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For: Yu L, Su Y, Liu Y, Zeng X. Review of unsupervised pretraining strategies for molecules representation. Brief Funct Genomics 2021;20:323-332. [PMID: 34342611 DOI: 10.1093/bfgp/elab036] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1
Mswahili ME, Hwang J, Rajapakse JC, Jo K, Jeong YS. Positional embeddings and zero-shot learning using BERT for molecular-property prediction. J Cheminform 2025;17:17. [PMID: 39910649 PMCID: PMC11800558 DOI: 10.1186/s13321-025-00959-9] [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: 09/19/2024] [Accepted: 01/18/2025] [Indexed: 02/07/2025]  Open
2
Mswahili ME, Jeong YS. Transformer-based models for chemical SMILES representation: A comprehensive literature review. Heliyon 2024;10:e39038. [PMID: 39640612 PMCID: PMC11620068 DOI: 10.1016/j.heliyon.2024.e39038] [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: 06/13/2024] [Revised: 09/26/2024] [Accepted: 10/05/2024] [Indexed: 12/07/2024]  Open
3
Wei L, Li Q, Song Y, Stefanov S, Dong R, Fu N, Siriwardane EMD, Chen F, Hu J. Crystal Composition Transformer: Self-Learning Neural Language Model for Generative and Tinkering Design of Materials. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2304305. [PMID: 39101275 PMCID: PMC11423232 DOI: 10.1002/advs.202304305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/09/2024] [Indexed: 08/06/2024]
4
Niu D, Zhang L, Zhang B, Zhang Q, Li Z. DAS-DDI: A dual-view framework with drug association and drug structure for drug-drug interaction prediction. J Biomed Inform 2024;156:104672. [PMID: 38857738 DOI: 10.1016/j.jbi.2024.104672] [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: 03/18/2024] [Revised: 05/09/2024] [Accepted: 06/06/2024] [Indexed: 06/12/2024]
5
Son YH, Shin DH, Kam TE. FTMMR: Fusion Transformer for Integrating Multiple Molecular Representations. IEEE J Biomed Health Inform 2024;28:4361-4372. [PMID: 38551824 DOI: 10.1109/jbhi.2024.3383221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
6
Tang X, Tran A, Tan J, Gerstein MB. MolLM: a unified language model for integrating biomedical text with 2D and 3D molecular representations. Bioinformatics 2024;40:i357-i368. [PMID: 38940177 PMCID: PMC11256921 DOI: 10.1093/bioinformatics/btae260] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]  Open
7
van Tilborg D, Brinkmann H, Criscuolo E, Rossen L, Özçelik R, Grisoni F. Deep learning for low-data drug discovery: Hurdles and opportunities. Curr Opin Struct Biol 2024;86:102818. [PMID: 38669740 DOI: 10.1016/j.sbi.2024.102818] [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: 01/29/2024] [Revised: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024]
8
Shen A, Yuan M, Ma Y, Du J, Wang M. Complementary multi-modality molecular self-supervised learning via non-overlapping masking for property prediction. Brief Bioinform 2024;25:bbae256. [PMID: 38801702 PMCID: PMC11129775 DOI: 10.1093/bib/bbae256] [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: 12/26/2023] [Revised: 04/25/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024]  Open
9
Zhao X, Xu J, Shui Y, Xu M, Hu J, Liu X, Che K, Wang J, Liu Y. PermuteDDS: a permutable feature fusion network for drug-drug synergy prediction. J Cheminform 2024;16:41. [PMID: 38622663 PMCID: PMC11017561 DOI: 10.1186/s13321-024-00839-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 04/03/2024] [Indexed: 04/17/2024]  Open
10
Ma M, Lei X. A deep learning framework for predicting molecular property based on multi-type features fusion. Comput Biol Med 2024;169:107911. [PMID: 38160501 DOI: 10.1016/j.compbiomed.2023.107911] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/18/2023] [Accepted: 12/24/2023] [Indexed: 01/03/2024]
11
