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In recent years, AI models that mine intrinsic patterns from molecular structures and protein sequences have shown promise in accelerating drug discovery.
Drug Discovery: A Historical Perspective
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The SWISS-PROT Protein Knowledgebase and Its Supplement TrEMBL in 2003
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KEGG for Linking Genomes to Life and the Environment
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A Network Integration Approach for Drug-Target Interaction Prediction and Computational Drug Repositioning from Heterogeneous Information
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Predicting Potential Drug-Drug Interactions by Integrating Chemical, Biological, Phenotypic and Network Data
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Enhancing Drug-Drug Interaction Extraction from Texts by Molecular Structure Information
Asada, M.; Miwa, M.; and Sasaki, Y. 2018 · 2018
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DeepDTA: Deep Drug–Target Binding Affinity Prediction
Öztürk, H.; Özgür, A.; and Ozkirimli, E. 2018 · 2018
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DrugBank 5.0: A Major Update to the DrugBank Database for 2018
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MoleculeNet: A Benchmark for Molecular Machine Learning
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Multifaceted Protein–Protein Interaction Prediction Based on Siamese Residual RCNN
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Drug-drug interaction prediction based on knowledge graph embeddings and convolutional-LSTM network
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Drug Repurposing: Progress, Challenges and Recommendations
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How Powerful Are Graph Neural Networks?
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Sparse transformer: Concentrated attention through explicit selection
Zhao, G.; Lin, J.; Zhang, Z.; Ren, X.; and Sun, X. 2019 · 2019
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Latent Representation Learning for Alzheimer’s Disease Diagnosis with Incomplete Multi-Modality Neuroimaging and Genetic Data
Zhou, T.; Liu, M.; Thung, K.-H.; and Shen, D. 2019 · 2019
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A Multimodal Deep Learning Framework For Predicting Drug–Drug Interaction Events
Deng, Y.; Xu, X.; Qiu, Y.; Xia, J.; Zhang, W.; and Liu, S. 2020 · 2020
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Physiological and Pathological Regulation of ACE2, the SARS-CoV-2 Receptor
Li, Y.; Zhou, W.; Yang, L.; and You, R. 2020 · 2020
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KGNN: Knowledge Graph Neural Network for Drug-Drug Interaction Prediction
Lin, X.; Quan, Z.; Wang, Z.-J.; Ma, T.; and Zeng, X. 2020 · 2020
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DeepR2cov: Deep Representation Learning on Heterogeneous Drug Networks to Discover Anti-Inflammatory Agents for COVID-19
Wang, X.; Xin, B.; Tan, W.; Xu, Z.; Li, K.; Li, F.; Zhong, W.; and Peng, S. 2021 · 2021
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A Unified Drug–Target Interaction Prediction Framework Based on Knowledge Graph and Recommendation System
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PharmKG: A Dedicated Knowledge Graph Benchmark for Biomedical Data Mining
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Knowledge Graphs: Introduction, History, and Perspectives
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Pre-training Molecular Graph Representation with 3D Geometry
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Qiu, J.; Chen, Q.; Dong, Y.; Zhang, J.; Yang, H.; Ding, M.; Wang, K.; and Tang, J. 2020 · 2020
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DTiGEMS+: Drug–Target Interaction Prediction Using Graph Embedding, Graph Mining, and Similarity-Based Techniques
Thafar, M. A.; Olayan, R. S.; Ashoor, H.; Albaradei, S.; Bajic, V. B.; Gao, X.; Gojobori, T.; and Essack, M. 2020 · 2020
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ACE2: Evidence of Role as Entry Receptor for SARS-CoV-2 and Implications in Comorbidities
Zamorano Cuervo, N.; and Grandvaux, N. 2020 · 2020
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Target Identification Among Known Drugs by Deep Learning from Heterogeneous Networks
Zeng, X.; Zhu, S.; Lu, W.; Liu, Z.; Huang, J.; Zhou, Y.; Fang, J.; Huang, Y.; Guo, H.; Li, L.; Trapp, B. D.; Nussinov, R.; Eng, C.; Loscalzo, J.; and Cheng, F. 2020 · 2020
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Domain-Specific Language Model Pretraining For Biomedical Natural Language Processing
Gu, Y.; Tinn, R.; Cheng, H.; Lucas, M.; Usuyama, N.; Liu, X.; Naumann, T.; Gao, J.; and Poon, H. 2021 · 2021
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Inhibition of ACE2 Expression by Ascorbic Acid Alone and Its Combinations with Other Natural Compounds
Ivanov, V.; Goc, A.; Ivanova, S.; Niedzwiecki, A.; and Rath, M. 2021 · 2021
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Learning Unknown from Correlations: Graph Neural Network for Inter-novel-protein Interaction Prediction
Lv, G.; Hu, Z.; Bi, Y.; and Zhang, S. 2021 · 2021
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Are multimodal transformers robust to missing modality?
