arXiv subjects

Rishikesan Kamaleswaran

Publications and source records attributed to Rishikesan Kamaleswaran.

At least 19 recordsLinked to original sources

arXiv2026

A doctrine-grounded visual question answering dataset for Tactical Combat Casualty Care

Tactical Combat Casualty Care (TC3) requires responders to connect visual observations of injuries and interventions with established clinical guidance. Developing vision-language models to support this process requires supervision that links visible evidence to traceable doctrine. We present TC3-VQA, a dataset constructed from public instructional and field TC3 videos and authoritative TC3 documents. It contains 581 items spanning 11 concepts, with 1,860 questions covering intervention recognition, doctrine, clinical reasoning, procedural guidance, and refusal when visual information is insufficient. Doctrine-based answers preserve verbatim source passages and character offsets. Construction combines visual annotation, passage retrieval, entailment checks, and verification across model families. Equipment boxes, anatomical labels, temporal segments, and source metadata accompany the question-answer pairs. Automated audits and ratings by two physicians and two medical students characterize annotation quality, with human ratings available for 88 retained items. The dataset provides a resource for adapting vision-language models to TC3, studying the connection between visual evidence and clinical knowledge, and evaluating recognition, doctrine recall, and abstention.

cs.CV↗

arXiv2026

Intervention Granularity Matters: Coherent Treatment Bundles in Counterfactual Simulation with Clinical World Models

Counterfactual simulation with a clinical world model means fixing a patient's history, changing the treatment, and reading off the predicted response. Doing so requires deciding what counts as one intervention. In clinical settings, interventions are documented as bundles: a co-occurrence audit of 945,707 patient-hours from MIMIC-IV shows groups of components, such as every parameter of a dialysis circuit, that never appear apart, so an edit that changes one component on its own describes an hour that never occurs in the data. We hypothesize that the granularity at which an intervention is edited changes how a world model responds, and test this with Clin-JEPA, a latent world model of patient trajectories conditioned on hourly treatment text. At 1,019 documented onsets of invasive ventilation, we keep the patient's history and other treatments fixed and compare editing one ventilator setting with editing the complete configuration recorded for a real patient with the most similar recent trajectory. The complete bundle moves the predicted next state further than any single setting, consistently across all five settings, and the difference remains after accounting for how much each edit changes the model's input. Intervention granularity therefore materially affects the response of a clinical world model: single-component edits may understate treatment sensitivity, and bundle-aware editing may offer a better-supported basis for counterfactual treatment simulation.

cs.LG↗

arXiv2026

Clin-JEPA: A Multi-Phase Co-Training Framework for Joint-Embedding Predictive Pretraining on EHR Patient Trajectories

Joint-embedding predictive architectures (JEPA) learn representations by predicting in latent space, as in computer vision; retaining the action-conditioned predictor at inference turns them into latent world models, enabling planning in robotics (V-JEPA 2-AC). Bringing this design to EHR patient trajectories---a predictor that simulates a patient's trajectory in latent space---has not been explored. We use an LLM as the encoder, reading the hourly record as text, avoiding feature engineering and vocabulary harmonisation. But an LLM adapted by supervised fine-tuning does not organise its latent space around physiological dynamics, and freezing it to train the predictor, as in V-JEPA 2-AC, leaves the encoder unaware of the rollout signal: the predictor degrades under rollout. We instead co-train encoder and predictor under one latent-prediction objective, grounding the encoder in the dynamics its predictor must follow. Naïve co-training, however, is unstable: the untrained predictor drags the encoder toward collapse, and the predictor's rollout diverges as its target space moves. We present Clin-JEPA, a five-phase curriculum that stably co-trains an LLM encoder with a latent trajectory predictor on MIMIC-IV. Three evaluations support the design: (1) under 48-hour autoregressive rollout the co-trained predictor degrades least (predictor degradation $\times$1.06, against $\times$1.23--1.36 for two-stage designs and $\times$6.3--66 for curriculum ablations) while the co-trained encoder resolves the progression of patient state most sharply (largest state displacement); (2) the co-trained encoder separates deteriorating from stable patients in its latent space with Cohen's $d{=}1.59$, against $\leq$0.50 for two-stage encoders; (3) one set of embeddings serves 34 downstream tasks across three benchmarks, outperforming strong per-task tuned baselines and a pretrained EHR foundation model.

