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For: Luo L, Lai PT, Wei CH, Arighi CN, Lu Z. BioRED: a rich biomedical relation extraction dataset. Brief Bioinform 2022;23:6645993. [PMID: 35849818 PMCID: PMC9487702 DOI: 10.1093/bib/bbac282] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 06/02/2022] [Accepted: 06/19/2022] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
1
Jia Y, Wang H, Yuan Z, Zhu L, Xiang ZL. Biomedical relation extraction method based on ensemble learning and attention mechanism. BMC Bioinformatics 2024;25:333. [PMID: 39425010 PMCID: PMC11488084 DOI: 10.1186/s12859-024-05951-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Accepted: 10/07/2024] [Indexed: 10/21/2024]  Open
2
Phan CP, Phan B, Chiang JH. Optimized biomedical entity relation extraction method with data augmentation and classification using GPT-4 and Gemini. Database (Oxford) 2024;2024:baae104. [PMID: 39383312 PMCID: PMC11463225 DOI: 10.1093/database/baae104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 08/21/2024] [Accepted: 09/04/2024] [Indexed: 10/11/2024]
3
Yin Y, Kim H, Xiao X, Wei CH, Kang J, Lu Z, Xu H, Fang M, Chen Q. Augmenting biomedical named entity recognition with general-domain resources. J Biomed Inform 2024;159:104731. [PMID: 39368529 DOI: 10.1016/j.jbi.2024.104731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 09/05/2024] [Accepted: 09/27/2024] [Indexed: 10/07/2024]
4
Košprdić M, Prodanović N, Ljajić A, Bašaragin B, Milošević N. From zero to hero: Harnessing transformers for biomedical named entity recognition in zero- and few-shot contexts. Artif Intell Med 2024;156:102970. [PMID: 39197375 DOI: 10.1016/j.artmed.2024.102970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 08/23/2024] [Accepted: 08/23/2024] [Indexed: 09/01/2024]
5
Sun J, Zhang C, Xing L, Zhang L, Cai H, Guo M. BAMRE: Joint extraction model of Chinese medical entities and relations based on Biaffine transformation with relation attention. J Biomed Inform 2024;158:104733. [PMID: 39368528 DOI: 10.1016/j.jbi.2024.104733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 09/03/2024] [Accepted: 09/28/2024] [Indexed: 10/07/2024]
6
Sänger M, Garda S, Wang XD, Weber-Genzel L, Droop P, Fuchs B, Akbik A, Leser U. HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization tools. Bioinformatics 2024;40:btae564. [PMID: 39302686 PMCID: PMC11453098 DOI: 10.1093/bioinformatics/btae564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 08/23/2024] [Accepted: 09/17/2024] [Indexed: 09/22/2024]  Open
7
Nastou K, Mehryary F, Ohta T, Luoma J, Pyysalo S, Jensen LJ. RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature. Database (Oxford) 2024;2024:baae095. [PMID: 39265993 PMCID: PMC11394941 DOI: 10.1093/database/baae095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/31/2024] [Accepted: 08/16/2024] [Indexed: 09/14/2024]
8
Lai PT, Coudert E, Aimo L, Axelsen K, Breuza L, de Castro E, Feuermann M, Morgat A, Pourcel L, Pedruzzi I, Poux S, Redaschi N, Rivoire C, Sveshnikova A, Wei CH, Leaman R, Luo L, Lu Z, Bridge A. EnzChemRED, a rich enzyme chemistry relation extraction dataset. Sci Data 2024;11:982. [PMID: 39251610 PMCID: PMC11384730 DOI: 10.1038/s41597-024-03835-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 08/23/2024] [Indexed: 09/11/2024]  Open
9
Nie P, Ning J, Lin M, Yang Z, Wang L. SSGU-CD: A combined semantic and structural information graph U-shaped network for document-level Chemical-Disease interaction extraction. J Biomed Inform 2024;157:104719. [PMID: 39214159 DOI: 10.1016/j.jbi.2024.104719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 08/20/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
10
Lu Z, Peng Y, Cohen T, Ghassemi M, Weng C, Tian S. Large language models in biomedicine and health: current research landscape and future directions. J Am Med Inform Assoc 2024;31:1801-1811. [PMID: 39169867 PMCID: PMC11339542 DOI: 10.1093/jamia/ocae202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Indexed: 08/23/2024]  Open
11
