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Biomedical knowledge graphs (KGs) hold rich information on entities such as diseases, drugs, and genes.
Fish oil, Raynaud’s syndrome, and undiscovered public knowledge
Don R. Swanson · 1986
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WordNet: a lexical database for English
George A. Miller · 1995
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Target discovery
Mark A Lindsay · 2003
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Freebase: A Collaboratively Created Graph Database For Structuring Human Knowledge
Kurt Bollacker, Colin Evans, Praveen K. Paritosh, Tim Sturge, and Jamie Taylor · 2008
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Scikit-learn: Machine Learning in Python
F. Pedregosa, G. Varoquaux, A. Gramfort, V. Michel, B. Thirion, O. Grisel, M. Blondel, G. Louppe, P. Prettenhofer, R. Weiss, J. Vanderplas, A. Passos, D. Cournapeau, M. Brucher, M. Perrot, and E. Duchesnay · 2011
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Translating Embeddings for Modeling Multi-relational Data
Antoine Bordes, Nicolas Usunier, Alberto García-Durán, Jason Weston, and Oksana Yakhnenko · 2013
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Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes
Daniel S. Himmelstein and Sergio E. Baranzini · 2015
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Adam: A Method for Stochastic Optimization
Diederik P. Kingma and Jimmy Ba · 2015
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Representing Text for Joint Embedding of Text and Knowledge Bases
Kristina Toutanova, Danqi Chen, Patrick Pantel, Hoifung Poon, Pallavi Choudhury, and Michael Gamon · 2015
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Embedding Entities and Relations for Learning and Inference in Knowledge Bases
Bishan Yang, Wen tau Yih, Xiadong He, Jianfeng Gao, and Li Deng · 2015
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XGBoost: A Scalable Tree Boosting System
Tianqi Chen and Carlos Guestrin · 2016
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Complex Embeddings for Simple Link Prediction
Théo Trouillon, Johannes Welbl, S. Riedel, Éric Gaussier, and Guillaume Bouchard · 2016
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Text-Enhanced Representation Learning for Knowledge Graph
Zhigang Wang and Juan-Zi Li · 2016
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Representation Learning of Knowledge Graphs with Entity Descriptions
Ruobing Xie, Zhiyuan Liu, Jia Jia, Huanbo Luan, and Maosong Sun · 2016
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A standard database for drug repositioning
Adam S. Brown and Chirag J. Patel · 2017
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Modeling Relational Data with Graph Convolutional Networks
Michael Schlichtkrull, Thomas Kipf, Peter Bloem, Rianne van den Berg, Ivan Titov, and Max Welling · 2018
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Modeling polypharmacy side effects with graph convolutional networks
Marinka Zitnik, Monica Agrawal, and Jure Leskovec · 2018
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Publicly Available Clinical BERT Embeddings
Emily Alsentzer, John R. Murphy, Willie Boag, Wei-Hung Weng, Di Jin, Tristan Naumann, and Matthew B. A. McDermott · 2019
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SciBERT: A Pretrained Language Model for Scientific Text
Iz Beltagy, Kyle Lo, and Arman Cohan · 2019
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BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding
Jacob Devlin, Ming-Wei Chang, Kenton Lee, and Kristina Toutanova · 2019
Explainable Link Prediction for Emerging Entities in Knowledge Graphs
Rajarshi Bhowmik and Gerard de Melo · 2020
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Benchmark and Best Practices for Biomedical Knowledge Graph Embeddings
David Chang, Ivana Balažević, Carl Allen, Daniel Chawla, Cynthia Brandt, and Andrew Taylor · 2020
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Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing
Yu Gu, Robert Tinn, Hao Cheng, Michael Lucas, Naoto Usuyama, Xiaodong Liu, Tristan Naumann, Jianfeng Gao, and Hoifung Poon · 2020
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Multi-Task Learning for Knowledge Graph Completion with Pre-trained Language Models
Bosung Kim, Taesuk Hong, Youngjoong Ko, and Jungyun Seo · 2020
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BioBERT: a pre-trained biomedical language representation model for biomedical text mining
Jinhyuk Lee, Wonjin Yoon, Sungdong Kim, Donghyeon Kim, Sunkyu Kim, Chan Ho So, and Jaewoo Kang · 2020
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A survey on literature based discovery approaches in biomedical domain
Vishrawas Gopalakrishnan, Kishlay Jha, Wei Jin, and Aidong Zhang · 2019
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RoBERTa: A Robustly Optimized BERT Pretraining Approach
Yinhan Liu, Myle Ott, Naman Goyal, Jingfei Du, Mandar Joshi, Danqi Chen, Omer Levy, Mike Lewis, Luke Zettlemoyer, and Veselin Stoyanov · 2019
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Knowledge Enhanced Contextual Word Representations
Matthew E. Peters, Mark Neumann, Robert Logan, Roy Schwartz, Vidur Joshi, Sameer Singh, and Noah A. Smith · 2019
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Language Models as Knowledge Bases?
Fabio Petroni, Tim Rocktäschel, Patrick Lewis, Anton Bakhtin, Yuxiang Wu, Alexander H. Miller, and Sebastien Riedel · 2019
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Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks
Nils Reimers and Iryna Gurevych · 2019
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RotatE: Knowledge Graph Embedding by Relational Rotation in Complex Space
Zhiqing Sun, Zhihong Deng, Jian-Yun Nie, and Jian Tang · 2019
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How Context Affects Language Models’ Factual Predictions
Fabio Petroni, Patrick Lewis, Aleksandra Piktus, Tim Rocktäschel, Yuxiang Wu, Alexander H Miller, and Sebastian Riedel · 2020
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Composition-based Multi-Relational Graph Convolutional Networks
Shikhar Vashishth, Soumya Sanyal, Vikram Nitin, and Partha Talukdar · 2020
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Application and evaluation of knowledge graph embeddings in biomedical data
Mona Alshahrani, Maha A. Thafar, and Magbubah Essack · 2021
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Inductive Entity Representations from Text via Link Prediction
Daniel Daza, Michael Cochez, and Paul T. Groth · 2021
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Biomedical data and computational models for drug repositioning: a comprehensive review
Huimin Luo, Min Li, Mengyun Yang, Fang-Xiang Wu, Yaohang Li, and Jianxin Wang · 2021
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Identification of disease treatment mechanisms through the multiscale interactome
Camilo Ruiz, Marinka Zitnik, and Jure Leskovec · 2021
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Structure-Augmented Text Representation Learning for Efficient Knowledge Graph Completion
Bo Wang, Tao Shen, Guodong Long, Tianyi Zhou, Ying Wang, and Yi Chang · 2021
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DOCENT: Learning Self-Supervised Entity Representations from Large Document Collections
Yury Zemlyanskiy, Sudeep Gandhe, Ruining He, Bhargav Kanagal, Anirudh Ravula, Juraj Gottweis, Fei Sha, and Ilya Eckstein · 2021
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