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Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities

29 September 2023

Valentina A. M. Tamma

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Papers citing "Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities"

33 / 33 papers shown

Title
Exploring a Large Language Model for Transforming Taxonomic Data into OWL: Lessons Learned and Implications for Ontology Development Filipi Miranda Soares Antonio Mauro Saraiva Luís Ferreira Pires Luiz Olavo Bonino da Silva Santos Dilvan de Abreu Moreira Fernando Elias Corrêa Kelly Rosa Braghetto Debora Pignatari Drucker Alexandre Cláudio Botazzo Delbem 69 0 0 25 Apr 2025
DeepOnto: A Python Package for Ontology Engineering with Deep Learning Yuan He Jiaoyan Chen Hang Dong Ian Horrocks Carlo Allocca Taehun Kim B. Sapkota 127 26 0 06 Jul 2023
Ontology Enrichment from Texts: A Biomedical Dataset for Concept Discovery and Placement Hang Dong Jiaoyan Chen Yuan He Ian Horrocks 87 8 0 26 Jun 2023
Otter-Knowledge: benchmarks of multimodal knowledge graph representation learning from different sources for drug discovery Hoang Thanh Lam M. Sbodio Marcos Martínez Galindo Mykhaylo Zayats Raúl Fernández-Díaz Víctor Valls Gabriele Picco Cesar Berrospi Ramis V. López 62 8 0 22 Jun 2023
Structured prompt interrogation and recursive extraction of semantics (SPIRES): A method for populating knowledge bases using zero-shot learning J. H. Caufield Harshad B. Hegde Vincent Emonet N. Harris marcin p. joachimiak ... Sierra A T Moxon Justin P Reese M. Haendel Peter N. Robinson Christopher J. Mungall 84 87 0 05 Apr 2023
Evaluating Language Models for Knowledge Base Completion Blerta Veseli Sneha Singhania Simon Razniewski Gerhard Weikum ALM 72 21 0 20 Mar 2023
NASTyLinker: NIL-Aware Scalable Transformer-based Entity Linker Nicolas Heist Heiko Paulheim 59 9 0 08 Mar 2023
Reveal the Unknown: Out-of-Knowledge-Base Mention Discovery with Entity Linking Hang Dong Jiaoyan Chen Yuan He Yinan Liu Ian Horrocks 77 10 0 14 Feb 2023
ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts Minghao Xu Xinyu Yuan Santiago Miret Jian Tang AI4TS 82 105 0 28 Jan 2023
Explainable AI for Bioinformatics: Methods, Tools, and Applications Md. Rezaul Karim Tanhim Islam Oya Beyan Christoph Lange Michael Cochez Dietrich-Rebholz Schuhmann Stefan Decker 82 75 0 25 Dec 2022
Ontology Development is Consensus Creation, Not (Merely) Representation Fabian Neuhaus Janna Hastings 103 18 0 21 Oct 2022
Construction and Applications of Billion-Scale Pre-Trained Multimodal Business Knowledge Graph Shumin Deng Chengming Wang Zhoubo Li Ningyu Zhang Zelin Dai ... Mosha Chen Jiaoyan Chen Jeff Z. Pan Bryan Hooi Huajun Chen VLM 78 21 0 30 Sep 2022
Extracting Biomedical Factual Knowledge Using Pretrained Language Model and Electronic Health Record Context Zonghai Yao Yi Cao Zhichao Yang Vijeta Deshpande Hong-ye Yu 187 20 0 26 Aug 2022
PLM-ICD: Automatic ICD Coding with Pretrained Language Models Chao-Wei Huang Shang-Chi Tsai Yun-Nung Chen 90 51 0 12 Jul 2022
Ontology-Driven and Weakly Supervised Rare Disease Identification from Clinical Notes Hang Dong Víctor Suárez-Paniagua Huayu Zhang Minhong Wang Arlene Casey E. Davidson Jiaoyan Chen Beatrice Alex W. Whiteley Honghan Wu 81 18 0 11 May 2022
