arXiv subjects

Shalmali Joshi

Publications and source records attributed to Shalmali Joshi.

At least 19 recordsLinked to original sources

arXiv2026

Positive-Unlabeled Preference Optimization For Chest X-ray Report Generation

Vision-Language Models (VLMs) for radiology report generation are typically trained on retrospective clinical reports, which suffer from omission noise: clinically present findings are left unreported due to the omission of subtle findings. For example, prior studies show that cardiomegaly may be omitted from ICU chest X-ray reports when the imaging request is focused on monitoring support device placement. As a result, models trained with standard approaches inherit these omissions, learning to under-report findings themselves. We propose PU-DPO, a preference optimization framework to prevent omission noise from corrupting the preference signal. We reformulate the objective under a positive-unlabeled (PU) learning framework, treating absent mentions as unlabeled rather than truly negative. Our framework provides preference supervision using constructed contrastive pairs, generated using edits to model responses, producing variants that explicitly mention or omit a specific finding. Generated responses that mention the finding are naturally preferred in the context of visual evidence. Across semi-synthetic experiments and analyses on real-world chest radiograph benchmarks where adjudicated labels are available, PU-DPO yields consistent gains in detection rates and recovery of hidden positives across multiple pathologies, and is more robust to omission noise than prior approaches.

cs.CV↗

arXiv2026

Causal Machine Learning Is Not a Panacea: A Roadmap for Observational Causal Inference in Health

Objective: The growing availability of large-scale observational clinical datasets and challenges in conducting randomized controlled trials have spurred enthusiasm in using causal machine learning (ML) for causal inference in observational data. We present a roadmap for applying causal ML to observational data. Materials and methods: We outline the importance of assessing validity assumptions within available data and applying causal ML responsibly for clinical experts using causal ML and ML practitioners with limited clinical expertise. Observations: Despite advances in causal ML, its limitations remain largely under-appreciated across disciplines. This gap in shared knowledge may impact the validity of findings. Discussion: Causal assumptions must be satisfied and modeling choices justified. Otherwise, these approaches risk producing biased or misleading results, with consequences for clinical research and patient care. Conclusion: Causal ML can be a powerful tool for generating causal hypotheses. We provide a template to strengthen the rigor and interpretability of causal analyses.

cs.LG↗

arXiv2026

One Loss to Rule Them All: Marked Time-to-Event for Structured EHR Foundation Models

Clinical events captured in Electronic Health Records (EHR) are irregularly sampled and may consist of a mixture of discrete events and numerical measurements, such as laboratory values or treatment dosages. The sequential nature of EHR, analogous to natural language, has motivated the use of next-token prediction to train prior EHR Foundation Models (FMs) over events. However, this training fails to capture the full structure of EHR. When a given event occurs must be captured, but the event value (abnormal lab) also modulates the likelihood of other clinical events. Most existing EHR FMs do not jointly model this likelihood and are unable to capture the full observation process, impacting downstream capabilities. We propose ORA, a marked time-to-event pretraining objective that jointly models event timing and associated measurements. Across multiple datasets, downstream tasks, and model backbones, this objective consistently yields more generalizable representations than next-token prediction and pretraining losses that ignore continuous measurements. Importantly, the proposed objective yields improvements beyond traditional classification evaluation, including better regression and time-to-event prediction. Beyond introducing a new family of FMs, our ablations suggest a broader takeaway: pretraining objectives that account for EHR structure are critical for expanding downstream capabilities and generalizability.

cs.LG↗

arXiv2026

A pipeline for enabling path-specific causal fairness in observational health data

When training machine learning (ML) models for potential deployment in a healthcare setting, it is essential to ensure that they do not replicate or exacerbate existing healthcare biases. Although many definitions of fairness exist, we focus on path-specific causal fairness, which allows us to better consider the social and medical contexts in which biases occur (e.g., direct discrimination by a clinician or model versus bias due to differential access to the healthcare system) and to characterize how these biases may appear in learned models. In this work, we map the structural fairness model to the observational healthcare setting and create a generalizable pipeline for training causally fair models. The pipeline explicitly considers specific healthcare context and disparities to define a target "fair" model. Our work fills two major gaps: first, we expand on characterizations of the "fairness-accuracy" tradeoff by detangling direct and indirect sources of bias and jointly presenting these fairness considerations alongside considerations of accuracy in the context of broadly known biases. Second, we demonstrate how a foundation model trained without fairness constraints on observational health data can be leveraged to generate causally fair downstream predictions in tasks with known social and medical disparities. This work presents a model-agnostic pipeline for training causally fair machine learning models that address both direct and indirect forms of healthcare bias.

