医学 AI

Comment on 'Interpretation of the Lempel-Ziv Complexity Measure in the context of Biomedical Signal Analysis'

Karthi Balasubramanian, Gayathri R Prabhu, Nithin Nagaraj

专题命中 生物医学文本 ：biomedical(title,abstract)

Comments Submitted for review to IEEE Transactions on Biomedical Engineering

BioSimplify: an open source sentence simplification engine to improve recall in automatic biomedical information extraction

Siddhartha Jonnalagadda, Graciela Gonzalez

专题命中 生物医学文本 ：biomedical(title,abstract)

Journal ref Siddhartha Jonnalagadda, Graciela Gonzalez. BioSimplify: an open source sentence simplification engine to improve recall in automatic biomedical information extraction. In Annual Proceedings of AMIA 2010

Parts-of-Speech Tagger Errors Do Not Necessarily Degrade Accuracy in Extracting Information from Biomedical Text

Maurice HT Ling, Christophe Lefevre, Kevin R. Nicholas

专题命中 生物医学文本 ：biomedical(title,abstract)

Journal ref Ling, Maurice HT, Lefevre, Christophe, Nicholas, Kevin R. 2008. Parts-of-Speech Tagger Errors Do Not Necessarily Degrade Accuracy in Extracting Information from Biomedical Text. The Python Papers 3 (1): 65-80

Open Biomedical Knowledge Graphs at Scale: Construction, Federation, and AI Agent Access with Samyama Graph Database

大规模开放生物医学知识图谱：基于Samyama图数据库的构建、联邦与AI代理访问

Madhulatha Mandarapu, Sandeep Kunkunuru

机构 * VaidhyaMegha Private Limited（维达希亚梅加私人有限公司） 纠错

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

AI总结 本文提出三种开源生物医学知识图谱，通过可重复的ETL模式构建大规模图谱，实现跨图谱联邦与AI代理访问，展示了高精度的领域特定工具。

Comments 12 pages, 7 tables, open-source code and data

Knowledge Graph Extraction from Biomedical Literature for Alkaptonuria Rare Disease

从生物医学文献中提取知识图谱用于阿尔富林尿症罕见疾病

Giang Pham, Rebecca Finetti, Caterina Graziani, Bianca Roncaglia, Asma Bendjeddou, Linda Brodo, Sara Brunetti, Moreno Falaschi, Stefano Forti, Silvia Giulia Galfré, Paolo Milazzo, Corrado Priami, Annalisa Santucci, Ottavia Spiga, Alina Sîrbu

机构 * Department of Computer Science, University of Pisa（计算机科学系，比萨大学） ； Department of Biotechnology, Chemistry and Pharmacy, University of Siena（生物技术、化学与药学系，锡耶纳大学） ； Department of Information Engineering and Mathematics, University of Siena（信息工程与数学系，锡耶纳大学） ； Department of Scienze Economiche e Aziendali, University of Sassari（经济与企业科学系，萨萨里大学） ； Department of Computer Science and Engineering, University of Bologna（计算机科学与工程系，博洛尼亚大学） 纠错

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

AI总结 本文利用PubTator3进行文本挖掘，构建了两个不同规模的知识图谱，用于提取与阿尔富林尿症相关的基因、疾病和治疗方案，揭示了该罕见代谢疾病的系统性相互作用及潜在治疗靶点。

Merged ChemProt-DrugProt for Relation Extraction from Biomedical Literature

融合ChemProt-DrugProt用于生物医学文献中的关系提取

Mai H. Nguyen, Shibani Likhite, Jiawei Tang, Darshini Mahendran, Bridget T. McInnes

机构 * San Diego Supercomputer Center, University of California San Diego 1 ； Department of Computer Science \& Engineering, University of California San Diego 2 ； Department of Computer Science, Virginia Commonwealth University 3 纠错

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

AI总结 本文通过融合ChemProt和DrugProt数据集，结合BioBERT和GCNs提升生物医学文献中化学-基因关系提取的准确率与召回率。

Bizard: A Community-Driven Platform for Accelerating and Enhancing Biomedical Data Visualization

