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The discovery of causal relationships from high-dimensional data is a major open problem in bioinformatics. Machine learning and feature attribution models have shown great promise in this context but lack causal interpretation. Here, we…

Machine Learning · Computer Science 2023-04-26 Payam Dibaeinia , Saurabh Sinha

We implement Ananke: an object-oriented Python package for causal inference with graphical models. At the top of our inheritance structure is an easily extensible Graph class that provides an interface to several broadly useful graph-based…

Methodology · Statistics 2023-01-30 Jaron J. R. Lee , Rohit Bhattacharya , Razieh Nabi , Ilya Shpitser

As cyber-physical systems grow increasingly interconnected and spatially distributed, ensuring their resilience against evolving cyberattacks has become a critical priority. Spatio-Temporal Anomaly detection plays an important role in…

Machine Learning · Computer Science 2025-07-14 Arun Vignesh Malarkkan , Haoyue Bai , Xinyuan Wang , Anjali Kaushik , Dongjie Wang , Yanjie Fu

We study the identification of causal effects, motivated by two improvements to identifiability which can be attained if one knows that some variables in a causal graph are functionally determined by their parents (without needing to know…

Artificial Intelligence · Computer Science 2024-05-24 Yizuo Chen , Adnan Darwiche

To make accurate predictions, understand mechanisms, and design interventions in systems of many variables, we wish to learn causal graphs from large scale data. Unfortunately the space of all possible causal graphs is enormous so scalably…

Machine Learning · Statistics 2024-06-19 Alan Nawzad Amin , Andrew Gordon Wilson

Causal Learner is a toolbox for learning causal structure and Markov blanket (MB) from data. It integrates functions for generating simulated Bayesian network data, a set of state-of-the-art global causal structure learning algorithms, a…

Machine Learning · Computer Science 2025-02-25 Zhaolong Ling , Kui Yu , Yiwen Zhang , Lin Liu , Jiuyong Li

In conventional supervised learning, a training dataset is given with ground-truth labels from a known label set, and the learned model will classify unseen instances to known labels. This paper studies a new problem setting in which there…

Machine Learning · Computer Science 2024-06-03 Peng Zhao , Jia-Wei Shan , Yu-Jie Zhang , Zhi-Hua Zhou

Learning on molecule graphs has become an increasingly important topic in AI for science, which takes full advantage of AI to facilitate scientific discovery. Existing solutions on modeling molecules utilize Graph Neural Networks (GNNs) to…

Machine Learning · Computer Science 2025-05-13 Limin Li , Kuo Yang , Wenjie Du , Pengkun Wang , Zhengyang Zhou , Yang Wang

Causal discovery aims to learn causal relationships between variables from targeted data, making it a fundamental task in machine learning. However, causal discovery algorithms often rely on unverifiable causal assumptions, which are…

Machine Learning · Computer Science 2025-10-15 Huiyang Yi , Yanyan He , Duxin Chen , Mingyu Kang , He Wang , Wenwu Yu

A fundamental challenge in the empirical sciences involves uncovering causal structure through observation and experimentation. Causal discovery entails linking the conditional independence (CI) invariances in observational data to their…

Machine Learning · Statistics 2025-11-04 Zihan Zhou , Muhammad Qasim Elahi , Murat Kocaoglu

Causal representation learning algorithms discover lower-dimensional representations of data that admit a decipherable interpretation of cause and effect; as achieving such interpretable representations is challenging, many causal learning…

Machine Learning · Computer Science 2023-11-09 Elise Walker , Jonas A. Actor , Carianne Martinez , Nathaniel Trask

Explainability is crucial for the application of black-box Graph Neural Networks (GNNs) in critical fields such as healthcare, finance, cybersecurity, and more. Various feature attribution methods, especially the perturbation-based methods,…

Machine Learning · Computer Science 2024-12-31 Xingping Xian , Jianlu Liu , Chao Wang , Tao Wu , Shaojie Qiao , Xiaochuan Tang , Qun Liu

Trajectory prediction is critical for autonomous driving vehicles. Most existing methods tend to model the correlation between history trajectory (input) and future trajectory (output). Since correlation is just a superficial description of…

Machine Learning · Computer Science 2023-07-13 Shengyi Li , Qifan Xue , Yezhuo Zhang , Xuanpeng Li

Recent advances in document image analysis (DIA) have been primarily driven by the application of neural networks. Ideally, research outcomes could be easily deployed in production and extended for further investigation. However, various…

Computer Vision and Pattern Recognition · Computer Science 2021-06-22 Zejiang Shen , Ruochen Zhang , Melissa Dell , Benjamin Charles Germain Lee , Jacob Carlson , Weining Li

It is crucial to consider the social and ethical consequences of AI and ML based decisions for the safe and acceptable use of these emerging technologies. Fairness, in particular, guarantees that the ML decisions do not result in…

Artificial Intelligence · Computer Science 2022-06-15 Rūta Binkytė-Sadauskienė , Karima Makhlouf , Carlos Pinzón , Sami Zhioua , Catuscia Palamidessi

There is growing interest in the study of causal methods in the Earth sciences. However, most applications have focused on causal discovery, i.e. inferring the causal relationships and causal structure from data. This paper instead examines…

Atmospheric and Oceanic Physics · Physics 2021-05-04 Adam Massmann , Pierre Gentine , Jakob Runge

Deep learning models have made significant progress in automatic program repair. However, the black-box nature of these methods has restricted their practical applications. To address this challenge, this paper presents an interpretable…

Software Engineering · Computer Science 2022-06-07 Jianzong Wang , Shijing Si , Zhitao Zhu , Xiaoyang Qu , Zhenhou Hong , Jing Xiao

Learning data representations that capture task-related features, but are invariant to nuisance variations remains a key challenge in machine learning. We introduce an automated Bayesian inference framework, called AutoBayes, that explores…

Machine Learning · Computer Science 2020-12-01 Andac Demir , Toshiaki Koike-Akino , Ye Wang , Deniz Erdogmus

In this guide, we present how to perform constraint-based causal discovery using three popular software packages: pcalg (with add-ons tpc and micd), bnlearn, and TETRAD. We focus on how these packages can be used with observational data and…

Applications · Statistics 2023-12-20 Ryan M. Andrews , Ronja Foraita , Vanessa Didelez , Janine Witte

Using computational notebooks (e.g., Jupyter Notebook), data scientists rationalize their exploratory data analysis (EDA) based on their prior experience and external knowledge such as online examples. For novices or data scientists who…

Human-Computer Interaction · Computer Science 2021-12-16 Xingjun Li , Yizhi Zhang , Justin Leung , Chengnian Sun , Jian Zhao