cs.LG↗

arXiv2025

Aligning Probabilistic Beliefs under Informative Missingness: LLM Steerability in Clinical Reasoning

Large Language Models (LLMs) are increasingly deployed for clinical reasoning tasks, which inherently require eliciting calibrated probabilistic beliefs based on available evidence. However, real-world clinical data are frequently incomplete, with missingness patterns often informative of patient prognosis; for example, ordering a rare laboratory test reflects a clinician's latent suspicion. In this work, we investigate whether LLMs can be steered to leverage this informative missingness for prognostic inference. To evaluate how well LLMs align their verbalized probabilistic beliefs with an underlying target distribution, we analyze three common prompt-based interventions: explicit serialization, instruction steering, and in-context learning. We introduce a bias-variance decomposition of the log-loss to clarify the mechanisms driving gains in predictive performance. Using a real-world intensive care testbed, we find that while explicit structural steering and in-context learning can improve probabilistic alignment, the models do not natively leverage informative missingness without careful interventions.

cs.AI↗

arXiv2025

Learning-To-Measure: In-Context Active Feature Acquisition

Active feature acquisition (AFA) is a sequential decision-making problem where the goal is to improve model performance for test instances by adaptively selecting which features to acquire. In practice, AFA methods often learn from retrospective data with systematic missingness in the features and limited task-specific labels. Most prior work addresses acquisition for a single predetermined task, limiting scalability. To address this limitation, we formalize the meta-AFA problem, where the goal is to learn acquisition policies across various tasks. We introduce Learning-to-Measure (L2M), which consists of i) reliable uncertainty quantification over unseen tasks, and ii) an uncertainty-guided greedy feature acquisition agent that maximizes conditional mutual information. We demonstrate a sequence-modeling or autoregressive pre-training approach that underpins reliable uncertainty quantification for tasks with arbitrary missingness. L2M operates directly on datasets with retrospective missingness and performs the meta-AFA task in-context, eliminating per-task retraining. Across synthetic and real-world tabular benchmarks, L2M matches or surpasses task-specific baselines, particularly under scarce labels and high missingness.

cs.LG↗

arXiv2025

ADHAM: Additive Deep Hazard Analysis Mixtures for Interpretable Survival Regression

Survival analysis is a fundamental tool for modeling time-to-event outcomes in healthcare. Recent advances have introduced flexible neural network approaches for improved predictive performance. However, most of these models do not provide interpretable insights into the association between exposures and the modeled outcomes, a critical requirement for decision-making in clinical practice. To address this limitation, we propose Additive Deep Hazard Analysis Mixtures (ADHAM), an interpretable additive survival model. ADHAM assumes a conditional latent structure that defines subgroups, each characterized by a combination of covariate-specific hazard functions. To select the number of subgroups, we introduce a post-training refinement that reduces the number of equivalent latent subgroups by merging similar groups. We perform comprehensive studies to demonstrate ADHAM's interpretability at the population, subgroup, and individual levels. Extensive experiments on real-world datasets show that ADHAM provides novel insights into the association between exposures and outcomes. Further, ADHAM remains on par with existing state-of-the-art survival baselines in terms of predictive performance, offering a scalable and interpretable approach to time-to-event prediction in healthcare.