WikiDiverse: A Multimodal Entity Linking Dataset with Diversified Contextual Topics and Entity Types Xuwu Wang Junfeng Tian Min Gui Zhixu Li Rui Wang Ming Yan Lihan Chen Yanghua Xiao VGen 71 50 0 13 Apr 2022
Contextual Semantic Embeddings for Ontology Subsumption Prediction Jiaoyan Chen Yuan He Yuxia Geng Ernesto Jiménez-Ruiz Hang Dong Ian Horrocks 89 53 0 20 Feb 2022
OntoProtein: Protein Pretraining With Gene Ontology Embedding Ningyu Zhang Zhen Bi Xiaozhuan Liang Shuyang Cheng Haosen Hong Shumin Deng J. Lian Qiang Zhang Huajun Chen 162 97 0 23 Jan 2022
Zero-shot and Few-shot Learning with Knowledge Graphs: A Comprehensive Survey Jiaoyan Chen Yuxia Geng Zhuo Chen Jeff Z. Pan Yuan He Wen Zhang Ian Horrocks Hua-zeng Chen 82 49 0 18 Dec 2021
Prediction of Adverse Biological Effects of Chemicals Using Knowledge Graph Embeddings E. B. Myklebust Ernesto Jiménez-Ruiz Jiaoyan Chen Raoul Wolf K. Tollefsen 67 9 0 08 Dec 2021
Can Language Models be Biomedical Knowledge Bases? Mujeen Sung Jinhyuk Lee Sean S. Yi Minji Jeon Sungdong Kim Jaewoo Kang AI4MH 187 107 0 15 Sep 2021
EXplainable Neural-Symbolic Learning (X-NeSyL) methodology to fuse deep learning representations with expert knowledge graphs: the MonuMAI cultural heritage use case Natalia Díaz Rodríguez Alberto Lamas Jules Sanchez Gianni Franchi Ivan Donadello Siham Tabik David Filliat P. Cruz Rosana Montes Francisco Herrera 136 78 0 24 Apr 2021
Does the Magic of BERT Apply to Medical Code Assignment? A Quantitative Study Shaoxiong Ji M. Holtta Pekka Marttinen 82 74 0 11 Mar 2021
Materializing Knowledge Bases via Trigger Graphs Efthymia Tsamoura David Carral Enrico Malizia Jacopo Urbani 40 30 0 04 Feb 2021
Discovering alignment relations with Graph Convolutional Networks: a biomedical case study Pierre Monnin Chedy Raïssi A. Napoli Adrien Coulet GNN 60 12 0 11 Nov 2020
An Empirical Meta-analysis of the Life Sciences (Linked?) Open Data on the Web Maulik R. Kamdar Mark A. Musen 36 14 0 07 Jun 2020
Low-Dimensional Hyperbolic Knowledge Graph Embeddings Ines Chami A. Wolf Da-Cheng Juan Frederic Sala Sujith Ravi Christopher Ré 58 395 0 01 May 2020
Network Medicine Framework for Identifying Drug Repurposing Opportunities for COVID-19 D. Gysi Ì. Valle Marinka Zitnik Asher Ameli Xiao Gan ... D. Ghiassian R. Baron Helia Sanchez J. Loscalzo Albert-László Barabási 59 441 0 15 Apr 2020
Explainable Artificial Intelligence (XAI): Concepts, Taxonomies, Opportunities and Challenges toward Responsible AI Alejandro Barredo Arrieta Natalia Díaz Rodríguez Javier Del Ser Adrien Bennetot Siham Tabik ... S. Gil-Lopez Daniel Molina Richard Benjamins Raja Chatila Francisco Herrera XAI 135 6,321 0 22 Oct 2019
Knowledge Graph Embedding for Ecotoxicological Effect Prediction E. B. Myklebust Ernesto Jiménez-Ruiz Jiaoyan Chen Raoul Wolf K. Tollefsen 67 22 0 02 Jul 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 182 5,684 0 25 Jan 2019
A Survey Of Methods For Explaining Black Box Models Riccardo Guidotti A. Monreale Salvatore Ruggieri Franco Turini D. Pedreschi F. Giannotti XAI 150 3,989 0 06 Feb 2018
Modeling polypharmacy side effects with graph convolutional networks Marinka Zitnik Monica Agrawal J. Leskovec GNN 124 1,093 0 02 Feb 2018