Wang X, Patil N, Li F, Wang Z, Zhan H, Schmidt D, Thompson P, Guo Y, Landersdorfer CB, Shen HH, Peleg AY, Li J, Song J. PmxPred: A data-driven approach for the identification of active polymyxin analogues against gram-negative bacteria. Comput Biol Med 2024;168:107681. [PMID: 37992470 DOI: 10.1016/j.compbiomed.2023.107681] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/07/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023]
12
Gao J, Shen Z, Xie Y, Lu J, Lu Y, Chen S, Bian Q, Guo Y, Shen L, Wu J, Zhou B, Hou T, He Q, Che J, Dong X. TransFoxMol: predicting molecular property with focused attention. Brief Bioinform 2023;24:bbad306. [PMID: 37605947 DOI: 10.1093/bib/bbad306] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/17/2023] [Accepted: 08/04/2023] [Indexed: 08/23/2023]  Open
13
Yang X, Niu Z, Liu Y, Song B, Lu W, Zeng L, Zeng X. Modality-DTA: Multimodality Fusion Strategy for Drug-Target Affinity Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:1200-1210. [PMID: 36083952 DOI: 10.1109/tcbb.2022.3205282] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
14
Zhang XC, Wu CK, Yi JC, Zeng XX, Yang CQ, Lu AP, Hou TJ, Cao DS. Pushing the Boundaries of Molecular Property Prediction for Drug Discovery with Multitask Learning BERT Enhanced by SMILES Enumeration. RESEARCH (WASHINGTON, D.C.) 2022;2022:0004. [PMID: 39285949 PMCID: PMC11404312 DOI: 10.34133/research.0004] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/19/2022] [Indexed: 09/19/2024]
15
Su Y, Wang M, Wang P, Zheng C, Liu Y, Zeng X. Deep learning joint models for extracting entities and relations in biomedical: a survey and comparison. Brief Bioinform 2022;23:6686739. [PMID: 36125190 DOI: 10.1093/bib/bbac342] [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: 05/23/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 12/14/2022]  Open
16
Zeng L, Liu Y, Yu ZG, Liu Y. iEnhancer-DLRA: identification of enhancers and their strengths by a self-attention fusion strategy for local and global features. Brief Funct Genomics 2022;21:399-407. [PMID: 35942693 DOI: 10.1093/bfgp/elac023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/30/2022] [Accepted: 07/12/2022] [Indexed: 11/14/2022]  Open
17
Zhang W, Hou J, Liu B. iPiDA-LTR: Identifying piwi-interacting RNA-disease associations based on Learning to Rank. PLoS Comput Biol 2022;18:e1010404. [PMID: 35969645 PMCID: PMC9410559 DOI: 10.1371/journal.pcbi.1010404] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 08/25/2022] [Accepted: 07/18/2022] [Indexed: 12/01/2022]  Open
18
Zhao L, Zhu Y, Wang J, Wen N, Wang C, Cheng L. A brief review of protein-ligand interaction prediction. Comput Struct Biotechnol J 2022;20:2831-2838. [PMID: 35765652 PMCID: PMC9189993 DOI: 10.1016/j.csbj.2022.06.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 01/21/2023]  Open
19
Jiao S, Chen Z, Zhang L, Zhou X, Shi L. ATGPred-FL: sequence-based prediction of autophagy proteins with feature representation learning. Amino Acids 2022;54:799-809. [PMID: 35286461 DOI: 10.1007/s00726-022-03145-5] [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: 09/26/2021] [Accepted: 01/28/2022] [Indexed: 11/26/2022]
20
Wan H, Zhang J, Ding Y, Wang H, Tian G. Immunoglobulin Classification Based on FC* and GC* Features. Front Genet 2022;12:827161. [PMID: 35140745 PMCID: PMC8819591 DOI: 10.3389/fgene.2021.827161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022]  Open
21
Lin C, Wang L, Shi L. AAPred-CNN: accurate predictor based on deep convolution neural network for identification of anti-angiogenic peptides. Methods 2022;204:442-448. [PMID: 35031486 DOI: 10.1016/j.ymeth.2022.01.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/28/2021] [Accepted: 01/09/2022] [Indexed: 12/13/2022]  Open
22
Song B, Luo X, Luo X, Liu Y, Niu Z, Zeng X. Learning spatial structures of proteins improves protein-protein interaction prediction. Brief Bioinform 2022;23:6501351. [PMID: 35018418 DOI: 10.1093/bib/bbab558] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 01/09/2023]  Open
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