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Genes, proteins and other biological entities influence one another via causal molecular networks. Causal relationships in such networks are mediated by complex and diverse mechanisms, through latent variables, and are often specific to…

Machine Learning · Computer Science 2025-03-07 Izzy Newsham , Luka Kovačević , Richard Moulange , Nan Rosemary Ke , Sach Mukherjee

To perform effective causal inference in high-dimensional datasets, initiating the process with causal discovery is imperative, wherein a causal graph is generated based on observational data. However, obtaining a complete and accurate…

Machine Learning · Computer Science 2025-04-18 Elahe Khatibi , Mahyar Abbasian , Zhongqi Yang , Iman Azimi , Amir M. Rahmani

Large Language Models (LLMs) have emerged as a transformative power in enhancing natural language comprehension, representing a significant stride toward artificial general intelligence. The application of LLMs extends beyond conventional…

Estimating individualized treatment effects from observational data presents a persistent challenge due to unmeasured confounding and structural bias. Causal Machine Learning (causal ML) methods, such as causal trees and doubly robust…

Machine Learning · Computer Science 2025-08-12 Po-Han Lee , Yu-Cheng Lin , Chan-Tung Ku , Chan Hsu , Pei-Cing Huang , Ping-Hsun Wu , Yihuang Kang

The integration of Large Language Models (LLMs) into the drug discovery and development field marks a significant paradigm shift, offering novel methodologies for understanding disease mechanisms, facilitating drug discovery, and optimizing…

Quantitative Methods · Quantitative Biology 2024-09-10 Yizhen Zheng , Huan Yee Koh , Maddie Yang , Li Li , Lauren T. May , Geoffrey I. Webb , Shirui Pan , George Church

Causal structure discovery methods are commonly applied to structured data where the causal variables are known and where statistical testing can be used to assess the causal relationships. By contrast, recovering a causal structure from…

Computation and Language · Computer Science 2024-10-10 Gaël Gendron , Jože M. Rožanec , Michael Witbrock , Gillian Dobbie

Cognitive diagnosis (CD) plays a crucial role in intelligent education, evaluating students' comprehension of knowledge concepts based on their test histories. However, current CD methods often model students, exercises, and knowledge…

Computation and Language · Computer Science 2025-05-21 Weiming Zhang , Lingyue Fu , Qingyao Li , Kounianhua Du , Jianghao Lin , Jingwei Yu , Wei Xia , Weinan Zhang , Ruiming Tang , Yong Yu

Autoregressive (AR) language models and Diffusion Language Models (DLMs) constitute the two principal paradigms of large language models. However, both paradigms suffer from insufficient reasoning capabilities. Human reasoning inherently…

Computation and Language · Computer Science 2025-12-01 Kairong Han , Nuanqiao Shan , Ziyu Zhao , Zijing Hu , Xinpeng Dong , Junjian Ye , Lujia Pan , Fei Wu , Kun Kuang

Causal discovery seeks to uncover causal relations from data, typically represented as causal graphs, and is essential for predicting the effects of interventions. While expert knowledge is required to construct principled causal graphs,…

Artificial Intelligence · Computer Science 2026-02-19 Zihao Li , Fabrizio Russo

The validity of medical studies based on real-world clinical data, such as observational studies, depends on critical assumptions necessary for drawing causal conclusions about medical interventions. Many published studies are flawed…

Artificial Intelligence · Computer Science 2024-07-30 Ahmed Alaa , Rachael V. Phillips , Emre Kıcıman , Laura B. Balzer , Mark van der Laan , Maya Petersen

Designing proper experiments and selecting optimal intervention targets is a longstanding problem in scientific or causal discovery. Identifying the underlying causal structure from observational data alone is inherently difficult.…

Artificial Intelligence · Computer Science 2025-03-05 Junyi Li , Yongqiang Chen , Chenxi Liu , Qianyi Cai , Tongliang Liu , Bo Han , Kun Zhang , Hui Xiong

Current approaches to data discovery match keywords between metadata and queries. This matching requires researchers to know the exact wording that other researchers previously used, creating a challenging process that could lead to missing…

Human-Computer Interaction · Computer Science 2025-10-03 Maura E Halstead , Mark A. Green , Caroline Jay , Richard Kingston , David Topping , Alexander Singleton

Large Language Models (LLMs) have revolutionised the field of Natural Language Processing (NLP) and have achieved state-of-the-art performance in practically every task in this field. However, the prevalent approach used in text generation,…

Computation and Language · Computer Science 2024-08-12 Nicolo Micheletti , Samuel Belkadi , Lifeng Han , Goran Nenadic

Large language models (LLMs) exhibit remarkable capabilities on not just language tasks, but also various tasks that are not linguistic in nature, such as logical reasoning and social inference. In the human brain, neuroscience has…

Computation and Language · Computer Science 2025-02-14 Badr AlKhamissi , Greta Tuckute , Antoine Bosselut , Martin Schrimpf

Large Language Models (LLMs) have shown their success in language understanding and reasoning on general topics. However, their capability to perform inference based on user-specified structured data and knowledge in corpus-rare concepts,…

Computation and Language · Computer Science 2024-10-29 Haitao Jiang , Lin Ge , Yuhe Gao , Jianian Wang , Rui Song

Despite impressive performance on language modelling and complex reasoning tasks, Large Language Models (LLMs) fall short on the same tasks in uncommon settings or with distribution shifts, exhibiting a lack of generalisation ability. By…

Computation and Language · Computer Science 2024-09-11 Gaël Gendron , Bao Trung Nguyen , Alex Yuxuan Peng , Michael Witbrock , Gillian Dobbie

Transforming a dynamic hypothesis into a causal loop diagram (CLD) is crucial for System Dynamics Modelling. Extracting key variables and causal relationships from text to build a CLD is often challenging and time-consuming for novice…

Machine Learning · Computer Science 2025-03-31 Ning-Yuan Georgia Liu , David R. Keith

With the rise of Large Language Models(LLMs), it has become crucial to understand their capabilities and limitations in deciphering and explaining the complex web of causal relationships that language entails. Current methods use either…

Large Language Models (LLMs) have seen rapid advancements in recent years, with models like ChatGPT and DeepSeek, showcasing their remarkable capabilities across diverse domains. While substantial research has been conducted on LLMs in…

Machine Learning · Computer Science 2026-03-31 Licheng Zhang , Bach Le , Naveed Akhtar , Siew-Kei Lam , Tuan Ngo

Causal inference is one of the hallmarks of human intelligence. While the field of CausalNLP has attracted much interest in the recent years, existing causal inference datasets in NLP primarily rely on discovering causality from empirical…

Computation and Language · Computer Science 2024-04-18 Zhijing Jin , Jiarui Liu , Zhiheng Lyu , Spencer Poff , Mrinmaya Sachan , Rada Mihalcea , Mona Diab , Bernhard Schölkopf