Navigating Healthcare Insights: A Birds Eye View of Explainability with Knowledge Graphs (2309.16593v1)
Abstract: Knowledge graphs (KGs) are gaining prominence in Healthcare AI, especially in drug discovery and pharmaceutical research as they provide a structured way to integrate diverse information sources, enhancing AI system interpretability. This interpretability is crucial in healthcare, where trust and transparency matter, and eXplainable AI (XAI) supports decision making for healthcare professionals. This overview summarizes recent literature on the impact of KGs in healthcare and their role in developing explainable AI models. We cover KG workflow, including construction, relationship extraction, reasoning, and their applications in areas like Drug-Drug Interactions (DDI), Drug Target Interactions (DTI), Drug Development (DD), Adverse Drug Reactions (ADR), and bioinformatics. We emphasize the importance of making KGs more interpretable through knowledge-infused learning in healthcare. Finally, we highlight research challenges and provide insights for future directions.
- NextMove Software — Pistachio — nextmovesoftware.com. https://www.nextmovesoftware.com/pistachio.html. [Accessed 30-07-2023].
- Shalom Akhai. From black boxes to transparent machines: The quest for explainable ai. Available at SSRN 4390887, 2023.
- Named entity extraction for knowledge graphs: A literature overview. IEEE Access, 8:32862–32881, 2020.
- Neuro-symbolic representation learning on biological knowledge graphs. Bioinformatics, 33(17):2723–2730, 2017.
- Famplex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining. BMC bioinformatics, 19:1–14, 2018.
- Knowledge graph prediction of unknown adverse drug reactions and validation in electronic health records. Scientific reports, 7(1):16416, 2017.
- Graph-to-sequence learning using gated graph neural networks. arXiv preprint arXiv:1806.09835, 2018.
- Codekgc: Code language model for generative knowledge graph construction. arXiv preprint arXiv:2304.09048, 2023.
- A standard database for drug repositioning. Scientific data, 4(1):1–7, 2017.
- Building a knowledge graph to enable precision medicine. Scientific Data, 10(1):67, 2023.
- Owl2vec*: Embedding of owl ontologies. Machine Learning, 110(7):1813–1845, 2021.
- A simple framework for contrastive learning of visual representations. In International conference on machine learning, pages 1597–1607. PMLR, 2020.
- A review: Knowledge reasoning over knowledge graph. Expert Systems with Applications, 141:112948, 2020.
- Knowledge graph completion: A review. Ieee Access, 8:192435–192456, 2020.
- Ctkg: A knowledge graph for clinical trials. medRxiv, pages 2021–11, 2021.
- Graph convolutional transformer: Learning the graphical structure of electronic health records. arXiv preprint arXiv:1906.04716, 2019.
- Kenneth Ward Church. Word2vec. Natural Language Engineering, 23(1):155–162, 2017.
- Wasserstein adversarial autoencoders for knowledge graph embedding based drug–drug interaction prediction. arXiv, page 07341, 2020.
- Drug–drug interaction prediction with wasserstein adversarial autoencoder-based knowledge graph embeddings. Briefings in Bioinformatics, 22(4):bbaa256, 2021.
- Comprehensive analysis of kinase inhibitor selectivity. Nature biotechnology, 29(11):1046–1051, 2011.
- The perils and pitfalls of explainable ai: Strategies for explaining algorithmic decision-making. Government information quarterly, 39(2):101666, 2022.
- Gate-variants of gated recurrent unit (gru) neural networks. In 2017 IEEE 60th international midwest symposium on circuits and systems (MWSCAS), pages 1597–1600. IEEE, 2017.
- Comparison of methods and resources for cell-cell communication inference from single-cell rna-seq data. Nature communications, 13(1):3224, 2022.
- Explainable ai (xai): Core ideas, techniques, and solutions. ACM Computing Surveys, 55(9):1–33, 2023.
- A guide to deep learning in healthcare. Nature medicine, 25(1):24–29, 2019.
- Knowledge graph-enhanced molecular contrastive learning with functional prompt. Nature Machine Intelligence, pages 1–12, 2023.
- Genomickb: a knowledge graph for the human genome. Nucleic Acids Research, 51(D1):D950–D956, 2023.
- Alvaro Fernandez-Quilez. Deep learning in radiology: ethics of data and on the value of algorithm transparency, interpretability and explainability. AI and Ethics, 3(1):257–265, 2023.
- Kg-predict: A knowledge graph computational framework for drug repurposing. Journal of biomedical informatics, 132:104133, 2022.
