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Bibhas Chakraborty

Publications and source records attributed to Bibhas Chakraborty.

At least 19 recordsLinked to original sources

PFN-TS: Thompson Sampling for Contextual Bandits via Prior-Data Fitted Networks

Thompson sampling is a widely used strategy for contextual bandits: at each round, it samples a reward function from a Bayesian posterior and acts greedily under that sample. Prior-data fitted networks (PFNs), such as TabPFN v2+ and TabICL v2, are attractive candidates for this purpose because they approximate Bayesian posterior predictive distributions in a single forward pass. However, PFNs predict noisy future rewards, while Thompson sampling requires uncertainty over the latent mean reward function. We propose PFN-TS, a Thompson sampling algorithm that converts PFN posterior predictives into mean-reward samples using a subsampled predictive central limit theorem. The method estimates posterior variance from a geometric grid of $O(\log n)$ dataset prefixes rather than the full $O(n)$ predictive sequence used in previous predictive-sequence approaches, and reuses TabICL's cached representations across rounds. We prove consistency of the subsampled variance estimator and give a Bayesian regret bound that decomposes PFN-TS regret into exact posterior-sampling regret under the PFN prior plus approximation terms. Empirically, PFN-TS achieves the best average rank across nonlinear synthetic and OpenML classification-to-bandit benchmarks, remains competitive on linear and BART-generated rewards, and attains the highest estimated policy value in an offline mobile-health evaluation. Code is available at https://anonymous.4open.science/r/PFN_TS-36ED/.

stat.ML

Bayesian integration G-formula for platform SMART designs allowing for adding new treatments

Dynamic treatment regimes (DTRs) are sequences of decision rules to guide treatment assignments in response to a patient's evolving, time-varying disease status. Sequential multiple assignment randomized trials (SMARTs) are considered the gold standard experimental design for evaluating DTRs. However, SMARTs often require more time to complete compared with a single stage RCT and new candidate treatments may become available or feasible during the trial. Platform trials are an adaptive trial design that allow new treatments to be added to the ongoing study according to a prespecified master protocol. In this paper, we introduce a novel platform SMART that integrates features from both platform trials and SMARTs, allowing new treatments to be added during the trial. Additionally, we propose the Bayesian integration G-formula (BIG) estimators for platform SMARTs to account for non-concurrent treatment comparisons. Extensive simulations are conducted to evaluate the performance of different BIG estimators against benchmark methods. We demonstrate the proposed BIG estimators based on the S. aureus Network Adaptive Platform (SNAP) trial.

stat.ME

BFTS: Thompson Sampling with Bayesian Additive Regression Trees

Contextual bandits are a core technology for personalized mobile health interventions, where decision-making requires adapting to complex, non-linear user behaviors. While Thompson Sampling (TS) is a preferred strategy for these problems, its performance hinges on the quality of the underlying reward model. Standard linear models suffer from high bias, while neural network approaches are often brittle and difficult to tune in online settings. Conversely, tree ensembles dominate tabular data prediction but typically rely on heuristic uncertainty quantification, lacking a principled probabilistic basis for TS. We propose Bayesian Forest Thompson Sampling (BFTS), the first contextual bandit algorithm to integrate Bayesian Additive Regression Trees (BART), a fully probabilistic sum-of-trees model, directly into the exploration loop. We prove that BFTS is theoretically sound, deriving an information-theoretic Bayesian regret bound of $\tilde{O}(\sqrt{T})$. As a complementary result, we establish frequentist minimax optimality for a "feel-good" variant, confirming the structural suitability of BART priors for non-parametric bandits. Empirically, BFTS achieves state-of-the-art regret on tabular benchmarks with near-nominal uncertainty calibration. Furthermore, in an offline policy evaluation on the Drink Less micro-randomized trial, BFTS improves engagement rates by over 30% compared to the deployed policy, demonstrating its practical effectiveness for behavioral interventions.