cs.LG↗

arXiv2026

Learning a Continuous Sepsis Severity Score Without Hour-by-Hour Supervision: A Two-Site Retrospective Study

Currently used sepsis severity indices rely on fixed variables and weights established decades ago, which are coarsely discretized and calibrated to a cohort that no longer reflects contemporary critical care. No alternative learned directly from patient trajectories is in routine use. We conducted a retrospective two-cohort study on a total of 29,116 and 7,691 adult patients meeting Sepsis-3 criteria from two hospital systems in Massachusetts and Georgie, respectively. We developed a sepsis index using 43 routinely charted variables over a 72-hour treatment window. Unlike previous studies, we use mortality as a treatment-level ranking signal rather than a per-state target, allowing credit to be redistributed non-uniformly across timesteps. Evaluation was done on a permanent 20% test holdout, using clinical vignettes and Spearman correlation. Uncertainty intervals were obtained by bootstrap resampling of whole patients. Under this ranking scheme, non-survivors scored 1.19-1.64 points higher than survivors on a 0-10 scale within all strata of baseline SOFA-2, with similar results stratifying within lactate, mean arterial pressure (MAP), and creatinine. Within-patient change in the index correlated with change in lactate (Spearman rho = 0.39; n = 1,854). Similar, weaker correlations were found for MAP and creatinine. On a cohort level, cross-institutional agreement measured by Spearman correlation between models trained on different sites, were 70-77% of same-site correlation. External within-patient correlations were 0.54 and 0.59 against ceilings of 0.92 and 0.90. Our index also correlated with established indices, while null controls stayed near zero. Our index demonstrated hourly prognostic information that meaningfully separates patient outcomes and is consistent with clinical expectation, indicating potential as a decision support tool complementing clinical judgement.

cs.AI↗

arXiv2026

Planner-Auditor Twin: Agentic Discharge Planning with FHIR-Based LLM Planning, Guideline Recall, Optional Caching and Self-Improvement

Objective: Large language models (LLMs) show promise for clinical discharge planning, but their use is constrained by hallucination, omissions, and miscalibrated confidence. We introduce a self-improving, cache-optional Planner-Auditor framework that improves safety and reliability by decoupling generation from deterministic validation and targeted replay. Materials and Methods: We implemented an agentic, retrospective, FHIR-native evaluation pipeline using MIMIC-IV-on-FHIR. For each patient, the Planner (LLM) generates a structured discharge action plan with an explicit confidence estimate. The Auditor is a deterministic module that evaluates multi-task coverage, tracks calibration (Brier score, ECE proxies), and monitors action-distribution drift. The framework supports two-tier self-improvement: (i) within-episode regeneration when enabled, and (ii) cross-episode discrepancy buffering with replay for high-confidence, low-coverage cases. Results: While context caching improved performance over baseline, the self-improvement loop was the primary driver of gains, increasing task coverage from 32% to 86%. Calibration improved substantially, with reduced Brier/ECE and fewer high-confidence misses. Discrepancy buffering further corrected persistent high-confidence omissions during replay. Discussion: Feedback-driven regeneration and targeted replay act as effective control mechanisms to reduce omissions and improve confidence reliability in structured clinical planning. Separating an LLM Planner from a rule-based, observational Auditor enables systematic reliability measurement and safer iteration without model retraining. Conclusion: The Planner-Auditor framework offers a practical pathway toward safer automated discharge planning using interoperable FHIR data access and deterministic auditing, supported by reproducible ablations and reliability-focused evaluation.

