Scientific Language Models for Biomedical Knowledge Base Completion: An Empirical Study

17 June 2021

Papers citing "Scientific Language Models for Biomedical Knowledge Base Completion: An Empirical Study"

27 / 27 papers shown

Title
IRIS: Interactive Research Ideation System for Accelerating Scientific Discovery Aniketh Garikaparthi Manasi Patwardhan Lovekesh Vig Arman Cohan VLM LRM 95 0 0 23 Apr 2025
What's In Your Field? Mapping Scientific Research with Knowledge Graphs and Large Language Models Abhipsha Das Nicholas Lourie Siavash Golkar Mariel Pettee 140 0 0 12 Mar 2025
ResearchAgent: Iterative Research Idea Generation over Scientific Literature with Large Language Models Jinheon Baek S. Jauhar Silviu Cucerzan Sung Ju Hwang AI4CE LLMAG LM&Ro 74 48 0 11 Apr 2024
Understanding the Performance of Knowledge Graph Embeddings in Drug Discovery Stephen Bonner Ian P Barrett Cheng Ye Rowan Swiers Ola Engkvist Charles Tapley Hoyt William L. Hamilton 68 51 0 17 May 2021
DOCENT: Learning Self-Supervised Entity Representations from Large Document Collections Yury Zemlyanskiy Sudeep Gandhe Ruining He Bhargav Kanagal Anirudh Ravula Juraj Gottweis Fei Sha Ilya Eckstein SSL 41 11 0 26 Feb 2021
A Review of Biomedical Datasets Relating to Drug Discovery: A Knowledge Graph Perspective Stephen Bonner Ian P Barrett Cheng Ye Rowan Swiers Ola Engkvist A. Bender Charles Tapley Hoyt William L. Hamilton 45 94 0 19 Feb 2021
Inductive Entity Representations from Text via Link Prediction Daniel Daza Michael Cochez Paul T. Groth 62 112 0 07 Oct 2020
Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing Yu Gu Robert Tinn Hao Cheng Michael R. Lucas Naoto Usuyama Xiaodong Liu Tristan Naumann Jianfeng Gao Hoifung Poon LM&MA AI4CE 66 1,734 0 31 Jul 2020
Benchmark and Best Practices for Biomedical Knowledge Graph Embeddings David Chang Ivana Balazevic Carl Allen Daniel Chawla C. Brandt R. Taylor 60 40 0 24 Jun 2020
How Context Affects Language Models' Factual Predictions Fabio Petroni Patrick Lewis Aleksandra Piktus Tim Rocktaschel Yuxiang Wu Alexander H. Miller Sebastian Riedel KELM 42 237 0 10 May 2020
Composition-based Multi-Relational Graph Convolutional Networks Shikhar Vashishth Soumya Sanyal Vikram Nitin Partha P. Talukdar GNN 111 827 0 08 Nov 2019
Knowledge Enhanced Contextual Word Representations Matthew E. Peters Mark Neumann IV RobertL.Logan Roy Schwartz Vidur Joshi Sameer Singh Noah A. Smith 269 657 0 09 Sep 2019
KG-BERT: BERT for Knowledge Graph Completion Liang Yao Chengsheng Mao Yuan Luo SLR 67 582 0 07 Sep 2019
Language Models as Knowledge Bases? Fabio Petroni Tim Rocktaschel Patrick Lewis A. Bakhtin Yuxiang Wu Alexander H. Miller Sebastian Riedel KELM AI4MH 545 2,639 0 03 Sep 2019
Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks Nils Reimers Iryna Gurevych 815 11,979 0 27 Aug 2019
RoBERTa: A Robustly Optimized BERT Pretraining Approach Yinhan Liu Myle Ott Naman Goyal Jingfei Du Mandar Joshi Danqi Chen Omer Levy M. Lewis Luke Zettlemoyer Veselin Stoyanov AIMat 467 24,160 0 26 Jul 2019
Publicly Available Clinical BERT Embeddings Emily Alsentzer John R. Murphy Willie Boag W. Weng Di Jin Tristan Naumann Matthew B. A. McDermott AI4MH 132 1,956 0 06 Apr 2019
SciBERT: A Pretrained Language Model for Scientific Text Iz Beltagy Kyle Lo Arman Cohan 92 2,948 0 26 Mar 2019
RotatE: Knowledge Graph Embedding by Relational Rotation in Complex Space Zhiqing Sun Zhihong Deng Jian-Yun Nie Jian Tang 95 2,108 0 26 Feb 2019
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 Jaewoo Kang OOD 127 5,579 0 25 Jan 2019
BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding Jacob Devlin Ming-Wei Chang Kenton Lee Kristina Toutanova VLM SSL SSeg 1.2K 93,936 0 11 Oct 2018
Modeling polypharmacy side effects with graph convolutional networks Marinka Zitnik Monica Agrawal J. Leskovec GNN 110 1,068 0 02 Feb 2018
Modeling Relational Data with Graph Convolutional Networks Michael Schlichtkrull Thomas Kipf Peter Bloem Rianne van den Berg Ivan Titov Max Welling GNN 172 4,772 0 17 Mar 2017
Complex Embeddings for Simple Link Prediction Théo Trouillon Johannes Welbl Sebastian Riedel Éric Gaussier Guillaume Bouchard BDL 88 2,955 0 20 Jun 2016
XGBoost: A Scalable Tree Boosting System Tianqi Chen Carlos Guestrin 474 37,815 0 09 Mar 2016
Adam: A Method for Stochastic Optimization Diederik P. Kingma Jimmy Ba ODL 1.1K 149,474 0 22 Dec 2014
Embedding Entities and Relations for Learning and Inference in Knowledge Bases Bishan Yang Wen-tau Yih Xiaodong He Jianfeng Gao Li Deng NAI 87 3,174 0 20 Dec 2014