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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

Conversational machine comprehension (MC) has proven significantly more challenging compared to traditional MC since it requires better utilization of conversation history. However, most existing approaches do not effectively capture…

Computation and Language · Computer Science 2020-07-16 Yu Chen , Lingfei Wu , Mohammed J. Zaki

Mental health disorders impose a substantial global socioeconomic burden. While large language models (LLMs) offer 24/7, non-judgmental interactions to address this gap, pretrained models lack contextual coherence and emotional alignment…

Computation and Language · Computer Science 2026-02-17 Eric Hua Qing Zhang , Julia Ive

Medical dialogue generation is an important yet challenging task. Most previous works rely on the attention mechanism and large-scale pretrained language models. However, these methods often fail to acquire pivotal information from the long…

Artificial Intelligence · Computer Science 2022-06-20 Yu Zhao , Yunxin Li , Yuxiang Wu , Baotian Hu , Qingcai Chen , Xiaolong Wang , Yuxin Ding , Min Zhang

We introduce a novel graph-based Retrieval-Augmented Generation (RAG) framework specifically designed for the medical domain, called \textbf{MedGraphRAG}, aimed at enhancing Large Language Model (LLM) capabilities for generating…

Computer Vision and Pattern Recognition · Computer Science 2024-10-17 Junde Wu , Jiayuan Zhu , Yunli Qi , Jingkun Chen , Min Xu , Filippo Menolascina , Vicente Grau

Data augmentation is necessary for graph representation learning due to the scarcity and noise present in graph data. Most of the existing augmentation methods overlook the context information inherited from the dataset as they rely solely…

Machine Learning · Computer Science 2025-02-20 Yushi Feng , Tsai Hor Chan , Guosheng Yin , Lequan Yu

Objective: Disease knowledge graphs are a way to connect, organize, and access disparate information about diseases with numerous benefits for artificial intelligence (AI). To create knowledge graphs, it is necessary to extract knowledge…

Machine Learning · Computer Science 2022-09-01 Yucong Lin , Keming Lu , Sheng Yu , Tianxi Cai , Marinka Zitnik

Gene expression datasets offer insights into gene regulation mechanisms, biochemical pathways, and cellular functions. Additionally, comparing gene expression profiles between disease and control patients can deepen the understanding of…

Machine Learning · Computer Science 2025-03-27 Rita T. Sousa , Heiko Paulheim

We present GLM-Dialog, a large-scale language model (LLM) with 10B parameters capable of knowledge-grounded conversation in Chinese using a search engine to access the Internet knowledge. GLM-Dialog offers a series of applicable techniques…

Computation and Language · Computer Science 2023-03-01 Jing Zhang , Xiaokang Zhang , Daniel Zhang-Li , Jifan Yu , Zijun Yao , Zeyao Ma , Yiqi Xu , Haohua Wang , Xiaohan Zhang , Nianyi Lin , Sunrui Lu , Juanzi Li , Jie Tang

Medical dialogue systems (MDS) have emerged as crucial online platforms for enabling multi-turn, context-aware conversations with patients. However, existing MDS often struggle to (1) identify relevant medical knowledge and (2) generate…

Computation and Language · Computer Science 2025-06-13 Hongda Sun , Jiaren Peng , Wenzhong Yang , Liang He , Bo Du , Rui Yan

Biomedical knowledge graphs are increasingly large, dynamic, and multimodal, driven by rapid advances in biotechnology such as high-throughput sequencing. Machine learning models can infer previously unobserved biomedical relationships and…

Machine Learning · Computer Science 2026-05-12 Yousef A. Radwan , Yao Li , Qing Qing , Ziqi Xu , Qixin Zhang , Yongcheng Jing , Renqiang Luo , Xikun Zhang

In Natural Language Processing (NLP), Machine Reading Comprehension (MRC) is the task of answering a question based on a given context. To handle questions in the medical domain, modern language models such as BioBERT, SciBERT and even…

Computation and Language · Computer Science 2024-12-16 Saptarshi Sengupta , Connor Heaton , Suhan Cui , Soumalya Sarkar , Prasenjit Mitra

Large language models (LLMs) offer new opportunities for constructing knowledge graphs (KGs) from unstructured clinical narratives. However, existing approaches often rely on structured inputs and lack robust validation of factual accuracy…

Artificial Intelligence · Computer Science 2026-01-06 Udiptaman Das , Krishnasai B. Atmakuri , Duy Ho , Chi Lee , Yugyung Lee

Large language models (LLMs) are rapidly transforming various domains, including biomedicine and healthcare, and demonstrate remarkable potential from scientific research to new drug discovery. Graph-based retrieval-augmented generation…

Quantitative Methods · Quantitative Biology 2025-11-14 Guofeng Meng , Li Shen , Qiuyan Zhong , Wei Wang , Haizhou Zhang , Xiaozhen Wang

Constructing responses in task-oriented dialogue systems typically relies on information sources such the current dialogue state or external databases. This paper presents a novel approach to knowledge-grounded response generation that…

Computation and Language · Computer Science 2023-10-23 Nicholas Thomas Walker , Stefan Ultes , Pierre Lison

Developing conversational agents to interact with patients and provide primary clinical advice has attracted increasing attention due to its huge application potential, especially in the time of COVID-19 Pandemic. However, the training of…

Computation and Language · Computer Science 2022-08-02 Wenge Liu , Jianheng Tang , Yi Cheng , Wenjie Li , Yefeng Zheng , Xiaodan Liang

Natural language generation (NLG) is an essential component of task-oriented dialogue systems. Despite the recent success of neural approaches for NLG, they are typically developed for particular domains with rich annotated training…

Computation and Language · Computer Science 2019-05-15 Fei Mi , Minlie Huang , Jiyong Zhang , Boi Faltings

Recent advances in natural language processing (NLP) owe their success to pre-training language models on large amounts of unstructured data. Still, there is an increasing effort to combine the unstructured nature of LMs with structured…

Computation and Language · Computer Science 2023-12-22 Juraj Vladika , Alexander Fichtl , Florian Matthes

Large language models (LLMs) have recently emerged as powerful tools, finding many medical applications. LLMs' ability to coalesce vast amounts of information from many sources to generate a response-a process similar to that of a human…

Large language models (LLMs) are transforming the way information is retrieved with vast amounts of knowledge being summarized and presented via natural language conversations. Yet, LLMs are prone to highlight the most frequently seen…

Computation and Language · Computer Science 2024-02-20 Julien Delile , Srayanta Mukherjee , Anton Van Pamel , Leonid Zhukov