- Prediction of lung and colon cancer through analysis of histopathological images by utilizing pre-trained cnn models with visualization of class activation and saliency maps. In Proceedings of the 2020 3rd Artificial Intelligence and Cloud Computing Conference, pages 38–45, 2020.
- Mofit: A framework to reduce obesity using machine learning and iot. In 2021 44th International Convention on Information, Communication and Electronic Technology (MIPRO), pages 1733–1740. IEEE, 2021.
- A birds eye view on knowledge graph embeddings, software libraries, applications and challenges. arXiv preprint arXiv:2205.09088, 2022.
- Explainable ai using knowledge graphs. In ACM CoDS-COMAD Conference, 2020.
- Semantics of the black-box: Can knowledge graphs help make deep learning systems more interpretable and explainable? IEEE Internet Computing, 25(1):51–59, 2021.
- Drugrep-kg: Toward learning a unified latent space for drug repurposing using knowledge graphs. Journal of Chemical Information and Modeling, 63(8):2532–2545, 2023.
- Smr: medical knowledge graph embedding for safe medicine recommendation. Big Data Research, 23:100174, 2021.
- Hybrid speech recognition with deep bidirectional lstm. In 2013 IEEE workshop on automatic speech recognition and understanding, pages 273–278. IEEE, 2013.
- Dgidb: mining the druggable genome. Nature methods, 10(12):1209–1210, 2013.
- node2vec: Scalable feature learning for networks. In Proceedings of the 22nd ACM SIGKDD international conference on Knowledge discovery and data mining, pages 855–864, 2016.
- Learning to automate follow-up question generation using process knowledge for depression triage on reddit posts. In Proceedings of the Eighth Workshop on Computational Linguistics and Clinical Psychology, pages 137–147, 2022.
- The challenges of explainable ai in biomedical data science, 2021.
- Research on construction of knowledge graph of intestinal cells. Journal of Artificial Intelligence for Medical Sciences, 1(1-2):15–22, 2020.
- Neural factorization machines for sparse predictive analytics. In Proceedings of the 40th International ACM SIGIR conference on Research and Development in Information Retrieval, pages 355–364, 2017.
- Machine learning-friendly biomedical datasets for equivalence and subsumption ontology matching. In International Semantic Web Conference, pages 575–591. Springer, 2022.
- Refining diagnosis paths for medical diagnosis based on an augmented knowledge graph. arXiv preprint arXiv:2204.13329, 2022.
- Heterogeneous network edge prediction: a data integration approach to prioritize disease-associated genes. PLoS computational biology, 11(7):e1004259, 2015.
- Open graph benchmark: Datasets for machine learning on graphs. Advances in neural information processing systems, 33:22118–22133, 2020.
- An integrated pipeline model for biomedical entity alignment. Frontiers of Computer Science, 15:1–15, 2021.
- Drkg-drug repurposing knowledge graph for covid-19. arXiv preprint arXiv:2010.09600, 2020.
- Causalkg: Causal knowledge graph explainability using interventional and counterfactual reasoning. IEEE Internet Computing, 26(1):43–50, 2022.
- A survey on knowledge graphs: Representation, acquisition, and applications. IEEE transactions on neural networks and learning systems, 33(2):494–514, 2021.
- Named entity recognition in traditional chinese medicine clinical cases combining bilstm-crf with knowledge graph. In Knowledge Science, Engineering and Management: 12th International Conference, KSEM 2019, Athens, Greece, August 28–30, 2019, Proceedings, Part I 12, pages 537–548. Springer, 2019.
- A knowledge graph embedding based approach to predict the adverse drug reactions using a deep neural network. Journal of Biomedical Informatics, 132:104122, 2022.
- Kegg: kyoto encyclopedia of genes and genomes. Nucleic acids research, 28(1):27–30, 2000.
- Kegg for representation and analysis of molecular networks involving diseases and drugs. Nucleic acids research, 38(suppl_1):D355–D360, 2010.
- Simple embedding for link prediction in knowledge graphs. Advances in neural information processing systems, 31, 2018.
- Question answering via integer programming over semi-structured knowledge. arXiv preprint arXiv:1604.06076, 2016.
- A semantically rich knowledge graph to automate hipaa regulations for cloud health it services. In 2021 7th IEEE Intl Conference on Big Data Security on Cloud (BigDataSecurity), IEEE Intl Conference on High Performance and Smart Computing,(HPSC) and IEEE Intl Conference on Intelligent Data and Security (IDS), pages 7–12. IEEE, 2021.
- The sider database of drugs and side effects. Nucleic acids research, 44(D1):D1075–D1079, 2016.
- Path-based knowledge reasoning with textual semantic information for medical knowledge graph completion. BMC medical informatics and decision making, 21:1–12, 2021.
