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From local explanations to global understanding with explainable AI for trees
Open accessAbstract
Tree-based machine learning models such as random forests, decision trees, and gradient boosted trees are popular non-linear predictive models, yet comparatively little attention has been paid to explaining their predictions. Here, we improve the interpretability of tree-based models through three main contributions: 1) The first polynomial time algorithm to compute optimal explanations based on game theory. 2) A new type of explanation that directly measures local feature interaction effects. 3) A new set of tools for understanding global model structure based on combining many local explanations of each prediction. We apply these tools to three medical machine learning problems and show how combining many high-quality local explanations allows us to represent global structure while retaining local faithfulness to the original model. These tools enable us to i) identify high magnitude but low frequency non-linear mortality risk factors in the US population, ii) highlight distinct population sub-groups with shared risk characteristics, iii) identify non-linear interaction effects among risk factors for chronic kidney disease, and iv) monitor a machine learning model deployed in a hospital by identifying which features are degrading the model's performance over time. Given the popularity of tree-based machine learning models, these improvements to their interpretability have implications across a broad set of domains.
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“SHAP [6] popularized this for machine learning feature importance, with extensions to tree models [5].”
From AgentSHAP: Interpreting LLM Agent Tool Importance with Monte Carlo Shapley Value Estimation (2025) · cites this paper as [5]
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“The algorithm provides interpretable explanations suitable for regression and classification of models with tree structure applied to tabular data [22,39].”
From Explainable AI (XAI): Core Ideas, Techniques, and Solutions (2023) · cites this paper as [39]
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“ML and AI techniques, such as social network analysis and agent-based modeling, can model the complex interactions between individuals and their social environments to identify key leverage points for interventions that promote health and well-being across communities [40, 47].”
From Integrating machine learning and artificial intelligence in life-course epidemiology: pathways to innovative public health solutions (2024) · cites this paper as [40]
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Lee, G., Kim, J., & Lee, C. (2022) · Expert Systems with Applications · doi:10.1016/j.eswa.2022.116817 · Cited by 75
Conceptual challenges for interpretable machine learning
Watson, D. S. (2022) · Synthese · doi:10.1007/s11229-022-03485-5 · Cited by 87
Yang, L., Fan, J., Xiao, B., & Zhu, W. (2023) · Chemical Engineering Journal · doi:10.1016/j.cej.2023.143823 · Cited by 75
Stef, N., Başağaoğlu, H., Chakraborty, D., & Jabeur, S. B. (2023) · Energy Economics · doi:10.1016/j.eneco.2023.106822 · Cited by 76
Counterfactual Shapley Additive Explanations
Albini, E., Long, J., Dervovic, D., & Magazzeni, D. (2022) · ACM Conference on Fairness, Accountability, and Transparency (FAccT) · doi:10.1145/3531146.3533168 · Cited by 86
Silva, S. J., Keller, C. A., & Hardin, J. C. (2022) · Journal of Advances in Modeling Earth Systems · doi:10.1029/2021ms002881 · Cited by 74
Lombardi, A., Diacono, D., Amoroso, N., Biecek, P., Monaco, A., Bellantuono, L., Pantaleo, E., Logroscino, G., Blasi, R. D., Tangaro, S., et al. (2022) · Brain Informatics · doi:10.1186/s40708-022-00165-5 · Cited by 82
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True to the Model or True to the Data?Preprint
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Metadata
- Authors
- Lundberg, S. M., Erion, G., Chen, H., DeGrave, A., Prutkin, J. M., Nair, B., Katz, R., Himmelfarb, J., Bansal, N., & Lee, S.-I.
- Affiliations
- Microsoft (United States) (US)
- University of Washington (US)
- Corresponding author
- Lee, Su-In
- ORCID
- Venue
- Nature Machine Intelligence
- Published
- 2020-01-17
- Volume
- 2
- Issue
- 1
- Pages
- 56-67
- ISSN
- 2522-5839 (ISSN-L)
- PMC
- PMC7326367
- OpenAlex
- W2999615587
- Cited by
- 10,551
- References
- 38
- Citations by year
- 2026: 3607 · 2025: 2330 · 2024: 1650 · 2023: 1197 · 2022: 959 · 2021: 614 · 2020: 187
- FWCI
- 291.51
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Machine Intelligence (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Science Foundation (DGE-1256082, DBI-1759487, DBI-1552309, DBI-1355899)
- American Cancer Society (127332-RSG-15-097-01-TBG)
- U.S. Department of Health & Human Services | National Institutes of Health (R35 GM 128638, R01 NIA AG 061132)
- Topics
- Physical Sciences › Computer Science › Artificial Intelligence › Explainable Artificial Intelligence (XAI)
- Health Sciences › Health Professions › Health Information Management › Artificial Intelligence in Healthcare
- Physical Sciences › Computer Science › Information Systems › Data Mining Algorithms and Applications
- Keywords
- explainable AI, tree-based models, local explanations, mortality risk, chronic kidney disease, model monitoring, machine learning in medicine
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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