cs.AI↗

arXiv2025

SpikGPT: A High-Accuracy and Interpretable Spiking Attention Framework for Single-Cell Annotation

Accurate and scalable cell type annotation remains a challenge in single-cell transcriptomics, especially when datasets exhibit strong batch effects or contain previously unseen cell populations. Here we introduce SpikGPT, a hybrid deep learning framework that integrates scGPT-derived cell embeddings with a spiking Transformer architecture to achieve efficient and robust annotation. scGPT provides biologically informed dense representations of each cell, which are further processed by a multi-head Spiking Self-Attention mechanism for energy-efficient feature extraction. Across multiple benchmark datasets, SpikGPT consistently matches or exceeds the performance of leading annotation tools. Notably, SpikGPT uniquely identifies unseen cell types by assigning low-confidence predictions to an "Unknown" category, allowing accurate rejection of cell states absent from the training reference. Together, these results demonstrate that SpikGPT is a versatile and reliable annotation tool capable of generalizing across datasets, resolving complex cellular heterogeneity, and facilitating discovery of novel or disease-associated cell populations.

q-bio.QM↗

arXiv2025

Performance of Large Language Models in Answering Critical Care Medicine Questions

Large Language Models have been tested on medical student-level questions, but their performance in specialized fields like Critical Care Medicine (CCM) is less explored. This study evaluated Meta-Llama 3.1 models (8B and 70B parameters) on 871 CCM questions. Llama3.1:70B outperformed 8B by 30%, with 60% average accuracy. Performance varied across domains, highest in Research (68.4%) and lowest in Renal (47.9%), highlighting the need for broader future work to improve models across various subspecialty domains.

cs.CL↗

arXiv2025

Open-Source Agentic Hybrid RAG Framework for Scientific Literature Review

The surge in scientific publications challenges traditional review methods, demanding tools that integrate structured metadata with full-text analysis. Hybrid Retrieval Augmented Generation (RAG) systems, combining graph queries with vector search offer promise but are typically static, rely on proprietary tools, and lack uncertainty estimates. We present an agentic approach that encapsulates the hybrid RAG pipeline within an autonomous agent capable of (1) dynamically selecting between GraphRAG and VectorRAG for each query, (2) adapting instruction-tuned generation in real time to researcher needs, and (3) quantifying uncertainty during inference. This dynamic orchestration improves relevance, reduces hallucinations, and promotes reproducibility. Our pipeline ingests bibliometric open-access data from PubMed, arXiv, and Google Scholar APIs, builds a Neo4j citation-based knowledge graph (KG), and embeds full-text PDFs into a FAISS vector store (VS) using the all-MiniLM-L6-v2 model. A Llama-3.3-70B agent selects GraphRAG (translating queries to Cypher for KG) or VectorRAG (combining sparse and dense retrieval with re-ranking). Instruction tuning refines domain-specific generation, and bootstrapped evaluation yields standard deviation for evaluation metrics. On synthetic benchmarks mimicking real-world queries, the Instruction-Tuned Agent with Direct Preference Optimization (DPO) outperforms the baseline, achieving a gain of 0.63 in VS Context Recall and a 0.56 gain in overall Context Precision. Additional gains include 0.24 in VS Faithfulness, 0.12 in both VS Precision and KG Answer Relevance, 0.11 in overall Faithfulness score, 0.05 in KG Context Recall, and 0.04 in both VS Answer Relevance and overall Precision. These results highlight the system's improved reasoning over heterogeneous sources and establish a scalable framework for autonomous, agentic scientific discovery.