stat.ML↗

arXiv2025

CEHR-XGPT: A Scalable Multi-Task Foundation Model for Electronic Health Records

Electronic Health Records (EHRs) provide a rich, longitudinal view of patient health and hold significant potential for advancing clinical decision support, risk prediction, and data-driven healthcare research. However, most artificial intelligence (AI) models for EHRs are designed for narrow, single-purpose tasks, limiting their generalizability and utility in real-world settings. Here, we present CEHR-XGPT, a general-purpose foundation model for EHR data that unifies three essential capabilities - feature representation, zero-shot prediction, and synthetic data generation - within a single architecture. To support temporal reasoning over clinical sequences, CEHR-XGPT incorporates a novel time-token-based learning framework that explicitly encodes patients' dynamic timelines into the model structure. CEHR-XGPT demonstrates strong performance across all three tasks and generalizes effectively to external datasets through vocabulary expansion and fine-tuning. Its versatility enables rapid model development, cohort discovery, and patient outcome forecasting without the need for task-specific retraining.

cs.LG↗

arXiv2025

Path-specific effects for pulse-oximetry guided decisions in critical care

Identifying and measuring biases associated with sensitive attributes is a crucial consideration in healthcare to prevent treatment disparities. One prominent issue is inaccurate pulse oximeter readings, which tend to overestimate oxygen saturation for dark-skinned patients and misrepresent supplemental oxygen needs. Most existing research has revealed statistical disparities linking device measurement errors to patient outcomes in intensive care units (ICUs) without causal formalization. This study causally investigates how racial discrepancies in oximetry measurements affect invasive ventilation in ICU settings. We employ a causal inference-based approach using path-specific effects to isolate the impact of bias by race on clinical decision-making. To estimate these effects, we leverage a doubly robust estimator, propose its self-normalized variant for improved sample efficiency, and provide novel finite-sample guarantees. Our methodology is validated on semi-synthetic data and applied to two large real-world health datasets: MIMIC-IV and eICU. Contrary to prior work, our analysis reveals minimal impact of racial discrepancies on invasive ventilation rates. However, path-specific effects mediated by oxygen saturation disparity are more pronounced on ventilation duration, and the severity differs across datasets. Our work provides a novel pipeline for investigating potential disparities in clinical decision-making and, more importantly, highlights the necessity of causal methods to robustly assess fairness in healthcare.

cs.LG↗

arXiv2025

FoMoH: A clinically meaningful foundation model evaluation for structured electronic health records

Foundation models (FMs) promise to address core limitations of traditional supervised machine learning: (i) reliance on large amounts of labeled data, (ii) task specificity, and (iii) poor transportability. Despite methodological advances in structured electronic health record (EHR) foundation models, no systematic benchmark has validated whether these models meaningfully deliver on these promises. We introduce a benchmark of 14 clinically meaningful prediction tasks spanning patient prognosis and early diagnosis of acute and chronic conditions. We benchmark 6 state-of-the-art EHR FMs beyond population-level discrimination, emphasizing the need for evaluating their calibration and fairness, with rigorous controls for data contamination and reproducibility across more than 6 million patients from Columbia University Irving Medical Center and MIMIC-IV. Our benchmark identifies that FMs deliver on some of their promises. In particular, top-performing FMs outperform traditional baselines on discriminative performance, especially under limited labeled data, and exhibit more equitable performance across socio-medical groups. However, these models may underperform in low-prevalence settings, as pretraining losses may discard discriminative information about such conditions, and present lower calibration under limited labeled data. Further, cross-institutional transportability remains a challenge for structured EHR FMs. Together, these findings advance our understanding of EHR FMs' potential for clinical utility, highlight critical gaps that remain to be addressed, and provide a reproducible framework to track progress.

cs.LG↗

arXiv2025

ICYM2I: The illusion of multimodal informativeness under missingness

Multimodal learning is of continued interest in artificial intelligence-based applications, motivated by the potential information gain from combining different data modalities. However, modalities observed in the source environment may differ from the modalities observed in the target environment due to multiple factors, including cost, hardware failure, or the perceived \textit{informativeness} of a given modality. This change in missingness patterns between the source and target environment has not been carefully studied. Na{\"i}ve estimation of the information gain associated with including an additional modality without accounting for missingness may result in improper estimates of that modality's value in the target environment. We formalize the problem of missingness, demonstrate its ubiquity, and show that the subsequent distribution shift induces bias when the missingness process is not explicitly accounted for. To address this issue, we introduce ICYM2I (In Case You Multimodal Missed It), a framework for the evaluation of predictive performance and information gain under missingness through inverse probability weighting-based correction. We demonstrate the importance of the proposed adjustment to estimate information gain under missingness on synthetic, semi-synthetic, and real-world datasets.

