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This comprehensive review aims to provide an overview of the current state of Healthcare Knowledge Graphs (HKGs), including their construction, utilization models, and applications across various healthcare and biomedical research domains.
Ontologies and knowledge graphs in oncology research
Silva MC, Eugénio P, Faria D, Pesquita C · 1906
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Detection, Disambiguation, Re-ranking: Autoregressive Entity Linking as a Multi-Task Problem
Mrini K, Nie S, Gu J, Wang S, Sanjabi M, Firooz H · 1972
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The cost of drug development
DiMasi JA, Grabowski HG, Hansen RW · 1972
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Inductive logic programming
Muggleton S · 1992
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Gene ontology: tool for the unification of biology
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al · 2000
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KEGG: kyoto encyclopedia of genes and genomes
Kanehisa M, Goto S · 2000
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The unified medical language system (UMLS): integrating biomedical terminology
Bodenreider O · 2004
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An ontology for cell types
Bard J, Rhee SY, Ashburner M · 2005
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Learning the structure of Markov logic networks
Kok S, Domingos P · 2005
Earlier work this paper cites.
SNOMED-CT: The advanced terminology and coding system for eHealth
Donnelly K, et al · 2006
Earlier work this paper cites.
Estimating the cost of new drug development: is it really $802 million?
Adams CP, Brantner VV · 2006
Earlier work this paper cites.
ICD-9 codes and surveillance for Clostridium difficile–associated disease
Dubberke ER, Reske KA, McDonald LC, Fraser VJ · 2006
Earlier work this paper cites.
When good drugs go bad
Giacomini KM, Krauss RM, Roden DM, Eichelbaum M, Hayden MR, Nakamura Y · 2007
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What is an ontology?
Guarino N, Oberle D, Staab S · 2009
Earlier work this paper cites.
PARIS: probabilistic alignment of relations, instances, and schema
Suchanek FM, Abiteboul S, Senellart P · 2011
Earlier work this paper cites.
Clinical decision support systems: potential with pitfalls
Eberhardt J, Bilchik A, Stojadinovic A · 2012
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Disease Ontology: a backbone for disease semantic integration
Schriml LM, Arze C, Nadendla S, Chang YWW, Mazaitis M, Felix V, et al · 2012
Earlier work this paper cites.
Translating embeddings for modeling multi-relational data
Bordes A, Usunier N, Garcia-Duran A, Weston J, Yakhnenko O · 2013
Earlier work this paper cites.
AMIE: association rule mining under incomplete evidence in ontological knowledge bases
Galárraga LA, Teflioudi C, Hose K, Suchanek F · 2013
Earlier work this paper cites.
Distant supervision for relation extraction with an incomplete knowledge base
Min B, Grishman R, Wan L, Wang C, Gondek D · 2013
Earlier work this paper cites.
Towards annotating potential incoherences in bioportal mappings
Faria D, Jiménez-Ruiz E, Pesquita C, Santos E, Couto FM · 2014
Earlier work this paper cites.
Formalizing mappings to optimize automated schema alignment: application to rare diseases
Maaroufi M, Choquet R, Landais P, Jaulent MC · 2014
Earlier work this paper cites.
Knowlife: a knowledge graph for health and life sciences
Ernst P, Meng C, Siu A, Weikum G · 2014
Earlier work this paper cites.
Clinical decision support systems for improving diagnostic accuracy and achieving precision medicine
Castaneda C, Nalley K, Mannion C, Bhattacharyya P, Blake P, Pecora A, et al · 2015
Earlier work this paper cites.
Heterogeneous network edge prediction: a data integration approach to prioritize disease-associated genes
Himmelstein DS, Baranzini SE · 2015
Earlier work this paper cites.
Knowlife: a versatile approach for constructing a large knowledge graph for biomedical sciences
Ernst P, Siu A, Weikum G · 2015
Earlier work this paper cites.
ICD-10: history and context
Hirsch J, Nicola G, McGinty G, Liu R, Barr R, Chittle M, et al · 2016
Earlier work this paper cites.
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability
Diehl AD, Meehan TF, Bradford YM, Brush MH, Dahdul WM, Dougall DS, et al · 2016
Earlier work this paper cites.
Drug–target interaction prediction: databases, web servers and computational models
Chen X, Yan CC, Zhang X, Zhang X, Dai F, Yin J, et al · 2016
Earlier work this paper cites.
Linnarsson S, Teichmann SA. Single-cell genomics: coming of age. Springer; 2016
2016
Earlier work this paper cites.
Semi-supervised classification with graph convolutional networks
Kipf TN, Welling M · 2016
Earlier work this paper cites.