Li Z, Wei Q, Huang LC, Li J, Hu Y, Chuang YS, He J, Das A, Keloth VK, Yang Y, Diala CS, Roberts KE, Tao C, Jiang X, Zheng WJ, Xu H. Ensemble pretrained language models to extract biomedical knowledge from literature. J Am Med Inform Assoc 2024;31:1904-1911. [PMID: 38520725 PMCID: PMC11339500 DOI: 10.1093/jamia/ocae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/14/2024] [Accepted: 03/12/2024] [Indexed: 03/25/2024]  Open
12
Zhou H, Li M, Xiao Y, Yang H, Zhang R. LEAP: LLM instruction-example adaptive prompting framework for biomedical relation extraction. J Am Med Inform Assoc 2024;31:2010-2018. [PMID: 38904416 PMCID: PMC11339510 DOI: 10.1093/jamia/ocae147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 05/26/2024] [Accepted: 06/03/2024] [Indexed: 06/22/2024]  Open
13
Luo L, Ning J, Zhao Y, Wang Z, Ding Z, Chen P, Fu W, Han Q, Xu G, Qiu Y, Pan D, Li J, Li H, Feng W, Tu S, Liu Y, Yang Z, Wang J, Sun Y, Lin H. Taiyi: a bilingual fine-tuned large language model for diverse biomedical tasks. J Am Med Inform Assoc 2024;31:1865-1874. [PMID: 38422367 PMCID: PMC11339499 DOI: 10.1093/jamia/ocae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/08/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024]  Open
14
Zong H, Wu R, Cha J, Feng W, Wu E, Li J, Shao A, Tao L, Li Z, Tang B, Shen B. Advancing Chinese biomedical text mining with community challenges. J Biomed Inform 2024;157:104716. [PMID: 39197732 DOI: 10.1016/j.jbi.2024.104716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 08/22/2024] [Accepted: 08/25/2024] [Indexed: 09/01/2024]
15
Sarol MJ, Hong G, Guerra E, Kilicoglu H. Integrating deep learning architectures for enhanced biomedical relation extraction: a pipeline approach. Database (Oxford) 2024;2024:baae079. [PMID: 39197056 PMCID: PMC11352595 DOI: 10.1093/database/baae079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/21/2024] [Accepted: 08/14/2024] [Indexed: 08/30/2024]
16
Nastou K, Koutrouli M, Pyysalo S, Jensen LJ. CoNECo: a Corpus for Named Entity recognition and normalization of protein Complexes. BIOINFORMATICS ADVANCES 2024;4:vbae116. [PMID: 39411448 PMCID: PMC11474106 DOI: 10.1093/bioadv/vbae116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/10/2024] [Accepted: 08/04/2024] [Indexed: 10/19/2024]
17
Islamaj R, Wei CH, Lai PT, Luo L, Coss C, Gokal Kochar P, Miliaras N, Rodionov O, Sekiya K, Trinh D, Whitman D, Lu Z. The biomedical relationship corpus of the BioRED track at the BioCreative VIII challenge and workshop. Database (Oxford) 2024;2024:baae071. [PMID: 39126204 PMCID: PMC11315767 DOI: 10.1093/database/baae071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/03/2024] [Accepted: 07/09/2024] [Indexed: 08/12/2024]
18
Islamaj R, Lai PT, Wei CH, Luo L, Almeida T, Jonker RAA, Conceição SIR, Sousa DF, Phan CP, Chiang JH, Li J, Pan D, Meesawad W, Tsai RTH, Sarol MJ, Hong G, Valiev A, Tutubalina E, Lee SM, Hsu YY, Li M, Verspoor K, Lu Z. The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII. Database (Oxford) 2024;2024:baae069. [PMID: 39114977 PMCID: PMC11306928 DOI: 10.1093/database/baae069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/27/2024] [Accepted: 07/09/2024] [Indexed: 08/11/2024]
19
Garda S, Leser U. BELHD: improving biomedical entity linking with homonym disambiguation. Bioinformatics 2024;40:btae474. [PMID: 39067036 PMCID: PMC11310454 DOI: 10.1093/bioinformatics/btae474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/14/2024] [Accepted: 07/25/2024] [Indexed: 07/30/2024]  Open
20
Cousins HC, Nayar G, Altman RB. Computational Approaches to Drug Repurposing: Methods, Challenges, and Opportunities. Annu Rev Biomed Data Sci 2024;7:15-29. [PMID: 38598857 DOI: 10.1146/annurev-biodatasci-110123-025333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
21
Jonker RAA, Almeida T, Antunes R, Almeida JR, Matos S. Multi-head CRF classifier for biomedical multi-class named entity recognition on Spanish clinical notes. Database (Oxford) 2024;2024:baae068. [PMID: 39083461 PMCID: PMC11290360 DOI: 10.1093/database/baae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/15/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024]