Ma, M.; Ren, J.; Zhao, L.; Testuggine, D.; and Peng, X. 2022 · 2022
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SMT-DTA: Improving Drug-Target Affinity Prediction with Semi-Supervised Multi-Task Training
Pei, Q.; Wu, L.; Zhu, J.; Xia, Y.; Xie, S.; Qin, T.; Liu, H.; and Liu, T.-Y. 2022 · 2022
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A biomedical knowledge graph-based method for drug–drug interactions prediction through combining local and global features with deep neural networks
Ren, Z.-H.; You, Z.-H.; Yu, C.-Q.; Li, L.-P.; Guan, Y.-J.; Guo, L.-X.; and Pan, J. 2022 · 2022
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Large-Scale Knowledge Synthesis and Complex Information Retrieval from Biomedical Documents
Saxena, S.; Sangani, R.; Prasad, S.; Kumar, S.; Athale, M.; Awhad, R.; and Vaddina, V. 2022 · 2022
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A Molecular Multimodal Foundation Model Associating Molecule Graphs with Natural Language
Su, B.; Du, D.; Yang, Z.; Zhou, Y.; Li, J.; Rao, A.; Sun, H.; Lu, Z.; and Wen, J.-R. 2022 · 2022
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Molecular Contrastive Learning of Representations via Graph Neural Networks
Wang, Y.; Wang, J.; Cao, Z.; and Barati Farimani, A. 2022 · 2022
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MGraphDTA: Deep Multiscale Graph Neural Network for Explainable Drug–Target Binding Affinity Prediction
Yang, Z.; Zhong, W.; Zhao, L.; and Chen, C. Y.-C. 2022 · 2022
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HGDTI: Predicting Drug–Target Interaction by Using Information Aggregation Based on Heterogeneous Graph Neural Network
Yu, L.; Qiu, W.; Lin, W.; Cheng, X.; Xiao, X.; and Dai, J. 2022 · 2022
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A Deep-Learning System Bridging Molecule Structure and Biomedical Text with Comprehension Comparable to Human Professionals
Zeng, Z.; Yao, Y.; Liu, Z.; and Sun, M. 2022 · 2022
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OntoProtein: Protein Pretraining with Gene Ontology Embedding
Zhang, N.; Bi, Z.; Liang, X.; Cheng, S.; Hong, H.; Deng, S.; Zhang, Q.; Lian, J.; and Chen, H. 2022 · 2022
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Vitamin C Is an Efficient Natural Product for Prevention of SARS-CoV-2 Infection by Targeting ACE2 in Both Cell and in Vivo Mouse Models
Zuo, Y.; Zheng, Z.; Huang, Y.; He, J.; Zang, L.; Ren, T.; Cao, X.; Miao, Y.; Yuan, Y.; Liu, Y.; et al. 2022 · 2022
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Multimodal Prompting with Missing Modalities for Visual Recognition
Lee, Y.-L.; Tsai, Y.-H.; Chiu, W.-C.; and Lee, C.-Y. 2023 · 2023
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Multimodal Data Fusion for Cancer Biomarker Discovery with Deep Learning
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Multitask Joint Strategies of Self-Supervised Representation Learning on Biomedical Networks for Drug Discovery
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