- Prediction of compound synthesis accessibility based on reaction knowledge graph. Molecules, 27(3):1039, 2022.
- Real-world data medical knowledge graph: construction and applications. Artificial intelligence in medicine, 103:101817, 2020.
- Kghc: a knowledge graph for hepatocellular carcinoma. BMC Medical Informatics and Decision Making, 20(3):1–11, 2020.
- Oerl: Enhanced representation learning via open knowledge graphs. IEEE Transactions on Knowledge and Data Engineering, 2022.
- K-bert: Enabling language representation with knowledge graph. In Proceedings of the AAAI Conference on Artificial Intelligence, volume 34, pages 2901–2908, 2020.
- Roberta: A robustly optimized bert pretraining approach. arXiv preprint arXiv:1907.11692, 2019.
- Open-world taxonomy and knowledge graph co-learning. In 4th Conference on Automated Knowledge Base Construction, 2022.
- Causal knowledge graph construction and evaluation for clinical decision support of diabetic nephropathy. Journal of Biomedical Informatics, 139:104298, 2023.
- Tecre: A novel temporal conflict resolution method based on temporal knowledge graph embedding. Information, 14(3):155, 2023.
- Biological applications of knowledge graph embedding models. Briefings in bioinformatics, 22(2):1679–1693, 2021.
- Inductive logic programming: Theory and methods. The Journal of Logic Programming, 19:629–679, 1994.
- A review on the attention mechanism of deep learning. Neurocomputing, 452:48–62, 2021.
- Amde: a novel attention-mechanism-based multidimensional feature encoder for drug–drug interaction prediction. Briefings in Bioinformatics, 23(1):bbab545, 2022.
- Heiko Paulheim. Knowledge graph refinement: A survey of approaches and evaluation methods. Semantic web, 8(3):489–508, 2017.
- Opening the black box: the promise and limitations of explainable machine learning in cardiology. Canadian Journal of Cardiology, 38(2):204–213, 2022.
- The disgenet knowledge platform for disease genomics: 2019 update. Nucleic acids research, 48(D1):D845–D855, 2020.
- Molecular sets (moses): a benchmarking platform for molecular generation models. Frontiers in pharmacology, 11:565644, 2020.
- Towards a knowledge graph-based explainable decision support hystem in healthcare. 2021.
- Knowledge-graph-based explainable ai: A systematic review. Journal of Information Science, page 01655515221112844, 2022.
- Generating novel molecule for target protein (sars-cov-2) using drug–target interaction based on graph neural network. Network Modeling Analysis in Health Informatics and Bioinformatics, 11:1–11, 2022.
- Kg-covid-19: a framework to produce customized knowledge graphs for covid-19 response. Patterns, 2(1), 2021.
- Proknow: Process knowledge for safety constrained and explainable question generation for mental health diagnostic assistance. Frontiers in big Data, 5:1056728, 2023.
- Process knowledge-infused learning for clinician-friendly explanations. arXiv preprint arXiv:2306.09824, 2023.
- Identification of disease treatment mechanisms through the multiscale interactome. Nature communications, 12(1):1796, 2021.
- Deep learning improves prediction of drug–drug and drug–food interactions. Proceedings of the national academy of sciences, 115(18):E4304–E4311, 2018.
- Clinical knowledge graph integrates proteomics data into clinical decision-making. bioRxiv, pages 2020–05, 2020.
- A knowledge graph to interpret clinical proteomics data. Nature biotechnology, 40(5):692–702, 2022.
- ” the human body is a black box” supporting clinical decision-making with deep learning. In Proceedings of the 2020 conference on fairness, accountability, and transparency, pages 99–109, 2020.
- Ehr-oriented knowledge graph system: toward efficient utilization of non-used information buried in routine clinical practice. IEEE Journal of Biomedical and Health Informatics, 25(7):2463–2475, 2021.
- N Sharma and R Bhatt. Privacy preserving knowledge graph for healthcare applications. In Journal of Physics: Conference Series, volume 2339, page 012013. IOP Publishing, 2022.
- Dockg: a knowledge graph framework for health with doctor-in-the-loop. In Health Information Science: 8th International Conference, HIS 2019, Xi’an, China, October 18–20, 2019, Proceedings 8, pages 3–14. Springer, 2019.
- Knowledge-graph-enabled biomedical entity linking: a survey. World Wide Web, pages 1–30, 2023.
- Communicative representation learning on attributed molecular graphs. In IJCAI, volume 2020, pages 2831–2838, 2020.
- Zinc 15–ligand discovery for everyone. Journal of chemical information and modeling, 55(11):2324–2337, 2015.
