arXiv subjects

Wouter A. C. van Amsterdam

Publications and source records attributed to Wouter A. C. van Amsterdam.

8 recordsLinked to original sources

arXiv2026

Optimizing for the decision not the prediction: an exploration of Smooth Net Benefit as a training objective

Objective Prediction models are commonly trained using objectives such as Bernoulli negative log-likelihood (NLL), although downstream clinical decisions may depend on specific risk thresholds. We introduce Smooth Net Benefit ($σ$NB), a differentiable approximation of Net Benefit designed to align model training with threshold-specific clinical utility. Materials and Methods We evaluated $σ$NB as a training objective for logistic regression, generalized additive models (GAMs), and XGBoost with three Hessian implementations. Experiments used the Framingham cardiovascular risk dataset and 44 TabZilla datasets comprising 72 dataset-threshold combinations. Results $σ$NB training did not consistently improve Net Benefit in Framingham. Across the TabZilla benchmark, mean standardized Net Benefit for logistic regression increased from 0.5669 with NLL to 0.5765 with $σ$NB (mean difference 0.0096, 95% CI -0.0001 to 0.0193). For GAMs, mean standardized Net Benefit decreased from 0.5921 to 0.5625 (mean difference -0.0296, 95% CI -0.0721 to 0.0129). For XGBoost, NLL achieved 0.6745 compared with 0.6723--0.6735 across $σ$NB implementations. In logistic regression, $σ$NB gains were positively associated with the performance advantage of XGBoost over NLL-trained logistic regression. Discussion The effect of $σ$NB was context dependent, with modest gains concentrated in logistic regression and little benefit for more flexible model classes. This suggests that decision-focused optimization may be most useful when limited model flexibility leaves greater scope for improvement. Conclusion Our results do not support $σ$NB as a general replacement for NLL training, but support further investigation of decision-focused objectives in settings where conventional likelihood-based training may not adequately capture decision-relevant structure.

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arXiv2026

Causal Meta-Analysis: Rethinking the Foundations of Evidence-Based Medicine

Meta-analysis, by synthesizing effect estimates from multiple studies conducted in diverse settings, stands at the top of the evidence hierarchy in clinical research. Yet, conventional approaches based on fixed- or random-effects models lack a causal framework, which may limit their interpretability and utility for public policy. Incorporating causal inference reframes meta-analysis as the estimation of well-defined causal effects on clearly specified populations, enabling a principled approach to handling study heterogeneity. We show that classical meta-analysis estimators have a clear causal interpretation when effects are measured as risk differences. However, this breaks down for nonlinear measures like the risk ratio and odds ratio. To address this, we introduce novel causal aggregation formulas that remain compatible with standard meta-analysis practices and do not require access to individual-level data. To evaluate real-world impact, we apply both classical and causal meta-analysis methods to 500 published meta-analyses. While the conclusions often align, notable discrepancies emerge, revealing cases where conventional methods may suggest a treatment is beneficial when, under a causal lens, it is in fact harmful.

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arXiv2025

A causal viewpoint on prediction model performance under changes in case-mix: discrimination and calibration respond differently for prognosis and diagnosis predictions

Prediction models need reliable predictive performance as they inform clinical decisions, aiding in diagnosis, prognosis, and treatment planning. The predictive performance of these models is typically assessed through discrimination and calibration. Changes in the distribution of the data impact model performance and there may be important changes between a model's current application and when and where its performance was last evaluated. In health-care, a typical change is a shift in case-mix. For example, for cardiovascular risk management, a general practitioner sees a different mix of patients than a specialist in a tertiary hospital. This work introduces a novel framework that differentiates the effects of case-mix shifts on discrimination and calibration based on the causal direction of the prediction task. When prediction is in the causal direction (often the case for prognosis predictions), calibration remains stable under case-mix shifts, while discrimination does not. Conversely, when predicting in the anti-causal direction (often with diagnosis predictions), discrimination remains stable, but calibration does not. A simulation study and empirical validation using cardiovascular disease prediction models demonstrate the implications of this framework. The causal case-mix framework provides insights for developing, evaluating and deploying prediction models across different clinical settings, emphasizing the importance of understanding the causal structure of the prediction task.