22
Almeida T, Jonker RAA, Antunes R, Almeida JR, Matos S. Towards discovery: an end-to-end system for uncovering novel biomedical relations. Database (Oxford) 2024;2024:baae057. [PMID: 38994795 PMCID: PMC11240158 DOI: 10.1093/database/baae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/20/2024] [Accepted: 06/19/2024] [Indexed: 07/13/2024]
23
Wei CH, Allot A, Lai PT, Leaman R, Tian S, Luo L, Jin Q, Wang Z, Chen Q, Lu Z. PubTator 3.0: an AI-powered literature resource for unlocking biomedical knowledge. Nucleic Acids Res 2024;52:W540-W546. [PMID: 38572754 PMCID: PMC11223843 DOI: 10.1093/nar/gkae235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/02/2024] [Accepted: 03/21/2024] [Indexed: 04/05/2024]  Open
24
Xu T, Gu Y, Xue M, Gu R, Li B, Gu X. Knowledge graph construction for heart failure using large language models with prompt engineering. Front Comput Neurosci 2024;18:1389475. [PMID: 39015745 PMCID: PMC11250484 DOI: 10.3389/fncom.2024.1389475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 06/13/2024] [Indexed: 07/18/2024]  Open
25
Yuan J, Zhang F, Qiu Y, Lin H, Zhang Y. Document-level biomedical relation extraction via hierarchical tree graph and relation segmentation module. BIOINFORMATICS (OXFORD, ENGLAND) 2024;40:btae418. [PMID: 38917409 DOI: 10.1093/bioinformatics/btae418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/27/2024] [Accepted: 06/24/2024] [Indexed: 06/27/2024]
26
Ming S, Zhang R, Kilicoglu H. Enhancing the coverage of SemRep using a relation classification approach. J Biomed Inform 2024;155:104658. [PMID: 38782169 DOI: 10.1016/j.jbi.2024.104658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/01/2024] [Accepted: 05/18/2024] [Indexed: 05/25/2024]
27
Purpura A, Mulligan N, Kartoun U, Koski E, Anand V, Bettencourt-Silva J. Investigating Cross-Domain Binary Relation Classification in Biomedical Natural Language Processing. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE PROCEEDINGS. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE 2024;2024:384-390. [PMID: 38827064 PMCID: PMC11141837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
28
Nachtegael C, De Stefani J, Cnudde A, Lenaerts T. DUVEL: an active-learning annotated biomedical corpus for the recognition of oligogenic combinations. Database (Oxford) 2024;2024:baae039. [PMID: 38805753 PMCID: PMC11131422 DOI: 10.1093/database/baae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/17/2024] [Accepted: 05/13/2024] [Indexed: 05/30/2024]
29
Huang MS, Han JC, Lin PY, You YT, Tsai RTH, Hsu WL. Surveying biomedical relation extraction: a critical examination of current datasets and the proposal of a new resource. Brief Bioinform 2024;25:bbae132. [PMID: 38609331 PMCID: PMC11014787 DOI: 10.1093/bib/bbae132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 11/06/2023] [Accepted: 03/02/2023] [Indexed: 04/14/2024]  Open
30
Smith E, Paloots R, Giagkos D, Baudis M, Stockinger K. Data-driven information extraction and enrichment of molecular profiling data for cancer cell lines. BIOINFORMATICS ADVANCES 2024;4:vbae045. [PMID: 38560553 PMCID: PMC10978572 DOI: 10.1093/bioadv/vbae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/12/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024]
31
Nachtegael C, De Stefani J, Lenaerts T. A study of deep active learning methods to reduce labelling efforts in biomedical relation extraction. PLoS One 2023;18:e0292356. [PMID: 38100453 PMCID: PMC10723703 DOI: 10.1371/journal.pone.0292356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/19/2023] [Indexed: 12/17/2023]  Open
32
Zhang Y, Sui X, Pan F, Yu K, Li K, Tian S, Erdengasileng A, Han Q, Wang W, Wang J, Wang J, Sun D, Chung H, Zhou J, Zhou E, Lee B, Zhang P, Qiu X, Zhao T, Zhang J. BioKG: a comprehensive, large-scale biomedical knowledge graph for AI-powered, data-driven biomedical research. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562216. [PMID: 38168218 PMCID: PMC10760044 DOI: 10.1101/2023.10.13.562216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