stat.ML

Toward Global Large Language Models in Medicine

Despite continuous advances in medical technology, the global distribution of health care resources remains uneven. The development of large language models (LLMs) has transformed the landscape of medicine and holds promise for improving health care quality and expanding access to medical information globally. However, existing LLMs are primarily trained on high-resource languages, limiting their applicability in global medical scenarios. To address this gap, we constructed GlobMed, a large multilingual medical dataset, containing over 500,000 entries spanning 12 languages, including four low-resource languages. Building on this, we established GlobMed-Bench, which systematically assesses 56 state-of-the-art proprietary and open-weight LLMs across multiple multilingual medical tasks, revealing significant performance disparities across languages, particularly for low-resource languages. Additionally, we introduced GlobMed-LLMs, a suite of multilingual medical LLMs trained on GlobMed, with parameters ranging from 1.7B to 8B. GlobMed-LLMs achieved an average performance improvement of over 40% relative to baseline models, with a more than threefold increase in performance on low-resource languages. Together, these resources provide an important foundation for advancing the equitable development and application of LLMs globally, enabling broader language communities to benefit from technological advances.

cs.CL

RELEAP: Reinforcement-Enhanced Label-Efficient Active Phenotyping for Electronic Health Records

Objective: Electronic health record (EHR) phenotyping often relies on noisy proxy labels, which undermine the reliability of downstream risk prediction. Active learning can reduce annotation costs, but most rely on fixed heuristics and do not ensure that phenotype refinement improves prediction performance. Our goal was to develop a framework that directly uses downstream prediction performance as feedback to guide phenotype correction and sample selection under constrained labeling budgets. Materials and Methods: We propose Reinforcement-Enhanced Label-Efficient Active Phenotyping (RELEAP), a reinforcement learning-based active learning framework. RELEAP adaptively integrates multiple querying strategies and, unlike prior methods, updates its policy based on feedback from downstream models. We evaluated RELEAP on a de-identified Duke University Health System (DUHS) cohort (2014-2024) for incident lung cancer risk prediction, using logistic regression and penalized Cox survival models. Performance was benchmarked against noisy-label baselines and single-strategy active learning. Results: RELEAP consistently outperformed all baselines. Logistic AUC increased from 0.774 to 0.805 and survival C-index from 0.718 to 0.752. Using downstream performance as feedback, RELEAP produced smoother and more stable gains than heuristic methods under the same labeling budget. Discussion: By linking phenotype refinement to prediction outcomes, RELEAP learns which samples most improve downstream discrimination and calibration, offering a more principled alternative to fixed active learning rules. Conclusion: RELEAP optimizes phenotype correction through downstream feedback, offering a scalable, label-efficient paradigm that reduces manual chart review and enhances the reliability of EHR-based risk prediction.

cs.LG

Bayesian Machine Learning for Estimating Optimal Dynamic Treatment Regimes with Ordinal Outcomes

Dynamic treatment regimes (DTRs) are sequences of decision rules designed to tailor treatment based on patients' treatment history and evolving disease status. Ordinal outcomes frequently serve as primary endpoints in clinical trials and observational studies. However, constructing optimal DTRs for ordinal outcomes has been underexplored. This paper introduces a Bayesian machine learning (BML) framework to handle ordinal outcomes in the DTR setting. To deal with potential nonlinear associations between outcomes and predictors, we first introduce ordinal Bayesian additive regression trees (OBART), a new model that integrates the latent variable framework within the traditional Bayesian additive regression trees (BART). We then incorporate OBART into the BML to estimate optimal DTRs based on ordinal data and quantify the associated uncertainties. Extensive simulation studies are conducted to evaluate the performance of the proposed approach against existing methods. We demonstrate the application of the proposed approach using data from a smoking cessation trial and provide the OBART R package along with R code for implementation.

stat.ME

A Penalized Shared-parameter Algorithm for Estimating Optimal Dynamic Treatment Regimens

A dynamic treatment regimen (DTR) is a set of decision rules to personalize treatments for an individual using their medical history. The Q-learning-based Q-shared algorithm has been used to develop DTRs that involve decision rules shared across multiple stages of intervention. We show that the existing Q-shared algorithm can suffer from non-convergence due to the use of linear models in the Q-learning setup, and identify the condition under which Q-shared fails. We develop a penalized Q-shared algorithm that not only converges in settings that violate the condition, but can outperform the original Q-shared algorithm even when the condition is satisfied. We give evidence for the proposed method in a real-world application and several synthetic simulations.

