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This paper introduces PROTEUS, a fully automated system that produces data-driven hypotheses from raw data files. We apply PROTEUS to clinical proteogenomics, a field where effective downstream data analysis and hypothesis proposal is…

Artificial Intelligence · Computer Science 2025-06-10 Shang Qu , Ning Ding , Linhai Xie , Yifei Li , Zaoqu Liu , Kaiyan Zhang , Yibai Xiong , Yuxin Zuo , Zhangren Chen , Ermo Hua , Xingtai Lv , Youbang Sun , Yang Li , Dong Li , Fuchu He , Bowen Zhou

With the development of artificial intelligence, its contribution to science is evolving from simulating a complex problem to automating entire research processes and producing novel discoveries. Achieving this advancement requires both…

Artificial Intelligence · Computer Science 2024-11-07 Ning Ding , Shang Qu , Linhai Xie , Yifei Li , Zaoqu Liu , Kaiyan Zhang , Yibai Xiong , Yuxin Zuo , Zhangren Chen , Ermo Hua , Xingtai Lv , Youbang Sun , Yang Li , Dong Li , Fuchu He , Bowen Zhou

The growing volume of academic publications poses significant challenges for researchers conducting timely and accurate Systematic Literature Reviews, particularly in fast-evolving fields like artificial intelligence. This growth of…

Artificial Intelligence · Computer Science 2024-10-23 João Pedro Fernandes Torres , Catherine Mulligan , Joaquim Jorge , Catarina Moreira

A plausible future mathematical claim must satisfy two constraints: it should follow the direction of prior work and respect the formal dependencies that constrain what can validly follow. Existing approaches typically model only one of…

Computation and Language · Computer Science 2026-05-29 David Busbib , Michael Werman

Large Language Models (LLMs) have shown remarkable capabilities in automating software engineering tasks, spurring the emergence of coding agents that scaffold LLMs with external tools to resolve repository-level problems. However, existing…

Software Engineering · Computer Science 2026-02-10 Yue Pan , Zimin Chen , Siyu Lu , Zhaoyang Chu , Xiang Li , Han Li , Yang Feng , Claire Le Goues , Federica Sarro , Martin Monperrus , He Ye

FEVEROUS is a benchmark and research initiative focused on fact extraction and verification tasks involving unstructured text and structured tabular data. In FEVEROUS, existing works often rely on extensive preprocessing and utilize…

Computation and Language · Computer Science 2024-03-27 Shirin Dabbaghi Varnosfaderani , Canasai Kruengkrai , Ramin Yahyapour , Junichi Yamagishi

Recently, using a powerful proprietary Large Language Model (LLM) (e.g., GPT-4) as an evaluator for long-form responses has become the de facto standard. However, for practitioners with large-scale evaluation tasks and custom criteria in…

Computation and Language · Computer Science 2024-03-12 Seungone Kim , Jamin Shin , Yejin Cho , Joel Jang , Shayne Longpre , Hwaran Lee , Sangdoo Yun , Seongjin Shin , Sungdong Kim , James Thorne , Minjoon Seo

New text as data techniques offer a great promise: the ability to inductively discover measures that are useful for testing social science theories of interest from large collections of text. We introduce a conceptual framework for making…

Machine Learning · Statistics 2018-02-08 Naoki Egami , Christian J. Fong , Justin Grimmer , Margaret E. Roberts , Brandon M. Stewart

Understanding climate change requires reasoning over complex causal networks. Yet, existing causal discovery datasets predominantly capture explicit, direct causal relations. We introduce ClimateCause, a manually expert-annotated dataset of…

Computation and Language · Computer Science 2026-04-17 Liesbeth Allein , Nataly Pineda-Castañeda , Andrea Rocci , Marie-Francine Moens

Structured (tabular) data in the preclinical and clinical domains contains valuable information about individuals and an efficient table-to-text summarization system can drastically reduce manual efforts to condense this data into reports.…

Computation and Language · Computer Science 2022-07-15 Heng-Yi Wu , Jingqing Zhang , Julia Ive , Tong Li , Vibhor Gupta , Bingyuan Chen , Yike Guo

AI-driven discovery can greatly reduce design time and enhance new therapeutics' effectiveness. Models using simulators explore broad design spaces but risk violating implicit constraints due to a lack of experimental priors. For example,…

Hypothetical induction is recognized as the main reasoning type when scientists make observations about the world and try to propose hypotheses to explain those observations. Past research on hypothetical induction is under a constrained…

Computation and Language · Computer Science 2024-06-13 Zonglin Yang , Xinya Du , Junxian Li , Jie Zheng , Soujanya Poria , Erik Cambria

The availability of large data sets is providing an impetus for driving current artificial intelligent developments. There are, however, challenges for developing solutions with small data sets due to practical and cost-effective deployment…

Machine Learning · Computer Science 2024-05-17 Luca Gherardini , Varun Ravi Varma , Karol Capala , Roger Woods , Jose Sousa

Contemporary approaches to assisted scientific discovery use language models to automatically generate large numbers of potential hypothesis to test, while also automatically generating code-based experiments to test those hypotheses. While…

Artificial Intelligence · Computer Science 2025-09-23 Peter Jansen , Samiah Hassan , Ruoyao Wang

Data analytics often involves hypothetical reasoning: repeatedly modifying the data and observing the induced effect on the computation result of a data-centric application. Previous work has shown that fine-grained data provenance can help…

Databases · Computer Science 2020-07-13 Daniel Deutch , Yuval Moskovitch , Noam Rinetzky

Besides the text content, documents and their associated words usually come with rich sets of meta informa- tion, such as categories of documents and semantic/syntactic features of words, like those encoded in word embeddings. Incorporating…

Computation and Language · Computer Science 2017-09-20 He Zhao , Lan Du , Wray Buntine , Gang Liu

The scientific claim verification task requires an NLP system to label scientific documents which Support or Refute an input claim, and to select evidentiary sentences (or rationales) justifying each predicted label. In this work, we…

Computation and Language · Computer Science 2022-05-11 David Wadden , Kyle Lo , Lucy Lu Wang , Arman Cohan , Iz Beltagy , Hannaneh Hajishirzi

From simulating galaxy formation to viral transmission in a pandemic, scientific models play a pivotal role in developing scientific theories and supporting government policy decisions that affect us all. Given these critical applications,…

Software Engineering · Computer Science 2023-07-03 Andrew G. Clark , Michael Foster , Benedikt Prifling , Neil Walkinshaw , Robert M. Hierons , Volker Schmidt , Robert D. Turner

Accurate trajectory prediction has long been a major challenge for autonomous driving (AD). Traditional data-driven models predominantly rely on statistical correlations, often overlooking the causal relationships that govern traffic…

Artificial Intelligence · Computer Science 2025-05-13 Bonan Wang , Haicheng Liao , Chengyue Wang , Bin Rao , Yanchen Guan , Guyang Yu , Jiaxun Zhang , Songning Lai , Chengzhong Xu , Zhenning Li

We introduce an explainability method for biomedical hypothesis generation systems, built on top of the novel Hypothesis Generation Context Retriever framework. Our approach combines semantic graph-based retrieval and relevant…

Information Retrieval · Computer Science 2025-11-11 Ilya Tyagin , Saeideh Valipour , Aliaksandra Sikirzhytskaya , Michael Shtutman , Ilya Safro
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