Paired Recipient-based Evaluation of Survival Prediction for Deceased Donor Kidney Transplants
Authors: Misaki Matsuura, Mohammadreza Nemati, Dulat Bekbolsynov, Stanislaw Stepkowski, Kevin S. Xu
Organizations: Department of Computer and Data Sciences Case Western Reserve University Cleveland, OH 44106, USA · Department of Medical Microbiology and Immunology University of Toledo Toledo, OH 43614, USA
There has been significant interest in using machine learning algorithms to predict kidney transplant outcomes, such as the number of years until a graft inevitably fails. These prediction algorithms could possibly be used for pre-transplant donor-recipient matching to identify more compatible donors and recipients and thus improve post-transplant outcomes. In this study, we explore the use of survival prediction models trained on deceased donor kidney transplant data from the Scientific Registry of Transplant Recipients (SRTR). We propose a novel paired recipient-based evaluation framework that compares graft outcomes between two recipients who received kidneys from the same deceased donor, allowing us to evaluate the counterfactual benefit of changing the recipient for a certain donor. We find that five different survival prediction models, ranging in complexity from linear to deep learning-based models, all result in ~60% paired recipient-based accuracy. We further translate this accuracy into an interpretable quantity of post-transplant years gained. We also highlight major limitations of the commonly used concordance index (C-index) metric for evaluating survival prediction accuracy in this setting and demonstrate that our proposed paired recipient-based accuracy metric is more clinically relevant and better reflects real-world allocation settings.
Machine learning predictors have become essential tools for guiding automated decision making. However, a major misalignment persists: predictive models are typically optimized in terms of standard statistical metrics in isolation from the algorithmic tasks they inform. We highlight this incongruity in the high-stakes domain of organ allocation by demonstrating that any algorithm relying on (even highly accurate) survival predictors optimized for standard metrics -- such as the Concordance index (C-index) -- can yield arbitrarily poor outcomes when used for allocation, failing to guarantee utility better than a uniform random selection. To bridge the gap between survival analysis and policy optimization, we introduce a decision-focused learning approach based on optimizing normalized discounted cumulative gain (NDCG), a mainstay metric in information retrieval. We establish the utility of NDCG in survival analysis by proving that it translates to guarantees on the performance of allocation. Empirically, we propose a bootstrapping approach to optimize the NDCG of existing survival models. Unlike prior work, we also address the challenge of right censorship when evaluating ranking. On historical heart transplant data from the US, our method dramatically boosts the NDCG of baseline models by 50-100%, which translates to tens of thousands of additional life years gained annually when deployed for transplant allocation. We anticipate that our framework will find broader applications in decision making with predictions.
Itai Zilberstein, Ioannis Anagnostides, Tuomas Sandholm
We convert black-box clinical prediction models for tabular data into standalone nomograms that can be audited term by term. PRiSM (Partial Responses in Structured Models) takes the shape of each effect and interaction from the source model, not merely which variables mattered, and lets the outcome select and weight them. We tested this in 50,356 heart transplant recipients, with validation in a later era than training. Nomograms from all 5 source models - a public clinical risk score, logistic regression, neural networks, random forests and extreme gradient boosting - met a prespecified noninferiority criterion for discrimination before any further simplification, and generally preserved calibration and clinical net benefit. Those from the 3 machine-learning models showed no detectable difference in discrimination from de novo generalized additive and explainable boosting models, exceeded neural additive models, and carried fewer terms than the explainable boosting model. PRiSM is released as an open-source Python package.
Henry Pigot, Paulo J. G. Lisboa, Sandra Ortega-Martorell +3
The early detection of Chronic Kidney Disease using machine learning has attracted significant interest in healthcare-related computer science. Despite rapid advancements in this field, many reported studies remain inconsistent and potentially misleading. A significant drawback is the lack of organized evaluation regarding methodological concerns. Key issues include data leakage, limited access to temporal patient records and inconsistency in reported clinical indicators. This research offers a systematic literature review of existing CKD prediction studies using interpretable machine learning techniques, where nineteen relevant studies were selected via systematic searches across major academic databases. To assess methodological reliability, this study introduces a structured taxonomy of information leakage and a quantitative leakage scoring framework to systematically evaluate reliability across CKD prediction studies. The analysis reveals a strong relationship between leakage and inflated performance. Here, High leakage-studies report an average accuracy of 95.48%, compared to 80.2% for leakage-free studies, reflecting an increase of approximately 15.28%. Furthermore, a cross-study feature stability analysis shows that only a small subset of predictors is consistently reproducible, with over 80% lacking reliability. Overall, the findings suggest that many reported performance improvements stem from methodological limitations rather than true predictive capability.