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Availability of research datasets is keystone for health and life science study reproducibility and scientific progress. Due to the heterogeneity and complexity of these data, a main challenge to be overcome by research data management…

Information Retrieval · Computer Science 2017-09-12 Douglas Teodoro , Luc Mottin , Julien Gobeill , Arnaud Gaudinat , Thérèse Vachon , Patrick Ruch

Generating novel and creative scientific hypotheses is a cornerstone in achieving Artificial General Intelligence. Large language and reasoning models have the potential to aid in the systematic creation, selection, and validation of…

Computation and Language · Computer Science 2025-04-18 Charles O'Neill , Tirthankar Ghosal , Roberta Răileanu , Mike Walmsley , Thang Bui , Kevin Schawinski , Ioana Ciucă

Summary: The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make modeling simpler, but largely exclude users from the process. We present an…

Biomolecules · Quantitative Biology 2017-02-08 Rowan Hatherley , David K. Brown , Özlem Tastan Bishop

Knowledge graphs, collectively as a knowledge network, have become critical tools for knowledge discovery in computable and explainable knowledge systems. Due to the semantic and structural complexities of biomedical data, these knowledge…

Other Quantitative Biology · Quantitative Biology 2025-09-29 Chunlei Wu , Hongfang Liu , Jason Flannick , Mark A. Musen , Andrew I. Su , Lawrence Hunter , Thomas M. Powers , Cathy H. Wu

Query answering routinely employs knowledge graphs to assist the user in the search process. Given a knowledge graph that represents entities and relationships among them, one aims at complementing the search with intuitive but effective…

Databases · Computer Science 2018-02-13 Davide Mottin , Bastian Grasnick , Axel Kroschk , Patrick Siegler , Emmanuel Mueller

High-quality labels are expensive to obtain for many machine learning tasks, such as medical image classification tasks. Therefore, probabilistic (weak) labels produced by weak supervision tools are used to seed a process in which…

Databases · Computer Science 2021-07-27 Yinjun Wu , James Weimer , Susan B. Davidson

Entity alignment has always had significant uses within a multitude of diverse scientific fields. In particular, the concept of matching entities across networks has grown in significance in the world of social science as communicative…

Social and Information Networks · Computer Science 2020-04-21 James Flamino , Christopher Abriola , Ben Zimmerman , Zhongheng Li , Joel Douglas

Scientific fact-checking aims to determine the veracity of scientific claims by retrieving and analysing evidence from research literature. The problem is inherently more complex than general fact-checking since it must accommodate the…

Information Retrieval · Computer Science 2025-08-18 Xingyu Deng , Xi Wang , Mark Stevenson

Verification of biomedical claims is critical for healthcare decision-making, public health policy and scientific research. We present an interactive biomedical claim verification system by integrating LLMs, transparent model explanations,…

Human-Computer Interaction · Computer Science 2025-03-03 Siting Liang , Daniel Sonntag

This article presents our steps to integrate complex and partly unstructured medical data into a clinical research database with subsequent decision support. Our main application is an integrated faceted search tool, accompanied by the…

Human-Computer Interaction · Computer Science 2018-10-31 Daniel Sonntag , Hans-Jürgen Profitlich

Data tables play a central role in scientific papers. However, their meaning is often co-constructed with surrounding text through narrative interplay, making comprehension cognitively demanding for readers. In this work, we explore how…

Human-Computer Interaction · Computer Science 2026-02-27 Liangwei Wang , Zhengxuan Zhang , Yifan Cao , Fugee Tsung , Yuyu Luo

Large language models (LLMs) are increasingly expected to go beyond simple factual queries toward Deep Research-tasks that require decomposing questions into sub-problems, coordinating multi-step reasoning, and synthesizing evidence from…

Computation and Language · Computer Science 2025-09-03 Ziyi Xia , Kun Luo , Hongjin Qian , Zheng Liu

English research articles (RAs) are an essential genre in academia, so the attempts to employ NLP to assist the development of academic writing ability have received considerable attention in the last two decades. However, there has been no…

Computation and Language · Computer Science 2021-11-16 Siyu Lei , Ruiying Yang , Chu-Ren Huang

The development of modern civil industry, energy and information technology is inseparable from the rapid explorations of new materials, which are hampered by months to years of painstaking attempts, resulting in only a small fraction of…

Chemical Physics · Physics 2023-03-22 Zhilong Wang , Junfei Cai , An Chen , Yanqiang Han , Kehao Tao , Simin Ye , Shiwei Wang , Imran Ali , Jinjin Li

Large pre-trained language models have been shown to encode large amounts of world and commonsense knowledge in their parameters, leading to substantial interest in methods for extracting that knowledge. In past work, knowledge was…

Computation and Language · Computer Science 2021-03-12 Adi Haviv , Jonathan Berant , Amir Globerson

Despite the success of PubMed and other search engines in managing the massive volume of biomedical literature and the retrieval of individual publications, grant-related data remains scattered and relatively inaccessible. This is…

Faced with the burgeoning volume of academic literature, researchers often need help with uncertain article quality and mismatches in term searches using traditional academic engines. We introduce IntellectSeeker, an innovative and…

Information Retrieval · Computer Science 2024-12-11 Weizhen Bian , Siyan Liu , Yubo Zhou , Dezhi Chen , Yijie Liao , Zhenzhen Fan , Aobo Wang

Polymers are a vital part of everyday life. Their chemical universe is so large that it presents unprecedented opportunities as well as significant challenges to identify suitable application-specific candidates. We present a complete…

Materials Science · Physics 2023-07-20 Christopher Kuenneth , Rampi Ramprasad

Antibiotic resistance presents a growing global health crisis, demanding new therapeutic strategies that target novel bacterial mechanisms. Recent advances in protein structure prediction and machine learning-driven molecule generation…

Biomolecules · Quantitative Biology 2025-05-22 Maximilian G. Schuh , Joshua Hesse , Stephan A. Sieber

In the extensive recommender systems literature, novelty and diversity have been identified as key properties of useful recommendations. However, these properties have received limited attention in the specific sub-field of research paper…

Information Retrieval · Computer Science 2024-11-06 Eoghan Cunningham , Derek Greene , Barry Smyth