin Herdeanu , Juan Nathaniel , Carla Roesch , Jatan Buch , Gregor Ramien , Johannes Haux , Pierre Gentine

Causal discovery from data affected by unobserved variables is an important but difficult problem to solve. The effects that unobserved variables have on the relationships between observed variables are more complex in nonlinear cases than…

Machine Learning · Computer Science 2021-06-07 Takashi Nicholas Maeda , Shohei Shimizu

Even when the causal graph underlying our data is unknown, we can use observational data to narrow down the possible values that an average treatment effect (ATE) can take by (1) identifying the graph up to a Markov equivalence class; and…

Machine Learning · Computer Science 2024-04-11 Shantanu Gupta , David Childers , Zachary C. Lipton

Causal graph discovery is a significant problem with applications across various disciplines. However, with observational data alone, the underlying causal graph can only be recovered up to its Markov equivalence class, and further…

Machine Learning · Computer Science 2024-02-14 Davin Choo , Kirankumar Shiragur , Caroline Uhler

Causal inference can estimate causal effects, but unless data are collected experimentally, statistical analyses must rely on pre-specified causal models. Causal discovery algorithms are empirical methods for constructing such causal models…

Methodology · Statistics 2022-05-17 Anne Helby Petersen , Joseph Ramsey , Claus Thorn Ekstrøm , Peter Spirtes

Controlling false positives (Type I errors) through statistical hypothesis testing is a foundation of modern scientific data analysis. Existing causal structure discovery algorithms either do not provide Type I error control or cannot scale…

Methodology · Statistics 2025-12-29 James Leiner , Brian Manzo , Aaditya Ramdas , Wesley Tansey

We present a sound and complete algorithm, called iterative causal discovery (ICD), for recovering causal graphs in the presence of latent confounders and selection bias. ICD relies on the causal Markov and faithfulness assumptions and…

Machine Learning · Computer Science 2022-01-19 Raanan Y. Rohekar , Shami Nisimov , Yaniv Gurwicz , Gal Novik

Through recognizing causal subgraphs, causal graph learning (CGL) has risen to be a promising approach for improving the generalizability of graph neural networks under out-of-distribution (OOD) scenarios. However, the empirical successes…

Machine Learning · Computer Science 2025-07-02 Yujia Yin , Tianyi Qu , Zihao Wang , Yifan Chen

We present a new method for causal discovery in linear structural equation models. We propose a simple ``trick'' based on statistical testing in linear models that can distinguish between ancestors and non-ancestors of any given variable.…

Methodology · Statistics 2023-03-15 Christoph Schultheiss , Peter Bühlmann

In recent years, many methods have been developed for detecting causal relationships in observational data. Some of them have the potential to tackle large data sets. However, these methods fail to discover a combined cause, i.e. a…

Artificial Intelligence · Computer Science 2015-10-16 Saisai Ma , Jiuyong Li , Lin Liu , Thuc Duy Le

Causal representation learning seeks to uncover causal relationships among high-level latent variables from low-level, entangled, and noisy observations. Existing approaches often either rely on deep neural networks, which lack…

Methodology · Statistics 2026-03-27 Wenjin Zhang , Yixin Wang , Yuqi Gu

We consider learning ancestral causal relationships in high dimensions. Our approach is driven by a supervised learning perspective, with discrete indicators of causal relationships treated as labels to be learned from available data. We…

Machine Learning · Statistics 2019-05-29 Umberto Noè , Bernd Taschler , Joachim Täger , Peter Heutink , Sach Mukherjee

Understanding causal relationships between variables is fundamental across scientific disciplines. Most causal discovery algorithms rely on two key assumptions: (i) all variables are observed, and (ii) the underlying causal graph is…

Machine Learning · Computer Science 2026-01-26 Muralikrishnna G. Sethuraman , Faramarz Fekri

Discovering causal relationships from time series data is significant in fields such as finance, climate science, and neuroscience. However, contemporary techniques rely on the simplifying assumption that data originates from the same…

Machine Learning · Computer Science 2024-06-25 Sumanth Varambally , Yi-An Ma , Rose Yu