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With the increasing availability and size of multi-omics datasets, investigating the casual relationships between molecular phenotypes has become an important aspect of exploring underlying biology and genetics. This paper aims to introduce…

Molecular Networks · Quantitative Biology 2022-01-31 Jack Kelly , Carlo Berzuini , Bernard Keavney , Maciej Tomaszewski , Hui Guo

Learning causal relationships between pairs of complex traits from observational studies is of great interest across various scientific domains. However, most existing methods assume the absence of unmeasured confounding and restrict causal…

Methodology · Statistics 2024-07-17 Wei Li , Rui Duan , Sai Li

The representation of the flow of information between neurons in the brain based on their activity is termed the causal functional connectome. Such representation incorporates the dynamic nature of neuronal activity and causal interactions…

Neurons and Cognition · Quantitative Biology 2022-11-16 Rahul Biswas , Eli Shlizerman

Causal inference permits us to discover covert relationships of various variables in time series. However, in most existing works, the variables mentioned above are the dimensions. The causality between dimensions could be cursory, which…

Machine Learning · Computer Science 2023-09-14 Yuanhao Liu , Dehui Du , Zihan Jiang , Anyan Huang , Yiyang Li

Inferring the coupling direction from measured time series of complex systems is challenging. We propose a new state space based causality measure obtained from cross-distance vectors for quantifying interaction strength. It is a model-free…

Data Analysis, Statistics and Probability · Physics 2023-05-04 Martin Brešar , Pavle Boškoski

We introduce a new approach to functional causal modeling from observational data, called Causal Generative Neural Networks (CGNN). CGNN leverages the power of neural networks to learn a generative model of the joint distribution of the…

Time series data are found in many areas of healthcare such as medical time series, electronic health records (EHR), measurements of vitals, and wearable devices. Causal discovery, which involves estimating causal relationships from…

Machine Learning · Computer Science 2023-10-18 Muhammad Hasan Ferdous , Uzma Hasan , Md Osman Gani

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

Actual causation is concerned with the question "what caused what?" Consider a transition between two states within a system of interacting elements, such as an artificial neural network, or a biological brain circuit. Which combination of…

Artificial Intelligence · Computer Science 2019-01-11 Larissa Albantakis , William Marshall , Erik Hoel , Giulio Tononi

Brain network provides important insights for the diagnosis of many brain disorders, and how to effectively model the brain structure has become one of the core issues in the domain of brain imaging analysis. Recently, various computational…

Neurons and Cognition · Quantitative Biology 2022-12-02 Zhengwang Xia , Tao Zhou , Saqib Mamoon , Amani Alfakih , Jianfeng Lu

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

We propose a novel approach for inferring the individualized causal effects of a treatment (intervention) from observational data. Our approach conceptualizes causal inference as a multitask learning problem; we model a subject's potential…

Machine Learning · Computer Science 2017-06-20 Ahmed M. Alaa , Michael Weisz , Mihaela van der Schaar

The inference of causal relationships using observational data from partially observed multivariate systems with hidden variables is a fundamental question in many scientific domains. Methods extracting causal information from conditional…

Machine Learning · Statistics 2020-10-13 Daniel Chicharro , Michel Besserve , Stefano Panzeri

A foremost challenge in modern network science is the inverse problem of reconstruction (inference) of coupling equations and network topology from the measurements of the network dynamics. Of particular interest are the methods that can…

Chaotic Dynamics · Physics 2019-10-31 Isao T. Tokuda , Zoran Levnajic , Kazuyoshi Ishimura

Understanding the functioning of a neural system in terms of its underlying circuitry is an important problem in neuroscience. Recent developments in electrophysiology and imaging allow one to simultaneously record activities of hundreds of…

Databases · Computer Science 2008-03-11 Debprakash Patnaik , P. S. Sastry , K. P. Unnikrishnan

Networks - collections of interacting elements or nodes - abound in the natural and manmade worlds. For many networks, complex spatiotemporal dynamics stem from patterns of physical interactions unknown to us. To infer these interactions,…

Quantitative Methods · Quantitative Biology 2015-05-13 Mark A. Kramer , Uri T. Eden , Sydney S. Cash , Eric D. Kolaczyk

Most causal discovery algorithms find causal structure among a set of observed variables. Learning the causal structure among latent variables remains an important open problem, particularly when using high-dimensional data. In this paper,…

Machine Learning · Computer Science 2020-09-09 Jonathan D. Young , Bryan Andrews , Gregory F. Cooper , Xinghua Lu

This paper introduces a novel decomposition framework to explain heterogeneity in causal effects observed across different studies, considering both observational and randomized settings. We present a formal decomposition of between-study…

Methodology · Statistics 2025-12-18 Brian Gilbert , Ivan Dıaz , Kara E. Rudolph , Nicholas Williams , Tat-Thang Vo

Recovering causal structure in the presence of latent variables is an important but challenging task. While many methods have been proposed to handle it, most of them require strict and/or untestable assumptions on the causal structure. In…

Machine Learning · Computer Science 2025-10-28 Wei Chen , Linjun Peng , Zhiyi Huang , Haoyue Dai , Zhifeng Hao , Ruichu Cai , Kun Zhang

Inferring causal relationships from observational data is often challenging due to endogeneity. This paper provides new identification results for causal effects of discrete, ordered and continuous treatments using multiple binary…

Econometrics · Economics 2024-10-21 Nadja van 't Hoff