Patient health record systems scope and functionalities: literature review and future directions
Bouayad L, Ialynytchev A, Padmanabhan B · 2017
Earlier work this paper cites.
Knowledge discovery in biological databases for revealing candidate genes linked to complex phenotypes
Hassani-Pak K, Rawlings C · 2017
Earlier work this paper cites.
Systematic integration of biomedical knowledge prioritizes drugs for repurposing
Himmelstein DS, Lizee A, Hessler C, Brueggeman L, Chen SL, Hadley D, et al · 2017
Earlier work this paper cites.
Ontology-driven weak supervision for clinical entity classification in electronic health records
Fries JA, Steinberg E, Khattar S, Fleming SL, Posada J, Callahan A, et al · 2017
Earlier work this paper cites.
Neuro-symbolic representation learning on biological knowledge graphs
Alshahrani M, Khan MA, Maddouri O, Kinjo AR, Queralt-Rosinach N, Hoehndorf R · 2017
Earlier work this paper cites.
How much do clinical trials cost
Martin L, Hutchens M, Hawkins C, Radnov A · 2017
Earlier work this paper cites.
GRAM: graph-based attention model for healthcare representation learning
Choi E, Bahadori MT, Song L, Stewart WF, Sun J · 2017
Earlier work this paper cites.
LEAP: learning to prescribe effective and safe treatment combinations for multimorbidity
Zhang Y, Chen R, Tang J, Stewart WF, Sun J · 2017
Earlier work this paper cites.
Scalable and accurate deep learning with electronic health records
Rajkomar A, Oren E, Chen K, Dai AM, Hajaj N, Hardt M, et al · 2018
Earlier work this paper cites.
Concurrence of big data analytics and healthcare: A systematic review
Mehta N, Pandit A · 2018
Earlier work this paper cites.
Personalized health knowledge graph
Gyrard A, Gaur M, Shekarpour S, Thirunarayan K, Sheth A · 2018
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FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining
Bachman JA, Gyori BM, Sorger PK · 2018
Earlier work this paper cites.
Open-world knowledge graph completion
Shi B, Weninger T · 2018
Earlier work this paper cites.
DrugBank 5.0: a major update to the DrugBank database for 2018
Wishart DS, Feunang YD, Guo AC, Lo EJ, Marcu A, Grant JR, et al · 2018
Earlier work this paper cites.
Explainable Prediction of Medical Codes from Clinical Text
Mullenbach J, Wiegreffe S, Duke J, Sun J, Eisenstein J · 2018
Earlier work this paper cites.
Kame: Knowledge-based attention model for diagnosis prediction in healthcare
Ma F, You Q, Xiao H, Chitta R, Zhou J, Gao J · 2018
Earlier work this paper cites.
Knowledge graph construction and applications for Web search and beyond
Wang P, Jiang H, Xu J, Zhang Q · 2019
Earlier work this paper cites.
Kgat: Knowledge graph attention network for recommendation
Wang X, He X, Cao Y, Liu M, Chua TS · 2019
Earlier work this paper cites.
KagNet: Knowledge-Aware Graph Networks for Commonsense Reasoning
Lin BY, Chen X, Chen J, Ren X · 2019
Earlier work this paper cites.
Big data in healthcare: management, analysis and future prospects
Dash S, Shakyawar SK, Sharma M, Kaushik S · 2019
Earlier work this paper cites.
BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding
Devlin J, Chang MW, Lee K, Toutanova K · 2019
Earlier work this paper cites.
ROBOKOP KG and KGB: integrated knowledge graphs from federated sources
Bizon C, Cox S, Balhoff J, Kebede Y, Wang P, Morton K, et al · 2019
Earlier work this paper cites.
ClaimsKG: A knowledge graph of fact-checked claims
Tchechmedjiev A, Fafalios P, Boland K, Gasquet M, Zloch M, Zapilko B, et al · 2019
Earlier work this paper cites.
Drug-drug interaction prediction based on knowledge graph embeddings and convolutional-LSTM network
Karim MR, Cochez M, Jares JB, Uddin M, Beyan O, Decker S · 2019
Earlier work this paper cites.
A network embedding model for pathogenic genes prediction by multi-path random walking on heterogeneous network
Xu B, Liu Y, Yu S, Wang L, Dong J, Lin H, et al · 2019
Earlier work this paper cites.
Criteria2Query: a natural language interface to clinical databases for cohort definition
Yuan C, Ryan PB, Ta C, Guo Y, Li Z, Hardin J, et al · 2019
Earlier work this paper cites.
Ehr coding with multi-scale feature attention and structured knowledge graph propagation
Xie X, Xiong Y, Yu PS, Zhu Y · 2019
Earlier work this paper cites.