Kexin Li, Hu Zheng, Kexin Huang, Yinying Chai, Yujie Peng, Chunyang Wang, Xuyang Yi, Zilun Jin, Hong Yang, Yun Peng, Ying Shi, Xinhe Lu, Jiarui Bian, Yirun Wang, Rongao Kou, Demin Gao, Hanbo Zhao, Juan Zhang, Dan Huang, Kaiyu Zhu, Chenxu Wu, Zeruo Yang, Zheng Kuang, Mo Liu, Zhiwei Bao, Yuzhong Peng, Benben Miao, Jianming Zeng, Jianfeng Li, Peng Luo, Shixiang Wang

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

Comments 28 pages, 5 figures, and 1 table

fastbmRAG: A Fast Graph-Based RAG Framework for Efficient Processing of Large-Scale Biomedical Literature

Guofeng Meng, Li Shen, Qiuyan Zhong, Wei Wang, Haizhou Zhang, Xiaozhen Wang

机构 * Changchun GeneScience Pharmaceuticals Co., Ltd.（长春基因科学制药有限公司） 纠错

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

Comments 8 pages, 2 figure, 1 table

Deciphering Scientific Collaboration in Biomedical LLM Research: Dynamics, Institutional Participation, and Resource Disparities

Lingyao Li, Zhijie Duan, Xuexin Li, Xiaoran Xu, Zhaoqian Xue, Siyuan Ma, Jin Jin

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

ModernBERT + ColBERT: Enhancing biomedical RAG through an advanced re-ranking retriever

Eduardo Martínez Rivera, Filippo Menolascina

机构 * School of Informatics University of Edinburgh（信息学院爱丁堡大学） ； School of Engineering University of Edinburgh（工程学院爱丁堡大学） 纠错

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

BioVERSE: Representation Alignment of Biomedical Modalities to LLMs for Multi-Modal Reasoning

Ching-Huei Tsou, Michal Ozery-Flato, Ella Barkan, Diwakar Mahajan, Ben Shapira

机构 * IBM T.J. Watson Research Center（IBM T.J. Watson研究所以） ； IBM Research（IBM研究所以） 纠错

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

Desiderata for a biomedical knowledge network: opportunities, challenges and future Directions

Chunlei Wu, Hongfang Liu, Jason Flannick, Mark A. Musen, Andrew I. Su, Lawrence Hunter, Thomas M. Powers, Cathy H. Wu

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

Comments 6 pages, 2 figures

Virtual Cells: From Conceptual Frameworks to Biomedical Applications

Saurabh Bhardwaj, Gaurav Kumar, Haochen Yang, Shaurya Bhardwaj, Qun Wang, Minjie Shen, Yizhi Wang, Cristabelle Madona De Souza

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

Comments 54 Pages, 7 Figures

Standards in the Preparation of Biomedical Research Metadata: A Bridge2AI Perspective

Harry Caufield, Satrajit Ghosh, Sek Wong Kong, Jillian Parker, Nathan Sheffield, Bhavesh Patel, Andrew Williams, Timothy Clark, Monica C. Munoz-Torres

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

Improving Biomedical Knowledge Graph Quality: A Community Approach

Katherina G Cortes, Shilpa Sundar, Sarah Gehrke, Keenan Manpearl, Junxia Lin, Daniel Robert Korn, Harry Caufield, Kevin Schaper, Justin Reese, Kushal Koirala, Lawrence E Hunter, E. Kathleen Carter, Marcello DeLuca, Arjun Krishnan, Chris Mungall, Melissa Haendel

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

STELLA: Self-Evolving LLM Agent for Biomedical Research

Ruofan Jin, Zaixi Zhang, Mengdi Wang, Le Cong

机构 * Princeton University（普林斯顿大学） ； Stanford University（斯坦福大学） 纠错

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

Quantum Dots as Functional Nanosystems for Enhanced Biomedical Applications

Pronama Biswas, Asmita Saha, Bhoomika Sridhar, Anwesha Patel, Belaguppa Manjunath Ashwin Desai

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

Comments Copyright: \c{opyright} 2024 The Author(s). Published by Biolife Sas. This is an open access article under the CC BY 4.0 license. Note: J. Biol. Regul. Homeost. Agents

Journal ref Journal of Biological Regulators and Homeostatic Agents. 2024, 38(3): 1831-1857