stat.ML

Skew-Probabilistic Neural Networks for Learning from Imbalanced Data

Real-world datasets often exhibit imbalanced data distribution, where certain class levels are severely underrepresented. In such cases, traditional pattern classifiers have shown a bias towards the majority class, impeding accurate predictions for the minority class. This paper introduces an imbalanced data-oriented classifier using probabilistic neural networks (PNN) with a skew-normal kernel function to address this major challenge. PNN is known for providing probabilistic outputs, enabling quantification of prediction confidence, interpretability, and the ability to handle limited data. By leveraging the skew-normal distribution, which offers increased flexibility, particularly for imbalanced and non-symmetric data, our proposed Skew-Probabilistic Neural Networks (SkewPNN) can better represent underlying class densities. Hyperparameter fine-tuning is imperative to optimize the performance of the proposed approach on imbalanced datasets. To this end, we employ a population-based heuristic algorithm, the Bat optimization algorithm, to explore the hyperparameter space effectively. We also prove the statistical consistency of the density estimates, suggesting that the true distribution will be approached smoothly as the sample size increases. Theoretical analysis of the computational complexity of the proposed SkewPNN and BA-SkewPNN is also provided. Numerical simulations have been conducted on different synthetic datasets, comparing various benchmark-imbalanced learners. Real-data analysis on several datasets shows that SkewPNN and BA-SkewPNN substantially outperform most state-of-the-art machine-learning methods for both balanced and imbalanced datasets (binary and multi-class categories) in most experimental settings.

stat.ML

Thompson sampling for zero-inflated count outcomes with an application to the Drink Less mobile health study

Mobile health (mHealth) interventions often aim to improve distal outcomes, such as clinical conditions, by optimizing proximal outcomes through just-in-time adaptive interventions. Contextual bandits provide a suitable framework for customizing such interventions according to individual time-varying contexts. However, unique challenges, such as modeling count outcomes within bandit frameworks, have hindered the widespread application of contextual bandits to mHealth studies. The current work addresses this challenge by leveraging count data models into online decision-making approaches. Specifically, we combine four common offline count data models (Poisson, negative binomial, zero-inflated Poisson, and zero-inflated negative binomial regressions) with Thompson sampling, a popular contextual bandit algorithm. The proposed algorithms are motivated by and evaluated on a real dataset from the Drink Less trial, where they are shown to improve user engagement with the mHealth platform. The proposed methods are further evaluated on simulated data, achieving improvement in maximizing cumulative proximal outcomes over existing algorithms. Theoretical results on regret bounds are also derived. The countts R package provides an implementation of our approach.

stat.ML

Artificial Intelligence-based Decision Support Systems for Precision and Digital Health

Precision health, increasingly supported by digital technologies, is a domain of research that broadens the paradigm of precision medicine, advancing everyday healthcare. This vision goes hand in hand with the groundbreaking advent of artificial intelligence (AI), which is reshaping the way we diagnose, treat, and monitor both clinical subjects and the general population. AI tools powered by machine learning have shown considerable improvements in a variety of healthcare domains. In particular, reinforcement learning (RL) holds great promise for sequential and dynamic problems such as dynamic treatment regimes and just-in-time adaptive interventions in digital health. In this work, we discuss the opportunity offered by AI, more specifically RL, to current trends in healthcare, providing a methodological survey of RL methods in the context of precision and digital health. Focusing on the area of adaptive interventions, we expand the methodological survey with illustrative case studies that used RL in real practice. This invited article has undergone anonymous review and is intended as a book chapter for the volume "Frontiers of Statistics and Data Science" edited by Subhashis Ghoshal and Anindya Roy for the International Indian Statistical Association Series on Statistics and Data Science, published by Springer. It covers the material from a short course titled "Artificial Intelligence in Precision and Digital Health" taught by the author Bibhas Chakraborty at the IISA 2022 Conference, December 26-30 2022, at the Indian Institute of Science, Bengaluru.

stat.ML

Reinforcement Learning in Modern Biostatistics: Constructing Optimal Adaptive Interventions

In recent years, reinforcement learning (RL) has acquired a prominent position in health-related sequential decision-making problems, gaining traction as a valuable tool for delivering adaptive interventions (AIs). However, in part due to a poor synergy between the methodological and the applied communities, its real-life application is still limited and its potential is still to be realized. To address this gap, our work provides the first unified technical survey on RL methods, complemented with case studies, for constructing various types of AIs in healthcare. In particular, using the common methodological umbrella of RL, we bridge two seemingly different AI domains, dynamic treatment regimes and just-in-time adaptive interventions in mobile health, highlighting similarities and differences between them and discussing the implications of using RL. Open problems and considerations for future research directions are outlined. Finally, we leverage our experience in designing case studies in both areas to showcase the significant collaborative opportunities between statistical, RL, and healthcare researchers in advancing AIs.