Domain knowledge guided deep learning with electronic health records
Yin C, Zhao R, Qian B, Lv X, Zhang P · 2019
Earlier work this paper cites.
KnowRisk: an interpretable knowledge-guided model for disease risk prediction
Zhang X, Qian B, Li Y, Yin C, Wang X, Zheng Q · 2019
Earlier work this paper cites.
Gamenet: Graph augmented memory networks for recommending medication combination
Shang J, Xiao C, Ma T, Li H, Sun J · 2019
Earlier work this paper cites.
Pre-training of graph augmented transformers for medication recommendation
Shang J, Ma T, Xiao C, Sun J · 2019
Earlier work this paper cites.
Constructing knowledge graphs and their biomedical applications
Nicholson DN, Greene CS · 2020
Earlier work this paper cites.
Interactive recommender system via knowledge graph-enhanced reinforcement learning
Zhou S, Dai X, Chen H, Zhang W, Ren K, Tang R, et al · 2020
Earlier work this paper cites.
Language models are few-shot learners
Brown T, Mann B, Ryder N, Subbiah M, Kaplan JD, Dhariwal P, et al · 2020
Cited alongside, same era.
Steam: Self-supervised taxonomy expansion with mini-paths
Yu Y, Li Y, Shen J, Feng H, Sun J, Zhang C · 2020
Cited alongside, same era.
Building a PubMed knowledge graph
Xu J, Kim S, Song M, Jeong M, Kim D, Kang J, et al · 2020
Cited alongside, same era.
Real-world data medical knowledge graph: construction and applications
Li L, Wang P, Yan J, Wang Y, Li S, Jiang J, et al · 2020
Cited alongside, same era.
BioRel: towards large-scale biomedical relation extraction
Xing R, Luo J, Song T · 2020
Cited alongside, same era.
Medical information extraction in the age of deep learning
Hahn U, Oleynik M · 2020
Cited alongside, same era.
Open-World Taxonomy and Knowledge Graph Co-Learning
Lu J, Yang C · 2022
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Knowledge integration and decision support for accelerated discovery of antibiotic resistance genes
Youn J, Rai N, Tagkopoulos I · 2022
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Machine Learning-Friendly Biomedical Datasets for Equivalence and Subsumption Ontology Matching
He Y, Chen J, Dong H, Jiménez-Ruiz E, Hadian A, Horrocks I · 2022
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Generative Knowledge Graph Construction: A Review
Ye H, Zhang N, Chen H, Chen H · 2022
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Copner: Contrastive learning with prompt guiding for few-shot named entity recognition
Huang Y, He K, Wang Y, Zhang X, Gong T, Mao R, et al · 2022
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QaNER: Prompting question answering models for few-shot named entity recognition
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Text-to-SQL generation for question answering on electronic medical records
Wang P, Shi T, Reddy CK · 2020
Cited alongside, same era.
Bond: Bert-assisted open-domain named entity recognition with distant supervision
Liang C, Yu Y, Jiang H, Er S, Wang R, Zhao T, et al · 2020
Cited alongside, same era.
Probabilistic Case-based Reasoning for Open-World Knowledge Graph Completion
Das R, Godbole A, Monath N, Zaheer M, McCallum A · 2020
Cited alongside, same era.
https://github.com/gnn4dr/DRKG/
Ioannidis VN, Song X, Manchanda S, Li M, Pan X, Zheng D, et al.. DRKG - Drug Repurposing Knowledge Graph for Covid-19; 2020 · 2020
Cited alongside, same era.
Retrieval augmented language model pre-training
Guu K, Lee K, Tung Z, Pasupat P, Chang M · 2020
Cited alongside, same era.
KGNN: Knowledge Graph Neural Network for Drug-Drug Interaction Prediction
Lin X, Quan Z, Wang ZJ, Ma T, Zeng X · 2020
Cited alongside, same era.