cs.IR↗

arXiv2025

Benchmarking Foundation Models with Multimodal Public Electronic Health Records

Foundation models have emerged as a powerful approach for processing electronic health records (EHRs), offering flexibility to handle diverse medical data modalities. In this study, we present a comprehensive benchmark that evaluates the performance, fairness, and interpretability of foundation models, both as unimodal encoders and as multimodal learners, using the publicly available MIMIC-IV database. To support consistent and reproducible evaluation, we developed a standardized data processing pipeline that harmonizes heterogeneous clinical records into an analysis-ready format. We systematically compared eight foundation models, encompassing both unimodal and multimodal models, as well as domain-specific and general-purpose variants. Our findings demonstrate that incorporating multiple data modalities leads to consistent improvements in predictive performance without introducing additional bias. Through this benchmark, we aim to support the development of effective and trustworthy multimodal artificial intelligence (AI) systems for real-world clinical applications. Our code is available at https://github.com/nliulab/MIMIC-Multimodal.

cs.LG↗

arXiv2025

CXR-TFT: Multi-Modal Temporal Fusion Transformer for Predicting Chest X-ray Trajectories

In intensive care units (ICUs), patients with complex clinical conditions require vigilant monitoring and prompt interventions. Chest X-rays (CXRs) are a vital diagnostic tool, providing insights into clinical trajectories, but their irregular acquisition limits their utility. Existing tools for CXR interpretation are constrained by cross-sectional analysis, failing to capture temporal dynamics. To address this, we introduce CXR-TFT, a novel multi-modal framework that integrates temporally sparse CXR imaging and radiology reports with high-frequency clinical data, such as vital signs, laboratory values, and respiratory flow sheets, to predict the trajectory of CXR findings in critically ill patients. CXR-TFT leverages latent embeddings from a vision encoder that are temporally aligned with hourly clinical data through interpolation. A transformer model is then trained to predict CXR embeddings at each hour, conditioned on previous embeddings and clinical measurements. In a retrospective study of 20,000 ICU patients, CXR-TFT demonstrated high accuracy in forecasting abnormal CXR findings up to 12 hours before they became radiographically evident. This predictive capability in clinical data holds significant potential for enhancing the management of time-sensitive conditions like acute respiratory distress syndrome, where early intervention is crucial and diagnoses are often delayed. By providing distinctive temporal resolution in prognostic CXR analysis, CXR-TFT offers actionable 'whole patient' insights that can directly improve clinical outcomes.

cs.LG↗

arXiv2025

Evaluating LLMs in Medicine: A Call for Rigor, Transparency

Objectives: To evaluate the current limitations of large language models (LLMs) in medical question answering, focusing on the quality of datasets used for their evaluation. Materials and Methods: Widely-used benchmark datasets, including MedQA, MedMCQA, PubMedQA, and MMLU, were reviewed for their rigor, transparency, and relevance to clinical scenarios. Alternatives, such as challenge questions in medical journals, were also analyzed to identify their potential as unbiased evaluation tools. Results: Most existing datasets lack clinical realism, transparency, and robust validation processes. Publicly available challenge questions offer some benefits but are limited by their small size, narrow scope, and exposure to LLM training. These gaps highlight the need for secure, comprehensive, and representative datasets. Conclusion: A standardized framework is critical for evaluating LLMs in medicine. Collaborative efforts among institutions and policymakers are needed to ensure datasets and methodologies are rigorous, unbiased, and reflective of clinical complexities.

cs.CL↗

arXiv2025

Contextual Phenotyping of Pediatric Sepsis Cohort Using Large Language Models

Clustering patient subgroups is essential for personalized care and efficient resource use. Traditional clustering methods struggle with high-dimensional, heterogeneous healthcare data and lack contextual understanding. This study evaluates Large Language Model (LLM) based clustering against classical methods using a pediatric sepsis dataset from a low-income country (LIC), containing 2,686 records with 28 numerical and 119 categorical variables. Patient records were serialized into text with and without a clustering objective. Embeddings were generated using quantized LLAMA 3.1 8B, DeepSeek-R1-Distill-Llama-8B with low-rank adaptation(LoRA), and Stella-En-400M-V5 models. K-means clustering was applied to these embeddings. Classical comparisons included K-Medoids clustering on UMAP and FAMD-reduced mixed data. Silhouette scores and statistical tests evaluated cluster quality and distinctiveness. Stella-En-400M-V5 achieved the highest Silhouette Score (0.86). LLAMA 3.1 8B with the clustering objective performed better with higher number of clusters, identifying subgroups with distinct nutritional, clinical, and socioeconomic profiles. LLM-based methods outperformed classical techniques by capturing richer context and prioritizing key features. These results highlight potential of LLMs for contextual phenotyping and informed decision-making in resource-limited settings.

