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Knowledge Science for AI-based biomedical and clinical applications
The document discusses the importance of knowledge science in enhancing trust in AI-based biomedical and clinical applications, particularly when dealing with complex and heterogeneous data. It emphasizes that trust can be achieved by representing model inputs, outputs, and processes and contextualizing them with domain and user knowledge. The integration of knowledge graphs and ontologies is suggested as a means to improve the explainability and reliability of AI systems in healthcare.
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Knowledge Science for AI-based biomedical and clinical applications
- 1. Knowledge Science forAI-based biomedical and clinical applications Catia Pesquita LASIGE, University of Lisbon @CPesquita clpesquita@fc.ul.pt TOWARDS TRUSTWORTHY DATA First International Workshop on Knowledge Science March 31, 2022 Eindhoven Artificial Intelligence Systems Institute
- 2. Why biomedical AIneeds Knowledge Science 1. Large amounts of data in non-standard formats which need to be converted, interpreted, and merged into readable formats. 2. Heterogeneous and complex data which current ML/AI approaches are processing without context 3. Lack of explainability hinders trust 2 Knowledge Science is key to tackle ALL challenges
- 3. Trust in AI •the user successfully comprehends how the model arrives at an outcome 🡪 represent inputs, outputs and processes • the model’s outcomes/workings match the user’s prior knowledge 🡪 build a shared context 3 Jacovi, Alon, et al. "Formalizing trust in artificial intelligence: Prerequisites, causes and goals of human trust in AI." Proceedings of the 2021 ACM conference on fairness, accountability, and transparency. 2021.
- 4. Trust in AI •the user successfully comprehends how the model arrives at an outcome 🡪 represent a model’s processes represent inputs, outputs and • the model’s outcomes/workings match the user’s prior knowledge 🡪 evaluation 4
- 5. What happens whendata is complex, multi-domain, heterogeneous, incomplete, ambiguous? 5
- 6. Trust in AIfor biomedical and clinical applications • the user successfully comprehends how the model arrives at an outcome 🡪 represent a model’s processes represent inputs, outputs and • the model’s outcomes/workings match the user’s prior knowledge 🡪 evaluation 6
- 7. Trust in AIfor biomedical and clinical applications • the user successfully comprehends how the model arrives at an outcome 🡪 represent a model’s inputs, outputs and processes • the model’s outcomes/workings match the user’s prior knowledge 🡪 evaluation 7
- 8. Trust in AIfor biomedical and clinical applications • the user successfully comprehends how the model arrives at an outcome 🡪 represent a model’s inputs, outputs and processes • the model’s outcomes/workings match the user’s prior knowledge 🡪 represent the scientific context 8
- 9. Knowledge Science canhelp mitigate bias in biomedical AI 9 10.1038/s43856-021-00028-w Mitigating bias in machine learning for medicine
- 10. Knowledge Science forTrust in Biomedical AI Assessing trustworthiness requires data, domain and user context Data context: represent data provenance and transformations/processing Domain/background knowledge: represent the scientific context of the data and application User context: different users will trust based on different expectations 10
- 11. Data Context Augment explanationswith the data creation and processing context • Provide a rich contextual semantic layer to the underlying data using domain ontologies and knowledge graphs. • Preserve uncertainty and highlight potential ambiguity and incompleteness at the data level 11
- 12. Data Context iskey for trust 25% of the works that developed ML approaches to diagnose COVID-19 in adults based on chest X-rays and CT scans used pediatric (ages 1-5) pneumonia images as control. 12 Roberts, Michael, et al. "Common pitfalls and recommendations for using machine learning to detect and prognosticate for COVID-19 using chest radiographs and CT scans." Nature Machine Intelligence 3.3 (2021): 199-217. 10.1016/j.cell.2018.02.0 10 COVID-19 10.1016/j.rxeng.2020.11.0 01
- 13. Domain Knowledge Context Contextualizean explanation within existing knowledge • Include prior knowledge through links to ontologies • Enrich the contextual semantic layer with links and relations across domains of knowledge 13
- 14. Domain Knowledge Contextis key for trust 14 Term 1 Term 2 Similarity Gingiva Gum 0.98
- 15. Domain Knowledge Contextis key for trust 15 Gingiva Gum 0.98 Term 1 Term 2 Similarity Gingiva Gum 0.98 Anatomical Part Chemical Substance
- 16. User Context Trusting anAI outcome depends on the user context: task, prior knowledge, expectation, etc. 16 Protein A and Protein B are not similar at all since they are involved in unrelated diseases… Protein A and Protein B are very similar because they perform the same molecular function! Biochemist Clinician
- 17. Ontologies, Knowledge Graphs andFAIR data principles can support data, domain and user context. 17
- 18. NextGen Biomedical AIrequires integration of complex and diverse data Molecular Cellular Anatomy Phenotype and Disease Clinical 18 Environmental
- 19. • 100s ofvery large files per patient covering genome sequence, mutations, transcriptome, clinical, etc. 19 NextGen Biomedical AI requires integration of complex and diverse data
- 20. What happens whendata is complex, multi-domain, heterogeneous, incomplete, ambiguous? 20
- 21. One ontology isnot enough Systems Biology, Systems Medicine and Personalized Medicine require holistic representations 21 JD Ferreira, DC Teixeira, C Pesquita. Biomedical Ontologies: Coverage, Access and Use. 2020 Systems Medicine Integrative, Qualitative and Computational Approaches, Academic Press, Elsevier
- 22. What do weneed to create holistic representations? Cover multiple domains Align multiple ontologies Scalability Ensure rich semantic integration Related but not equal domains Complex relations involving more than one ontology Provide high quality alignments Support human interaction Visualizing the context of a mapping Balancing cognitive overload and informativeness 22 MC Silva, D Faria, and C Pesquita. Integrating knowledge graphs for explainable artificial intelligence in biomedicine. Ontology Matching workshop 2021
- 23. Rethinking biomedical ontology alignment Covermultiple domains Pairwise ontology alignment Holistic ontology alignment of multiple ontologies Ensure rich semantic integration Simple equivalence ontology alignment Complex ontology alignment Provide high quality alignments User validation Human-in-the-loop Interactive Alignment 23 MC Silva, D Faria, and C Pesquita. Integrating knowledge graphs for explainable artificial intelligence in biomedicine. Ontology Matching workshop 2021
- 24. Holistic Matching withclustering and incremental matching 24 Silva, M.C., Faria, D. & Pesquita, C. (2022). Matching Multiple Ontologies to Build a Knowledge Graph for Personalized Medicine. ESWC2022 (accepted) Can we ensure the scalability of matching tasks with many ontologies?