- ibkh: The integrative biomedical knowledge hub. medRxiv, page 21253461, 2021.
- Biomedical discovery through the integrative biomedical knowledge hub (ibkh). Iscience, 26(4), 2023.
- Attention-based knowledge graph representation learning for predicting drug-drug interactions. Briefings in bioinformatics, 23(3):bbac140, 2022.
- Rotate: Knowledge graph embedding by relational rotation in complex space. arXiv preprint arXiv:1902.10197, 2019.
- Data-driven prediction of drug effects and interactions. Science translational medicine, 4(125):125ra31–125ra31, 2012.
- Complex embeddings for simple link prediction, November 23 2017. US Patent App. 15/156,849.
- Interacte: Improving convolution-based knowledge graph embeddings by increasing feature interactions. In Proceedings of the AAAI conference on artificial intelligence, volume 34, pages 3009–3016, 2020.
- Composition-based multi-relational graph convolutional networks. In International Conference on Learning Representations, 2019.
- Biokg: A knowledge graph for relational learning on biological data. In Proceedings of the 29th ACM International Conference on Information & Knowledge Management, pages 3173–3180, 2020.
- Covid-19 literature knowledge graph construction and drug repurposing report generation. In Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies: Demonstrations, pages 66–77, 2021.
- Disease comorbidity-guided drug repositioning: a case study in schizophrenia. In AMIA Annual Symposium Proceedings, volume 2018, page 1300. American Medical Informatics Association, 2018.
- Kg-dti: a knowledge graph based deep learning method for drug-target interaction predictions and alzheimer’s disease drug repositions. Applied Intelligence, 52(1):846–857, 2022.
- Explainable reasoning over knowledge graphs for recommendation. In Proceedings of the AAAI conference on artificial intelligence, volume 33, pages 5329–5336, 2019.
- Drugbank: a comprehensive resource for in silico drug discovery and exploration. Nucleic acids research, 34(suppl_1):D668–D672, 2006.
- Building attention and edge message passing neural networks for bioactivity and physical–chemical property prediction. Journal of cheminformatics, 12(1):1–18, 2020.
- Knowledge graph analysis and visualization of ai technology applied in covid-19. Environmental Science and Pollution Research, 29(18):26396–26408, 2022.
- Prediction of drug–target interaction networks from the integration of chemical and genomic spaces. Bioinformatics, 24(13):i232–i240, 2008.
- Leveraging knowledge bases in lstms for improving machine reading. In Proceedings of the 55th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers), pages 1436–1446, 2017.
- Embedding entities and relations for learning and inference in knowledge bases. In Proceedings of the International Conference on Learning Representations (ICLR) 2015, 2015.
- Kg-bert: Bert for knowledge graph completion. arXiv preprint arXiv:1909.03193, 2019.
- Generative knowledge graph construction: A review. In Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing, pages 1–17, 2022.
- A unified drug–target interaction prediction framework based on knowledge graph and recommendation system. Nature communications, 12(1):6775, 2021.
- Knowledge integration and decision support for accelerated discovery of antibiotic resistance genes. Nature Communications, 13(1):2360, 2022.
- Sumgnn: multi-typed drug interaction prediction via efficient knowledge graph summarization. Bioinformatics, 37(18):2988–2995, 2021.
- Drug-path: a database for drug-induced pathways. Database, 2015:bav061, 2015.
- Toward better drug discovery with knowledge graph. Current opinion in structural biology, 72:114–126, 2022.
- Discovering dti and ddi by knowledge graph with mhrw and improved neural network. In 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pages 588–593. IEEE, 2021.
- Graph convolutional networks: a comprehensive review. Computational Social Networks, 6(1):1–23, 2019.
- Hkgb: an inclusive, extensible, intelligent, semi-auto-constructed knowledge graph framework for healthcare with clinicians’ expertise incorporated. Information Processing & Management, 57(6):102324, 2020.
- Pharmkg: a dedicated knowledge graph benchmark for bomedical data mining. Briefings in bioinformatics, 22(4):bbaa344, 2021.
- Graph neural networks: A review of methods and applications. AI open, 1:57–81, 2020.
- Rdkg-115: Assisting drug repurposing and discovery for rare diseases by trimodal knowledge graph embedding. Computers in Biology and Medicine, page 107262, 2023.
- Neural-symbolic models for logical queries on knowledge graphs. In International Conference on Machine Learning, pages 27454–27478. PMLR, 2022.
- Modeling polypharmacy side effects with graph convolutional networks. Bioinformatics, 34(13):i457–i466, 2018.
- Satvik Garg (8 papers)
- Shivam Parikh (1 paper)
- Somya Garg (4 papers)