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We present BioLunar, developed using the Lunar framework, as a tool for supporting biological analyses, with a particular emphasis on molecular-level evidence enrichment for biomarker discovery in oncology. The platform integrates Large…

This paper presents OG-RAG, an Ontology-Grounded Retrieval Augmented Generation method designed to enhance LLM-generated responses by anchoring retrieval processes in domain-specific ontologies. While LLMs are widely used for tasks like…

Computation and Language · Computer Science 2024-12-23 Kartik Sharma , Peeyush Kumar , Yunqing Li

This paper addresses the challenge of improving information retrieval from semi-structured eXtensible Markup Language (XML) documents. Traditional information retrieval systems (IRS) often overlook user-specific needs and return identical…

Information Retrieval · Computer Science 2026-03-24 Ounnaci Iddir , Ahmed-ouamer Rachid , Tai Dinh

Multi-objective optimization is a common problem in practical applications, and multi-objective evolutionary algorithm (MOEA) is considered as one of the effective methods to solve these problems. However, their randomness sometimes…

Neural and Evolutionary Computing · Computer Science 2024-10-04 Wanyi Liu , Long Chen , Zhenzhou Tang

Entity matching (EM) is a critical step in entity resolution (ER). Recently, entity matching based on large language models (LLMs) has shown great promise. However, current LLM-based entity matching approaches typically follow a binary…

Computation and Language · Computer Science 2024-12-13 Tianshu Wang , Xiaoyang Chen , Hongyu Lin , Xuanang Chen , Xianpei Han , Hao Wang , Zhenyu Zeng , Le Sun

Large language models have emerged as a promising approach towards achieving general-purpose AI agents. The thriving open-source LLM community has greatly accelerated the development of agents that support human-machine dialogue interaction…

Computer Vision and Pattern Recognition · Computer Science 2023-11-07 Zhenfei Yin , Jiong Wang , Jianjian Cao , Zhelun Shi , Dingning Liu , Mukai Li , Lu Sheng , Lei Bai , Xiaoshui Huang , Zhiyong Wang , Jing Shao , Wanli Ouyang

Generative Artificial Intelligence (GenAI), particularly Large Language Models (LLMs), offer powerful capabilities for interpreting the complex data landscape in healthcare. In this paper, we present a comprehensive overview of the…

Machine Learning · Computer Science 2025-09-05 Ankit Shetgaonkar , Dipen Pradhan , Lakshit Arora , Sanjay Surendranath Girija , Shashank Kapoor , Aman Raj

Large Language Models (LLMs) have been extensively adopted in Knowledge Graph Completion (KGC), showcasing significant research advancements. However, as black-box models driven by deep neural architectures, current LLM-based KGC methods…

Computation and Language · Computer Science 2025-10-22 Wenbin Guo , Xin Wang , Jiaoyan Chen , Zhao Li , Zirui Chen

In the realm of Business Process Management (BPM), process modeling plays a crucial role in translating complex process dynamics into comprehensible visual representations, facilitating the understanding, analysis, improvement, and…

Software Engineering · Computer Science 2024-07-01 Humam Kourani , Alessandro Berti , Daniel Schuster , Wil M. P. van der Aalst

Ontologies form the basic interest in various computer science disciplines such as semantic web, information retrieval, database design, etc. They aim at providing a formal, explicit and shared conceptualization and understanding of common…

Information Retrieval · Computer Science 2020-05-04 M. Maree , M. Belkhatir

The heterogeneity of data poses a great challenge when data from different sources is to be merged for one application. Solutions for this are offered, for example, by ontology-based data management (OBDM). A challenge of OBDM is the…

Information Retrieval · Computer Science 2020-05-15 Andreas Burgdorf , André Pomp , Tobias Meisen

The paper introduces a framework for the evaluation of the encoding of factual scientific knowledge, designed to streamline the manual evaluation process typically conducted by domain experts. Inferring over and extracting information from…

Computation and Language · Computer Science 2024-10-21 Magdalena Wysocka , Oskar Wysocki , Maxime Delmas , Vincent Mutel , Andre Freitas

Clinical trial matching is the task of identifying trials for which patients may be potentially eligible. Typically, this task is labor-intensive and requires detailed verification of patient electronic health records (EHRs) against the…

The explainability of recommendation systems is crucial for enhancing user trust and satisfaction. Leveraging large language models (LLMs) offers new opportunities for comprehensive recommendation logic generation. However, in existing…

Information Retrieval · Computer Science 2024-07-04 Hongke Zhao , Songming Zheng , Likang Wu , Bowen Yu , Jing Wang

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

The rapid advancement of Large Language Models (LLMs) has resulted in interest in their potential applications within manufacturing systems, particularly in the context of Industry 5.0. However, determining when to implement LLMs versus…

Human-Computer Interaction · Computer Science 2025-05-27 John Oyekan , Christopher Turner , Michael Bax , Erich Graf

Semantic reasoning aims to infer new knowledge from existing knowledge, with OWL ontologies serving as a standardized framework for organizing information. A key challenge in semantic reasoning is verifying ontology consistency. However,…

Artificial Intelligence · Computer Science 2025-04-29 Justin Mücke , Ansgar Scherp

Large Language Models (LLMs) are a class of generative AI models built using the Transformer network, capable of leveraging vast datasets to identify, summarize, translate, predict, and generate language. LLMs promise to revolutionize…

Information Retrieval · Computer Science 2024-03-05 Chunhe Ni , Jiang Wu , Hongbo Wang , Wenran Lu , Chenwei Zhang

Large Language Models (LLMs) possess substantial reasoning capabilities and are increasingly applied to optimization tasks, particularly in synergy with evolutionary computation. However, while recent surveys have explored specific aspects…

Neural and Evolutionary Computing · Computer Science 2026-01-08 Yisong Zhang , Ran Cheng , Guoxing Yi , Kay Chen Tan

Domain experts often rely on most recent knowledge for apprehending and disseminating specific biological processes that help them design strategies for developing prevention and therapeutic decision-making in various disease scenarios. A…

Computation and Language · Computer Science 2023-11-21 Md. Rezaul Karim , Lina Molinas Comet , Md Shajalal , Oya Deniz Beyan , Dietrich Rebholz-Schuhmann , Stefan Decker