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arXiv2025

Time After Time: Deep-Q Effect Estimation for Interventions on When and What to do

Problems in fields such as healthcare, robotics, and finance requires reasoning about the value both of what decision or action to take and when to take it. The prevailing hope is that artificial intelligence will support such decisions by estimating the causal effect of policies such as how to treat patients or how to allocate resources over time. However, existing methods for estimating the effect of a policy struggle with \emph{irregular time}. They either discretize time, or disregard the effect of timing policies. We present a new deep-Q algorithm that estimates the effect of both when and what to do called Earliest Disagreement Q-Evaluation (EDQ). EDQ makes use of recursion for the Q-function that is compatible with flexible sequence models, such as transformers. EDQ provides accurate estimates under standard assumptions. We validate the approach through experiments on survival time and tumor growth tasks.

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arXiv2024

When accurate prediction models yield harmful self-fulfilling prophecies

Prediction models are popular in medical research and practice. By predicting an outcome of interest for specific patients, these models may help inform difficult treatment decisions, and are often hailed as the poster children for personalized, data-driven healthcare. We show however, that using prediction models for decision making can lead to harmful decisions, even when the predictions exhibit good discrimination after deployment. These models are harmful self-fulfilling prophecies: their deployment harms a group of patients but the worse outcome of these patients does not invalidate the predictive power of the model. Our main result is a formal characterization of a set of such prediction models. Next we show that models that are well calibrated before and after deployment are useless for decision making as they made no change in the data distribution. These results point to the need to revise standard practices for validation, deployment and evaluation of prediction models that are used in medical decisions.

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arXiv2024

From algorithms to action: improving patient care requires causality

In cancer research there is much interest in building and validating outcome predicting outcomes to support treatment decisions. However, because most outcome prediction models are developed and validated without regard to the causal aspects of treatment decision making, many published outcome prediction models may cause harm when used for decision making, despite being found accurate in validation studies. Guidelines on prediction model validation and the checklist for risk model endorsement by the American Joint Committee on Cancer do not protect against prediction models that are accurate during development and validation but harmful when used for decision making. We explain why this is the case and how to build and validate models that are useful for decision making.

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arXiv2023

Conditional average treatment effect estimation with marginally constrained models

Treatment effect estimates are often available from randomized controlled trials as a single average treatment effect for a certain patient population. Estimates of the conditional average treatment effect (CATE) are more useful for individualized treatment decision making, but randomized trials are often too small to estimate the CATE. Examples in medical literature make use of the relative treatment effect (e.g. an odds-ratio) reported by randomized trials to estimate the CATE using large observational datasets. One approach to estimating these CATE models is by using the relative treatment effect as an offset, while estimating the covariate-specific untreated risk. We observe that the odds-ratios reported in randomized controlled trials are not the odds-ratios that are needed in offset models because trials often report the marginal odds-ratio. We introduce a constraint or regularizer to better use marginal odds-ratios from randomized controlled trials and find that under the standard observational causal inference assumptions this approach provides a consistent estimate of the CATE. Next, we show that the offset approach is not valid for CATE estimation in the presence of unobserved confounding. We study if the offset assumption and the marginal constraint lead to better approximations of the CATE relative to the alternative of using the average treatment effect estimate from the randomized trial. We empirically show that when the underlying CATE has sufficient variation, the constraint and offset approaches lead to closer approximations to the CATE.

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arXiv2019

Controlling for Biasing Signals in Images for Prognostic Models: Survival Predictions for Lung Cancer with Deep Learning

Deep learning has shown remarkable results for image analysis and is expected to aid individual treatment decisions in health care. To achieve this, deep learning methods need to be promoted from the level of mere associations to being able to answer causal questions. We present a scenario with real-world medical images (CT-scans of lung cancers) and simulated outcome data. Through the sampling scheme, the images contain two distinct factors of variation that represent a collider and a prognostic factor. We show that when this collider can be quantified, unbiased individual prognosis predictions are attainable with deep learning. This is achieved by (1) setting a dual task for the network to predict both the outcome and the collider and (2) enforcing independence of the activation distributions of the last layer with ordinary least squares. Our method provides an example of combining deep learning and structural causal models for unbiased individual prognosis predictions.

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