Digital Pathway Curation (DPC): a pipeline able to assess the reproducibility, consensus and accuracy in biomedical search retrieval by comparing Gemini, PubMed, and Scientific Reviewers

Flavio Lichtenstein, Daniel Alexandre de Souza, Carlos Eduardo Madureira Trufen, Victor Wendel da Silva Gonçalves, Juliana de Paula Bernardes, Vinicius Miranda Baroni, Carlos DeOcesano-Pereira, Leonardo Fontoura Ormundo, Fabio Augusto Labre de Souza, Olga Celia Martinez Ibañez, Nancy Starobinas, Luciano Rodrigo Lopes, Aparecida Maria Fontes, Sonia Aparecida de Andrade, Ana Marisa Chudzinski-Tavassi

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

Comments Main article: 7 figures and 10 tables. Supplementary information: 22 figures and 59 tables

Quantum machine learning framework for longitudinal biomedical studies

Maria Demidik, Filippo Utro, Alexey Galda, Karl Jansen, Daniel Blankenberg, Laxmi Parida

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

Comments 5 pages, 4 figures

Can Large Language Models Replace Data Scientists in Biomedical Research?

Zifeng Wang, Benjamin Danek, Ziwei Yang, Zheng Chen, Jimeng Sun

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

BMRetriever: Tuning Large Language Models as Better Biomedical Text Retrievers

Ran Xu, Wenqi Shi, Yue Yu, Yuchen Zhuang, Yanqiao Zhu, May D. Wang, Joyce C. Ho, Chao Zhang, Carl Yang

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

Comments Accepted to EMNLP 2024. The model and data are uploaded to \url{https://github.com/ritaranx/BMRetriever}

Journal ref EMNLP 2024

Autonomous self-evolving research on biomedical data: the DREAM paradigm

Luojia Deng, Yijie Wu, Yongyong Ren, Hui Lu

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

Comments 11 pages, 4 figures, content added, typos in figure corrected, references revised and font changed

An LLM-based Knowledge Synthesis and Scientific Reasoning Framework for Biomedical Discovery

Oskar Wysocki, Magdalena Wysocka, Danilo Carvalho, Alex Teodor Bogatu, Danilo Miranda Gusicuma, Maxime Delmas, Harriet Unsworth, Andre Freitas

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

Comments accepted for ACL 2024 System Demonstration Track

Advancing Biomedical Applications: Antioxidant and Biocompatible Cerium Oxide Nanoparticle-Integrated Poly-ε- caprolactone Fibers

Ummay Mowshome Jahan, Brianna Blevins, Sergiy Minko, Vladimir Reukov

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Information

Qiao Jin, Yifan Yang, Qingyu Chen, Zhiyong Lu

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

Journal ref Bioinformatics, 2024

A Platform for the Biomedical Application of Large Language Models

Sebastian Lobentanzer, Shaohong Feng, The BioChatter Consortium, Andreas Maier, Cankun Wang, Jan Baumbach, Nils Krehl, Qin Ma, Julio Saez-Rodriguez

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

Comments 31 pages, 3 figures

PubTator 3.0: an AI-powered Literature Resource for Unlocking Biomedical Knowledge

Chih-Hsuan Wei, Alexis Allot, Po-Ting Lai, Robert Leaman, Shubo Tian, Ling Luo, Qiao Jin, Zhizheng Wang, Qingyu Chen, Zhiyong Lu

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

MedCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrieval

Qiao Jin, Won Kim, Qingyu Chen, Donald C. Comeau, Lana Yeganova, W. John Wilbur, Zhiyong Lu

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

Comments The MedCPT code and API are available at https://github.com/ncbi/MedCPT

Divergent Characteristics of Biomedical Research across Publication Types: A Quantitative Analysis on the Aging-related Research

Chenxing Qian, Qingyue Guo

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

Comments 43 pages, 3 tables, 9 figures, supplementary figures and tables attached in latex code

Development and application of SEM/EDS in biological, biomedical & nanotechnological research

Aniruddha Acharya

专题命中 生物医学文本 ：biomedical(title,abstract)；分类 q-bio

Comments 32 pages, 5 figures, 1 table, unpublished work