Liu AT, Xiao W, Zhu H, Zhang D, Li SW, Arnold A · 2022
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ReSel: N-ary Relation Extraction from Scientific Text and Tables by Learning to Retrieve and Select
Zhuang Y, Li Y, Zhang J, Yu Y, Mou Y, Chen X, et al · 2022
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Unified Structure Generation for Universal Information Extraction
Lu Y, Liu Q, Dai D, Xiao X, Lin H, Han X, et al · 2022
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A large language model for electronic health records
Yang X, Chen A, PourNejatian N, Shin HC, Smith KE, Parisien C, et al · 2022
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Unsupervised Entity Linking with Guided Summarization and Multiple-Choice Selection
Cho YM, Zhang L, Callison-Burch C · 2022
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Sequence-to-Sequence Knowledge Graph Completion and Question Answering
Saxena A, Kochsiek A, Gemulla R · 2022
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From discrimination to generation: knowledge graph completion with generative transformer
Xie X, Zhang N, Li Z, Deng S, Chen H, Xiong F, et al · 2022
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PALT: Parameter-Lite Transfer of Language Models for Knowledge Graph Completion
Shen J, Wang C, Yuan Y, Han J, Ji H, Sen K, et al · 2022
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Large language models are few-shot clinical information extractors
Agrawal M, Hegselmann S, Lang H, Kim Y, Sontag D · 2022
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Enhancing Entity Representations with Prompt Learning for Biomedical Entity Linking
Zhu T, Qin Y, Chen Q, Hu B, Xiang Y · 2022
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OERL: Enhanced Representation Learning Via Open Knowledge Graphs
Li Q, Wang D, Song SFK, Zhang Y, Yu G · 2022
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Generating novel molecule for target protein (SARS-CoV-2) using drug–target interaction based on graph neural network
Ranjan A, Shukla S, Datta D, Misra R · 2022
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Prediction of compound synthesis accessibility based on reaction knowledge graph
Li B, Chen H · 2022
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Intelligent generation of optimal synthetic pathways based on knowledge graph inference and retrosynthetic predictions using reaction big data
Jeong J, Lee N, Shin Y, Shin D · 2022
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Kg-predict: a knowledge graph computational framework for drug repurposing
Gao Z, Ding P, Xu R · 2022
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Uncertainty-Aware Text-to-Program for Question Answering on Structured Electronic Health Records
Kim D, Bae S, Kim S, Choi E · 2022
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DEAP-FAKED: Knowledge graph based approach for fake news detection
Mayank M, Sharma S, Sharma R · 2022
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Empowering COVID-19 Fact-Checking with Extended Knowledge Graphs
Mengoni P, Yang J · 2022
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Attention-based knowledge graph representation learning for predicting drug-drug interactions
Su X, Hu L, You Z, Hu P, Zhao B · 2022
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Neural-symbolic models for logical queries on knowledge graphs
Zhu Z, Galkin M, Zhang Z, Tang J · 2022
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KG-DTI: a knowledge graph based deep learning method for drug-target interaction predictions and Alzheimer’s disease drug repositions
Wang S, Du Z, Ding M, Rodriguez-Paton A, Song T · 2022
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HINT: Hierarchical interaction network for clinical-trial-outcome predictions
Fu T, Huang K, Xiao C, Glass LM, Sun J · 2022
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Automated clinical coding: what, why, and where we are?
Dong H, Falis M, Whiteley W, Alex B, Matterson J, Ji S, et al · 2022
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HiCu: Leveraging Hierarchy for Curriculum Learning in Automated ICD Coding
Ren W, Zeng R, Wu T, Zhu T, Krishnan RG · 2022
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Multimodal Learning on Graphs for Disease Relation Extraction
Lin Y, Lu K, Yu S, Cai T, Zitnik M · 2022
Later among the works it cites.
Leveraging multiple types of domain knowledge for safe and effective drug recommendation
Wu J, Qian B, Li Y, Gao Z, Ju M, Yang Y, et al · 2022
Later among the works it cites.
4SDrug: Symptom-based Set-to-set Small and Safe Drug Recommendation
Tan Y, Kong C, Yu L, Li P, Chen C, Zheng X, et al · 2022
Later among the works it cites.
Knowledge-Driven New Drug Recommendation
Wu Z, Yao H, Su Z, Liebovitz DM, Glass LM, Zou J, et al · 2022
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Using logical constraints to validate statistical information about disease outbreaks in collaborative knowledge graphs: the case of COVID-19 epidemiology in Wikidata
Turki H, Jemielniak D, Taieb MAH, Gayo JEL, Aouicha MB, Banat M, et al · 2022
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Ontological Representation of Causal Relations for a Deep Understanding of Associations Between Variables in Epidemiology
Pressat Laffouilhère T, Grosjean J, Pinson J, Darmoni SJ, Leveque E, Lanoy E, et al · 2022
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Improving chronic disease management for children with knowledge graphs and artificial intelligence
Yu G, Tabatabaei M, Mezei J, Zhong Q, Chen S, Li Z, et al · 2022
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CausalKG: Causal Knowledge Graph Explainability using interventional and counterfactual reasoning
Jaimini U, Sheth A · 2022
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Large Language Models Encode Clinical Knowledge
Singhal K, Azizi S, Tu T, Mahdavi SS, Wei J, Chung HW, et al · 2022
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New meaning for NLP: the trials and tribulations of natural language processing with GPT-3 in ophthalmology
Nath S, Marie A, Ellershaw S, Korot E, Keane PA · 2022
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Building a knowledge graph to enable precision medicine
Chandak P, Huang K, Zitnik M · 2023
Closest in time.