stat.ML

Incorporating nonparametric methods for estimating causal excursion effects in mobile health with zero-inflated count outcomes

In mobile health, tailoring interventions for real-time delivery is of paramount importance. Micro-randomized trials have emerged as the "gold-standard" methodology for developing such interventions. Analyzing data from these trials provides insights into the efficacy of interventions and the potential moderation by specific covariates. The "causal excursion effect", a novel class of causal estimand, addresses these inquiries. Yet, existing research mainly focuses on continuous or binary data, leaving count data largely unexplored. The current work is motivated by the Drink Less micro-randomized trial from the UK, which focuses on a zero-inflated proximal outcome, i.e., the number of screen views in the subsequent hour following the intervention decision point. To be specific, we revisit the concept of causal excursion effect, specifically for zero-inflated count outcomes, and introduce novel estimation approaches that incorporate nonparametric techniques. Bidirectional asymptotics are established for the proposed estimators. Simulation studies are conducted to evaluate the performance of the proposed methods. As an illustration, we also implement these methods to the Drink Less trial data.

stat.ME

Fairness-Aware Interpretable Modeling (FAIM) for Trustworthy Machine Learning in Healthcare

The escalating integration of machine learning in high-stakes fields such as healthcare raises substantial concerns about model fairness. We propose an interpretable framework - Fairness-Aware Interpretable Modeling (FAIM), to improve model fairness without compromising performance, featuring an interactive interface to identify a "fairer" model from a set of high-performing models and promoting the integration of data-driven evidence and clinical expertise to enhance contextualized fairness. We demonstrated FAIM's value in reducing sex and race biases by predicting hospital admission with two real-world databases, MIMIC-IV-ED and SGH-ED. We show that for both datasets, FAIM models not only exhibited satisfactory discriminatory performance but also significantly mitigated biases as measured by well-established fairness metrics, outperforming commonly used bias-mitigation methods. Our approach demonstrates the feasibility of improving fairness without sacrificing performance and provides an a modeling mode that invites domain experts to engage, fostering a multidisciplinary effort toward tailored AI fairness.

cs.LG

Developing Federated Time-to-Event Scores Using Heterogeneous Real-World Survival Data

Survival analysis serves as a fundamental component in numerous healthcare applications, where the determination of the time to specific events (such as the onset of a certain disease or death) for patients is crucial for clinical decision-making. Scoring systems are widely used for swift and efficient risk prediction. However, existing methods for constructing survival scores presume that data originates from a single source, posing privacy challenges in collaborations with multiple data owners. We propose a novel framework for building federated scoring systems for multi-site survival outcomes, ensuring both privacy and communication efficiency. We applied our approach to sites with heterogeneous survival data originating from emergency departments in Singapore and the United States. Additionally, we independently developed local scores at each site. In testing datasets from each participant site, our proposed federated scoring system consistently outperformed all local models, evidenced by higher integrated area under the receiver operating characteristic curve (iAUC) values, with a maximum improvement of 11.6%. Additionally, the federated score's time-dependent AUC(t) values showed advantages over local scores, exhibiting narrower confidence intervals (CIs) across most time points. The model developed through our proposed method exhibits effective performance on each local site, signifying noteworthy implications for healthcare research. Sites participating in our proposed federated scoring model training gained benefits by acquiring survival models with enhanced prediction accuracy and efficiency. This study demonstrates the effectiveness of our privacy-preserving federated survival score generation framework and its applicability to real-world heterogeneous survival data.