cs.LG↗

arXiv2025

A Planning Framework for Adaptive Labeling

Ground truth labels/outcomes are critical for advancing scientific and engineering applications, e.g., evaluating the treatment effect of an intervention or performance of a predictive model. Since randomly sampling inputs for labeling can be prohibitively expensive, we introduce an adaptive labeling framework where measurement effort can be reallocated in batches. We formulate this problem as a Markov decision process where posterior beliefs evolve over time as batches of labels are collected (state transition), and batches (actions) are chosen to minimize uncertainty at the end of data collection. We design a computational framework that is agnostic to different uncertainty quantification approaches including those based on deep learning, and allows a diverse array of policy gradient approaches by relying on continuous policy parameterizations. On real and synthetic datasets, we demonstrate even a one-step lookahead policy can substantially outperform common adaptive labeling heuristics, highlighting the virtue of planning. On the methodological side, we note that standard REINFORCE-style policy gradient estimators can suffer high variance since they rely only on zeroth order information. We propose a direct backpropagation-based approach, Smoothed-Autodiff, based on a carefully smoothed version of the original non-differentiable MDP. Our method enjoys low variance at the price of introducing bias, and we theoretically and empirically show that this trade-off can be favorable.

cs.LG↗

arXiv2023

"Why did the Model Fail?": Attributing Model Performance Changes to Distribution Shifts

Machine learning models frequently experience performance drops under distribution shifts. The underlying cause of such shifts may be multiple simultaneous factors such as changes in data quality, differences in specific covariate distributions, or changes in the relationship between label and features. When a model does fail during deployment, attributing performance change to these factors is critical for the model developer to identify the root cause and take mitigating actions. In this work, we introduce the problem of attributing performance differences between environments to distribution shifts in the underlying data generating mechanisms. We formulate the problem as a cooperative game where the players are distributions. We define the value of a set of distributions to be the change in model performance when only this set of distributions has changed between environments, and derive an importance weighting method for computing the value of an arbitrary set of distributions. The contribution of each distribution to the total performance change is then quantified as its Shapley value. We demonstrate the correctness and utility of our method on synthetic, semi-synthetic, and real-world case studies, showing its effectiveness in attributing performance changes to a wide range of distribution shifts.

cs.LG↗

arXiv2022

Learning-to-defer for sequential medical decision-making under uncertainty

Learning-to-defer is a framework to automatically defer decision-making to a human expert when ML-based decisions are deemed unreliable. Existing learning-to-defer frameworks are not designed for sequential settings. That is, they defer at every instance independently, based on immediate predictions, while ignoring the potential long-term impact of these interventions. As a result, existing frameworks are myopic. Further, they do not defer adaptively, which is crucial when human interventions are costly. In this work, we propose Sequential Learning-to-Defer (SLTD), a framework for learning-to-defer to a domain expert in sequential decision-making settings. Contrary to existing literature, we pose the problem of learning-to-defer as model-based reinforcement learning (RL) to i) account for long-term consequences of ML-based actions using RL and ii) adaptively defer based on the dynamics (model-based). Our proposed framework determines whether to defer (at each time step) by quantifying whether a deferral now will improve the value compared to delaying deferral to the next time step. To quantify the improvement, we account for potential future deferrals. As a result, we learn a pre-emptive deferral policy (i.e. a policy that defers early if using the ML-based policy could worsen long-term outcomes). Our deferral policy is adaptive to the non-stationarity in the dynamics. We demonstrate that adaptive deferral via SLTD provides an improved trade-off between long-term outcomes and deferral frequency on synthetic, semi-synthetic, and real-world data with non-stationary dynamics. Finally, we interpret the deferral decision by decomposing the propagated (long-term) uncertainty around the outcome, to justify the deferral decision.