- 25. Holistic Matching (CIA)runs in half the time, ensures high recall within similar domains and high precision across domains 25 Silva, M.C., Faria, D. & Pesquita, C. (2022). Matching Multiple Ontologies to Build a Knowledge Graph for Personalized Medicine. ESWC2022 (accepted)
- 26. Compound Matching forontology triples Can we find mappings involving multiple ontologies using lexical approaches and search space pruning? 26 HP:0001650 aortic stenosis PATO:0001847 constricted Step 1 FMA:3734 aorta Step 2 HP:0001650 (…) stenosis Filter unmapped source classes Remove mapped words from class labels. Selection of best scoring mappings Oliveira, D., & Pesquita, C. (2018). Improving the interoperability of biomedical ontologies with compound alignments. J. Biomedical Semantics. Ontology sets Correct (New) MP-CL-PATO 47.1% (17.6%) MP-GO-PATO 86.9% (22.3%) MP-NBO-PATO 70.4% (20.7%) MP-UBERON-PATO 83.5% (24.7%) WBP-GO-PATO 44.9% (33.3%) HP-FMA-PATO 81.5% (44.1%)
- 27. https://github.com/liseda-lab/VOWLMap Supporting contextualized ontologyalignment validation 27 Guerreiro, A., Faria, D. & Pesquita, C. (2021) VOWLMap: Graph-based Ontology Alignment Visualization and Editing. VOILA workshop (ISWC 2021)
- 28. Trustworthy biomedical AI requirestrustworthy data.
- 29. Explainable AI forPersonalized Oncology 29 katy-project.eu
- 30. 30 Is this DataTrustworthy?
- 31. Building a KGfor Explainable AI for Personalized Oncology 31
- 32. Patient Ex-smoker Smoker Diabetes MET HLA-A2 cytokine-mediated signaling pathway Renal cell carcinoma,somatic Sunitinib Antineoplastic Agent Tyrosine kinase activity Cancer AI recommendation presents has mutation inhibits The KG can be used to contextualize the patient and the drug recommendation promotes treats Patient treated with 32 is risk factor
- 33. Patient Ex-smoker Smoker Diabetes MET HLA-A2 cytokine-mediated signaling pathway Renal cell carcinoma,somatic Sunitinib Antineoplastic Agent Tyrosine kinase activity Cancer AI recommendation presents has mutation inhibits The KG can be used to contextualize the patient and the drug recommendation promotes treats Patient treated with 33 is risk factor How diverse is my dataset in terms of patient features?
- 34. Patient Ex-smoker Smoker Diabetes MET HLA-A2 cytokine-mediated signaling pathway Renal cell carcinoma,somatic Sunitinib Antineoplastic Agent Tyrosine kinase activity Cancer AI recommendation presents has mutation inhibits The KG can be used to contextualize the patient and the drug recommendation promotes treats Patient treated with 34 is risk factor How **similar** are my negative and positive cases?
- 35. Patient Ex-smoker Smoker Diabetes MET HLA-A2 cytokine-mediated signaling pathway Renal cell carcinoma,somatic Sunitinib Antineoplastic Agent Tyrosine kinase activity Cancer AI recommendation presents has mutation inhibits The KG can be used to contextualize the patient and the drug recommendation promotes treats Patient treated with 35 is risk factor How does the prediction match current scientific knowledge?
- 36. Patient Ex-smoker Smoker Diabetes MET HLA-A2 cytokine-mediated signaling pathway Renal cell carcinoma,somatic Sunitinib Antineoplastic Agent Tyrosine kinase activity Cancer AI recommendation presents has mutation inhibits The KG can be used to contextualize the patient and the drug recommendation promotes treats Patient treated with 36 is risk factor How **similar** are patients treated with the same drug?
- 37. The great barrierto AI adoption in healthcare and biomedical research is lack of trust. Knowledge Science is the answer. Photo by National Cancer Institute on Unsplash 37
- 38. Acknowledgements Daniel Faria, LASIGE/Biodata.pt,Portugal Isabel Cruz, U. Illinois, USA Ernesto Jimenez-Ruiz, City, U. of London, UK Daniela Oliveira, Novartis Patrick Lambrix, U. Linkoping, Sweden Valentina Ivanova, RISE, Sweden Booma S. Balasubramani, Microsoft and many others Past and present students: Rita Sousa Marta Silva Susana Nunes Ana Guerreiro Patrícia Eugénio Filipa Serrano Beatriz Lima Carlota Cardoso and many others 38 https://liseda-lab.github.io/ https://github.com/liseda-lab/ https://github.com/AgreementMakerLight @CPesquita clpesquita@fc.ul.pt This work was supported by FCT through the LASIGEResearch Unit (UIDB/00408/2020 and UIDP/00408/2020). It was also partially supported by the KATY project which has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 101017453.