q-bio.QM↗

arXiv2025

Improving Clinical Decision Support through Interpretable Machine Learning and Error Handling in Electronic Health Records

The objective of this work is to develop an Electronic Medical Record (EMR) data processing tool that confers clinical context to Machine Learning (ML) algorithms for error handling, bias mitigation and interpretability. We present Trust-MAPS, an algorithm that translates clinical domain knowledge into high-dimensional, mixed-integer programming models that capture physiological and biological constraints on clinical measurements. EMR data is projected onto this constrained space, effectively bringing outliers to fall within a physiologically feasible range. We then compute the distance of each data point from the constrained space modeling healthy physiology to quantify deviation from the norm. These distances, termed "trust-scores," are integrated into the feature space for downstream ML applications. We demonstrate the utility of Trust-MAPS by training a binary classifier for early sepsis prediction on data from the 2019 PhysioNet Computing in Cardiology Challenge, using the XGBoost algorithm and applying SMOTE for overcoming class-imbalance. The Trust-MAPS framework shows desirable behavior in handling potential errors and boosting predictive performance. We achieve an AUROC of 0.91 (0.89, 0.92 : 95% CI) for predicting sepsis 6 hours before onset - a marked 15% improvement over a baseline model trained without Trust-MAPS. Trust-scores emerge as clinically meaningful features that not only boost predictive performance for clinical decision support tasks, but also lend interpretability to ML models. This work is the first to translate clinical domain knowledge into mathematical constraints, model cross-vital dependencies, and identify aberrations in high-dimensional medical data. Our method allows for error handling in EMR, and confers interpretability and superior predictive power to models trained for clinical decision support.

cs.LG↗

arXiv2025

NeuroSep-CP-LCB: A Deep Learning-based Contextual Multi-armed Bandit Algorithm with Uncertainty Quantification for Early Sepsis Prediction

In critical care settings, timely and accurate predictions can significantly impact patient outcomes, especially for conditions like sepsis, where early intervention is crucial. We aim to model patient-specific reward functions in a contextual multi-armed bandit setting. The goal is to leverage patient-specific clinical features to optimize decision-making under uncertainty. This paper proposes NeuroSep-CP-LCB, a novel integration of neural networks with contextual bandits and conformal prediction tailored for early sepsis detection. Unlike the algorithm pool selection problem in the previous paper, where the primary focus was identifying the most suitable pre-trained model for prediction tasks, this work directly models the reward function using a neural network, allowing for personalized and adaptive decision-making. Combining the representational power of neural networks with the robustness of conformal prediction intervals, this framework explicitly accounts for uncertainty in offline data distributions and provides actionable confidence bounds on predictions.

cs.LG↗

arXiv2025

Sepsyn-OLCP: An Online Learning-based Framework for Early Sepsis Prediction with Uncertainty Quantification using Conformal Prediction

Sepsis is a life-threatening syndrome with high morbidity and mortality in hospitals. Early prediction of sepsis plays a crucial role in facilitating early interventions for septic patients. However, early sepsis prediction systems with uncertainty quantification and adaptive learning are scarce. This paper proposes Sepsyn-OLCP, a novel online learning algorithm for early sepsis prediction by integrating conformal prediction for uncertainty quantification and Bayesian bandits for adaptive decision-making. By combining the robustness of Bayesian models with the statistical uncertainty guarantees of conformal prediction methodologies, this algorithm delivers accurate and trustworthy predictions, addressing the critical need for reliable and adaptive systems in high-stakes healthcare applications such as early sepsis prediction. We evaluate the performance of Sepsyn-OLCP in terms of regret in stochastic bandit setting, the area under the receiver operating characteristic curve (AUROC), and F-measure. Our results show that Sepsyn-OLCP outperforms existing individual models, increasing AUROC of a neural network from 0.64 to 0.73 without retraining and high computational costs. And the model selection policy converges to the optimal strategy in the long run. We propose a novel reinforcement learning-based framework integrated with conformal prediction techniques to provide uncertainty quantification for early sepsis prediction. The proposed methodology delivers accurate and trustworthy predictions, addressing a critical need in high-stakes healthcare applications like early sepsis prediction.