Towards electronic health record-based medical knowledge graph construction, completion, and applications: A literature study
Murali L, Gopakumar G, Viswanathan DM, Nedungadi P · 2023
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Healthcare knowledge graph construction: A systematic review of the state-of-the-art, open issues, and opportunities
Abu-Salih B, Al-Qurishi M, Alweshah M, Al-Smadi M, Alfayez R, Saadeh H · 2023
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Biomedical discovery through the integrative biomedical knowledge hub (iBKH)
Su C, Hou Y, Zhou M, Rajendran S, Maasch JR, Abedi Z, et al · 2023
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TeCre: A Novel Temporal Conflict Resolution Method Based on Temporal Knowledge Graph Embedding
Ma J, Zhou C, Chen Y, Wang Y, Hu G, Qiao Y · 2023
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One Model for All Domains: Collaborative Domain-Prefix Tuning for Cross-Domain NER
Chen X, Li L, Fei Q, Zhang N, Tan C, Jiang Y, et al · 2023
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GraphPrompt: Biomedical Entity Normalization Using Graph-based Prompt Templates
Zhang J, Wang Z, Zhang S, Bhalerao MM, Liu Y, Zhu D, et al · 2023
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Zero-shot Clinical Entity Recognition using ChatGPT
Hu Y, Ameer I, Zuo X, Peng X, Zhou Y, Li Z, et al · 2023
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HiPrompt: Few-Shot Biomedical Knowledge Fusion via Hierarchy-Oriented Prompting
Lu J, Shen J, Xiong B, Ma W, Steffen S, Yang C · 2023
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The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest
Szklarczyk D, Kirsch R, Koutrouli M, Nastou K, Mehryary F, Hachilif R, et al · 2023
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DrugRep-KG: Toward Learning a Unified Latent Space for Drug Repurposing Using Knowledge Graphs
Ghorbanali Z, Zare-Mirakabad F, Akbari M, Salehi N, Masoudi-Nejad A · 2023
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Weakly-Supervised Scientific Document Classification via Retrieval-Augmented Multi-Stage Training
Xu R, Yu Y, Ho JC, Yang C · 2023
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REPLUG: Retrieval-Augmented Black-Box Language Models
Shi W, Min S, Yasunaga M, Seo M, James R, Lewis M, et al · 2023
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GA-ENs: A novel drug–target interactions prediction method by incorporating prior Knowledge Graph into dual Wasserstein Generative Adversarial Network with gradient penalty
Li G, Sun W, Xu J, Hu L, Zhang W, Zhang P · 2023
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AIMedGraph: A Comprehensive Multi-Relational Knowledge Graph for Precision Medicine
Quan X, Cai W, Xi C, Wang C, Yan L · 2023
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GenomicKB: a knowledge graph for the human genome
Feng F, Tang F, Gao Y, Zhu D, Li T, Yang S, et al · 2023
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SPOT: Sequential Predictive Modeling of Clinical Trial Outcome with Meta-Learning
Wang Z, Xiao C, Sun J · 2023
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Exploring Partial Knowledge Base Inference in Biomedical Entity Linking
Yuan H, Lu K, Yuan Z · 2023
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Knowledge graph of wastewater-based epidemiology development: A data-driven analysis based on research topics and trends
Gao Z, Gao M, Chen Ch, Zhou Y, Zhan ZH, Ren Y · 2023
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BioBLP: a modular framework for learning on multimodal biomedical knowledge graphs
Daza D, Alivanistos D, Mitra P, Pijnenburg T, Cochez M, Groth P · 2023
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Foundation models for generalist medical artificial intelligence
Moor M, Banerjee O, Abad ZSH, Krumholz HM, Leskovec J, Topol EJ, et al · 2023
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Biomedical knowledge graph-optimized prompt generation for large language models
Soman K, Rose PW, Morris JH, Akbas RE, Smith B, Peetoom B, et al · 2024
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Advancing entity recognition in biomedicine via instruction tuning of large language models
Keloth VK, Hu Y, Xie Q, Peng X, Wang Y, Zheng A, et al · 2024
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Geometric molecular graph representation learning model for drug-drug interactions prediction
Jiang Z, Ding P, Shen C, Dai X · 2024
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Interpretable emotion analysis based on knowledge graph and OCC model
Wang S, Zhang Y, Lin B, Li B · 2038
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