33
Millikin RJ, Raja K, Steill J, Lock C, Tu X, Ross I, Tsoi LC, Kuusisto F, Ni Z, Livny M, Bockelman B, Thomson J, Stewart R. Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models. BMC Bioinformatics 2023;24:412. [PMID: 37915001 PMCID: PMC10619245 DOI: 10.1186/s12859-023-05539-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/19/2023] [Indexed: 11/03/2023]  Open
34
Lai PT, Wei CH, Luo L, Chen Q, Lu Z. BioREx: Improving biomedical relation extraction by leveraging heterogeneous datasets. J Biomed Inform 2023;146:104487. [PMID: 37673376 DOI: 10.1016/j.jbi.2023.104487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/18/2023] [Accepted: 09/02/2023] [Indexed: 09/08/2023]
35
Rey CA, Danguilan JL, Mendoza KP, Remolona MF. Transformer-based approach to variable typing. Heliyon 2023;9:e20505. [PMID: 37842594 PMCID: PMC10568320 DOI: 10.1016/j.heliyon.2023.e20505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 09/19/2023] [Accepted: 09/27/2023] [Indexed: 10/17/2023]  Open
36
Zhao D, Yang Y, Chen P, Meng J, Sun S, Wang J, Lin H. Biomedical document relation extraction with prompt learning and KNN. J Biomed Inform 2023;145:104459. [PMID: 37531999 DOI: 10.1016/j.jbi.2023.104459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 06/26/2023] [Accepted: 07/22/2023] [Indexed: 08/04/2023]
37
Buonocore TM, Crema C, Redolfi A, Bellazzi R, Parimbelli E. Localizing in-domain adaptation of transformer-based biomedical language models. J Biomed Inform 2023;144:104431. [PMID: 37385327 DOI: 10.1016/j.jbi.2023.104431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 06/09/2023] [Accepted: 06/17/2023] [Indexed: 07/01/2023]
38
Yoon W, Yi S, Jackson R, Kim H, Kim S, Kang J. Biomedical relation extraction with knowledge base-refined weak supervision. Database (Oxford) 2023;2023:baad054. [PMID: 37551911 PMCID: PMC10407973 DOI: 10.1093/database/baad054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/13/2023] [Accepted: 07/04/2023] [Indexed: 08/09/2023]
39
Millikin RJ, Raja K, Steill J, Lock C, Tu X, Ross I, Tsoi LC, Kuusisto F, Ni Z, Livny M, Bockelman B, Thomson J, Stewart R. Serial KinderMiner (SKiM) Discovers and Annotates Biomedical Knowledge Using Co-Occurrence and Transformer Models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542911. [PMID: 37397987 PMCID: PMC10312590 DOI: 10.1101/2023.05.30.542911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
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Luo L, Wei CH, Lai PT, Leaman R, Chen Q, Lu Z. AIONER: all-in-one scheme-based biomedical named entity recognition using deep learning. Bioinformatics 2023;39:btad310. [PMID: 37171899 PMCID: PMC10212279 DOI: 10.1093/bioinformatics/btad310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/12/2023] [Accepted: 05/11/2023] [Indexed: 05/14/2023]  Open
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Guo M, Zhou Z, Gotz D, Wang Y. GRAFS: Graphical Faceted Search System to Support Conceptual Understanding in Exploratory Search. ACM T INTERACT INTEL 2023. [DOI: 10.1145/3588319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Wang Z, Gu Y, Zheng S, Yang L, Li J. MGREL: A multi-graph representation learning-based ensemble learning method for gene-disease association prediction. Comput Biol Med 2023;155:106642. [PMID: 36805231 DOI: 10.1016/j.compbiomed.2023.106642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 01/15/2023] [Accepted: 02/05/2023] [Indexed: 02/12/2023]
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Ivanisenko TV, Demenkov PS, Kolchanov NA, Ivanisenko VA. The New Version of the ANDDigest Tool with Improved AI-Based Short Names Recognition. Int J Mol Sci 2022;23:ijms232314934. [PMID: 36499269 PMCID: PMC9738852 DOI: 10.3390/ijms232314934] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/19/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022]  Open
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