cs.LG↗

arXiv2022

Machine Learning for Health symposium 2022 -- Extended Abstract track

A collection of the extended abstracts that were presented at the 2nd Machine Learning for Health symposium (ML4H 2022), which was held both virtually and in person on November 28, 2022, in New Orleans, Louisiana, USA. Machine Learning for Health (ML4H) is a longstanding venue for research into machine learning for health, including both theoretical works and applied works. ML4H 2022 featured two submission tracks: a proceedings track, which encompassed full-length submissions of technically mature and rigorous work, and an extended abstract track, which would accept less mature, but innovative research for discussion. All the manuscripts submitted to ML4H Symposium underwent a double-blind peer-review process. Extended abstracts included in this collection describe innovative machine learning research focused on relevant problems in health and biomedicine.

cs.LG↗

arXiv2022

Towards Robust Off-Policy Evaluation via Human Inputs

Off-policy Evaluation (OPE) methods are crucial tools for evaluating policies in high-stakes domains such as healthcare, where direct deployment is often infeasible, unethical, or expensive. When deployment environments are expected to undergo changes (that is, dataset shifts), it is important for OPE methods to perform robust evaluation of the policies amidst such changes. Existing approaches consider robustness against a large class of shifts that can arbitrarily change any observable property of the environment. This often results in highly pessimistic estimates of the utilities, thereby invalidating policies that might have been useful in deployment. In this work, we address the aforementioned problem by investigating how domain knowledge can help provide more realistic estimates of the utilities of policies. We leverage human inputs on which aspects of the environments may plausibly change, and adapt the OPE methods to only consider shifts on these aspects. Specifically, we propose a novel framework, Robust OPE (ROPE), which considers shifts on a subset of covariates in the data based on user inputs, and estimates worst-case utility under these shifts. We then develop computationally efficient algorithms for OPE that are robust to the aforementioned shifts for contextual bandits and Markov decision processes. We also theoretically analyze the sample complexity of these algorithms. Extensive experimentation with synthetic and real world datasets from the healthcare domain demonstrates that our approach not only captures realistic dataset shifts accurately, but also results in less pessimistic policy evaluations.

cs.LG↗

arXiv2022

Counterfactually Guided Off-policy Transfer in Clinical Settings

Domain shift, encountered when using a trained model for a new patient population, creates significant challenges for sequential decision making in healthcare since the target domain may be both data-scarce and confounded. In this paper, we propose a method for off-policy transfer by modeling the underlying generative process with a causal mechanism. We use informative priors from the source domain to augment counterfactual trajectories in the target in a principled manner. We demonstrate how this addresses data-scarcity in the presence of unobserved confounding. The causal parametrization of our sampling procedure guarantees that counterfactual quantities can be estimated from scarce observational target data, maintaining intuitive stability properties. Policy learning in the target domain is further regularized via the source policy through KL-divergence. Through evaluation on a simulated sepsis treatment task, our counterfactual policy transfer procedure significantly improves the performance of a learned treatment policy when assumptions of "no-unobserved confounding" are relaxed.

cs.LG↗

arXiv2022

Generalizing Off-Policy Evaluation From a Causal Perspective For Sequential Decision-Making

Assessing the effects of a policy based on observational data from a different policy is a common problem across several high-stake decision-making domains, and several off-policy evaluation (OPE) techniques have been proposed. However, these methods largely formulate OPE as a problem disassociated from the process used to generate the data (i.e. structural assumptions in the form of a causal graph). We argue that explicitly highlighting this association has important implications on our understanding of the fundamental limits of OPE. First, this implies that current formulation of OPE corresponds to a narrow set of tasks, i.e. a specific causal estimand which is focused on prospective evaluation of policies over populations or sub-populations. Second, we demonstrate how this association motivates natural desiderata to consider a general set of causal estimands, particularly extending the role of OPE for counterfactual off-policy evaluation at the level of individuals of the population. A precise description of the causal estimand highlights which OPE estimands are identifiable from observational data under the stated generative assumptions. For those OPE estimands that are not identifiable, the causal perspective further highlights where more experimental data is necessary, and highlights situations where human expertise can aid identification and estimation. Furthermore, many formalisms of OPE overlook the role of uncertainty entirely in the estimation process.We demonstrate how specifically characterising the causal estimand highlights the different sources of uncertainty and when human expertise can naturally manage this uncertainty. We discuss each of these aspects as actionable desiderata for future OPE research at scale and in-line with practical utility.

cs.LG↗