cs.LG↗

arXiv2024

Detecting algorithmic bias in medical-AI models using trees

With the growing prevalence of machine learning and artificial intelligence-based medical decision support systems, it is equally important to ensure that these systems provide patient outcomes in a fair and equitable fashion. This paper presents an innovative framework for detecting areas of algorithmic bias in medical-AI decision support systems. Our approach efficiently identifies potential biases in medical-AI models, specifically in the context of sepsis prediction, by employing the Classification and Regression Trees (CART) algorithm with conformity scores. We verify our methodology by conducting a series of synthetic data experiments, showcasing its ability to estimate areas of bias in controlled settings precisely. The effectiveness of the concept is further validated by experiments using electronic medical records from Grady Memorial Hospital in Atlanta, Georgia. These tests demonstrate the practical implementation of our strategy in a clinical environment, where it can function as a vital instrument for guaranteeing fairness and equity in AI-based medical decisions.

stat.ML↗

arXiv2024

Meta-learning in healthcare: A survey

As a subset of machine learning, meta-learning, or learning to learn, aims at improving the model's capabilities by employing prior knowledge and experience. A meta-learning paradigm can appropriately tackle the conventional challenges of traditional learning approaches, such as insufficient number of samples, domain shifts, and generalization. These unique characteristics position meta-learning as a suitable choice for developing influential solutions in various healthcare contexts, where the available data is often insufficient, and the data collection methodologies are different. This survey discusses meta-learning broad applications in the healthcare domain to provide insight into how and where it can address critical healthcare challenges. We first describe the theoretical foundations and pivotal methods of meta-learning. We then divide the employed meta-learning approaches in the healthcare domain into two main categories of multi/single-task learning and many/few-shot learning and survey the studies. Finally, we highlight the current challenges in meta-learning research, discuss the potential solutions, and provide future perspectives on meta-learning in healthcare.

cs.LG↗

arXiv2024

Deep Representation Learning-Based Dynamic Trajectory Phenotyping for Acute Respiratory Failure in Medical Intensive Care Units

Sepsis-induced acute respiratory failure (ARF) is a serious complication with a poor prognosis. This paper presents a deep representation learningbased phenotyping method to identify distinct groups of clinical trajectories of septic patients with ARF. For this retrospective study, we created a dataset from electronic medical records (EMR) consisting of data from sepsis patients admitted to medical intensive care units who required at least 24 hours of invasive mechanical ventilation at a quarternary care academic hospital in southeast USA for the years 2016-2021. A total of N=3349 patient encounters were included in this study. Clustering Representation Learning on Incomplete Time Series Data (CRLI) algorithm was applied to a parsimonious set of EMR variables in this data set. To validate the optimal number of clusters, the K-means algorithm was used in conjunction with dynamic time warping. Our model yielded four distinct patient phenotypes that were characterized as liver dysfunction/heterogeneous, hypercapnia, hypoxemia, and multiple organ dysfunction syndrome by a critical care expert. A Kaplan-Meier analysis to compare the 28-day mortality trends exhibited significant differences (p < 0.005) between the four phenotypes. The study demonstrates the utility of our deep representation learning-based approach in unraveling phenotypes that reflect the heterogeneity in sepsis-induced ARF in terms of different mortality outcomes and severity. These phenotypes might reveal important clinical insights into an effective prognosis and tailored treatment strategies.

eess.SP↗