cs.AI

Optimal Adaptive SMART Designs with Binary Outcomes

In a sequential multiple-assignment randomized trial (SMART), a sequence of treatments is given to a patient over multiple stages. In each stage, randomization may be done to allocate patients to different treatment groups. Even though SMART designs are getting popular among clinical researchers, the methodologies for adaptive randomization at different stages of a SMART are few and not sophisticated enough to handle the complexity of optimal allocation of treatments at every stage of a trial. Lack of optimal allocation methodologies can raise serious concerns about SMART designs from an ethical point of view. In this work, we develop an optimal adaptive allocation procedure to minimize the expected number of treatment failures for a SMART with a binary primary outcome. Issues related to optimal adaptive allocations are explored theoretically with supporting simulations. The applicability of the proposed methodology is demonstrated using a recently conducted SMART study named M-Bridge for developing universal and resource-efficient dynamic treatment regimes (DTRs) for incoming first-year college students as a bridge to desirable treatments to address alcohol-related risks.

stat.ME

Incorporating Participants' Welfare into Sequential Multiple Assignment Randomized Trials

Dynamic treatment regimes (DTRs) are sequences of decision rules that recommend treatments based on patients' time-varying clinical conditions. The sequential multiple assignment randomized trial (SMART) is an experimental design that can provide high-quality evidence for constructing optimal DTRs. In a conventional SMART, participants are randomized to available treatments at multiple stages with balanced randomization probabilities. Despite its relative simplicity of implementation and desirable performance in comparing embedded DTRs, the conventional SMART faces inevitable ethical issues including assigning many participants to the empirically inferior treatment or the treatment they dislike, which might slow down the recruitment procedure and lead to higher attrition rates, ultimately leading to poor internal and external validities of the trial results. In this context, we propose a SMART under the Experiment-as-Market framework (SMART-EXAM), a novel SMART design that holds the potential to improve participants' welfare by incorporating their preferences and predicted treatment effects into the randomization procedure. We describe the steps of conducting a SMART-EXAM and evaluate its performance compared to the conventional SMART. The results indicate that the SMART-EXAM can improve the welfare of the participants enrolled in the trial, while also achieving a desirable ability to construct an optimal DTR when the experimental parameters are suitably specified. We finally illustrate the practical potential of the SMART-EXAM design using data from a SMART for children with attention-deficit/hyperactivity disorder (ADHD).

stat.ME

A Flexible Micro-Randomized Trial Design and Sample Size Considerations

Technological advancements have made it possible to deliver mobile health interventions to individuals. A novel framework that has emerged from such advancements is the just-in-time adaptive intervention (JITAI), which aims to suggest the right support to the individuals when their needs arise. The micro-randomized trial (MRT) design has been proposed recently to test the proximal effects of these JITAIs. However, the extant MRT framework only considers components with a fixed number of categories added at the beginning of the study. We propose a flexible MRT (FlexiMRT) design which allows addition of more categories to the components during the study. The proposed design is motivated by collaboration on the DIAMANTE study, which learns to deliver text messages to encourage physical activity among the patients with diabetes and depression. We developed a new test statistic and the corresponding sample size calculator for the FlexiMRT using an approach similar to the generalized estimating equation for longitudinal data. Simulation studies were conducted to evaluate the sample size calculators and an R shiny application for the calculators was developed.

stat.ME

Federated and distributed learning applications for electronic health records and structured medical data: A scoping review

Federated learning (FL) has gained popularity in clinical research in recent years to facilitate privacy-preserving collaboration. Structured data, one of the most prevalent forms of clinical data, has experienced significant growth in volume concurrently, notably with the widespread adoption of electronic health records in clinical practice. This review examines FL applications on structured medical data, identifies contemporary limitations and discusses potential innovations. We searched five databases, SCOPUS, MEDLINE, Web of Science, Embase, and CINAHL, to identify articles that applied FL to structured medical data and reported results following the PRISMA guidelines. Each selected publication was evaluated from three primary perspectives, including data quality, modeling strategies, and FL frameworks. Out of the 1160 papers screened, 34 met the inclusion criteria, with each article consisting of one or more studies that used FL to handle structured clinical/medical data. Of these, 24 utilized data acquired from electronic health records, with clinical predictions and association studies being the most common clinical research tasks that FL was applied to. Only one article exclusively explored the vertical FL setting, while the remaining 33 explored the horizontal FL setting, with only 14 discussing comparisons between single-site (local) and FL (global) analysis. The existing FL applications on structured medical data lack sufficient evaluations of clinically meaningful benefits, particularly when compared to single-site analyses. Therefore, it is crucial for future FL applications to prioritize clinical motivations and develop designs and methodologies that can effectively support and aid clinical practice and research.

cs.LG