ClinTraceBench: Source-Verifiable Longitudinal Clinical Reasoning over EHR-Derived Dialogues

Clinical LLM assistants must reason over multi-visit patient trajectories, yet whether the compact history representations used to scale them---retrieval, structured timelines, LLM summaries, agentic memory---preserve the longitudinal signal clinical reasoning needs has not been measured. We introduce ClinTraceBench: 385 MIMIC-IV-derived verified dialogues with event-ID provenance, a nine-task taxonomy (T1--T9), and L0--L4 deterministic + L5 human-audit validation (98.92\% agreement). We evaluate eight history representation strategies---a no-context floor, \textit{last-visit-only}, \textit{full-context}, BGE-M3 \textit{dense-retrieval}, two compression schemes, and two agentic-memory systems (\textit{Mem0}, \textit{A-Mem})---across four backbones (DeepSeek-V3, GPT-4o-mini, Haiku~4.5, Sonnet~4.6) on 6{,}271 questions: 32 cells, 200{,}672 predictions. Four findings: (SP4) a controlled T3 injection probe isolates compression-induced \textit{relation} loss---with the attribution sentence present \textit{before} construction, \textit{Mem0}, \textit{A-Mem} and \textit{llm-summary} still recover only 0--5.3\% of the injected positives; (SP1) compressed strategies pay an aggregation tax on multi-visit trends and cross-patient comparisons; (SP2) the blind-to-full gap spans $+29.8$~pp (GPT-4o-mini) to $+62.7$~pp (Haiku); (SP3) abstention scales non-monotonically with context length. On the Pareto frontier Haiku dominates Sonnet under \textit{full-context} (\$25.76 vs.\ \$106.21), inverting the ``biggest backbone wins'' heuristic.

Scalable Clinical Data Infrastructure and Comparative ML Evaluation for Hospitalisation Risk Prediction in Elderly Patients with Multiple Long-Term Conditions using CPRD

Deep learning architectures are increasingly proposed for patient trajectory modeling in electronic health records (EHRs), yet their advantage over simpler, more interpretable models is rarely subjected to rigorous empirical scrutiny in real-world clinical settings. We present a comprehensive patient timeline pipeline applied to elderly patients in CPRD Aurum, incorporating 260 clinical conditions classified via a three-tier automated framework including specialised detection logic for 17 complex conditions. Using this infrastructure, we benchmark Temporal Graph Convolutional Neural Networks (TG-CNN) against Logistic Regression with LASSO regularisation and Random Forests for predicting 12-month all-cause emergency hospitalisation risk, motivated by (but not filtered to) the elevated risk of adverse drug reactions. Under cross-validation, TG-CNN achieves a marginally higher mean AUC-ROC than LASSO (0.712 vs. 0.705), whereas on the held-out test set LASSO achieves the highest discrimination of three models (AUC-ROC 0.733, versus 0.710 for Random Forest and 0.702 for TG-CNN). We show, that discrimination alone is an incomplete criterion for clinical deployment: after Platt calibration, LASSO is the only model with an acceptable calibration slope (0.817), while Random Forest (0.759) and, TG-CNN (0.391) remain substantially miscalibrated. We argue that LASSO, not the highest-discriminating model, is the model best suited to direct clinical deployment. We present lessons for the machine learning and healthcare community regarding data infrastructure, model selection, and value of calibration and interpretability in high-stakes decision support.

From Analytics to Tumor Boards: An Evidence-Linked Multi-Agent Workflow for Oncology Feature Extraction

Clinically relevant oncology information is distributed across heterogeneous, longitudinal documentation, creating substantial abstraction burden and requiring accurate attribution across specimens, tumors, biomarkers, and time points, while manual cancer-registry abstraction can require 27.2 minutes per case, highlighting the need for scalable methods that preserve clinical context while converting documentation into structured data. We evaluate an oncology information-extraction workflow in which OncoLens supplies multi-source, oncology-aware document selection, aggregation, and normalization from integrated EHRs, while the NimbleMind Multi-Agent System (nMAS) is a configurable oncology information-extraction workflow that extracts clinically relevant structured fields from fragmented oncology documentation. The extraction task uses a clinician-informed schema of 328 attributes spanning report metadata, diagnosis, staging, and cancer-type-specific information. nMAS separates clinician-defined field specifications from model execution and combines complexity-aware extraction, report-level consolidation, and source-grounded validation. The retrospective evaluation included 230 de-identified oncology documents from 40 patients and 418 clinician-reviewed document-field pairs containing 1,126 non-empty reference values. Evaluation focused on fields identified by clinicians as present in the source documents rather than exhaustively annotating all 328 schema fields. nMAS achieved a rank-weighted value-level precision of 82.6%, recall of 87.5%, and F1 of 85.0%, compared with an F1 of 66.4% for an independently implemented UMA-style MiniMax M2.5 comparator. These findings support the feasibility of using a configurable, source-grounded extraction workflow to convert fragmented oncology documentation into reusable structured data.

MultiSigBERT: Beyond Survival Analysis through Multimodal and Sequential Modeling in Oncology

Machine learning has become an essential component of modern healthcare, where the integration of heterogeneous data sources offers unprecedented opportunities to improve clinical decision-making. Electronic Health Records (EHR) contain complementary information -- including narrative clinical reports, numerical measurements, and structured variables -- yet most survival models remain limited to a single modality or fail to exploit the temporal nature of patient trajectories. We propose MultiSigBERT, a unified framework for multimodal sequential survival modeling in oncology based on path signature representations. Here, narrative medical reports (free-text) are converted into sentence embeddings by extracting and averaging contextual word embeddings. These representations are then compressed via modality-specific PCA and concatenated with structured covariates to form joint temporal trajectories which are then encoded using the Signature transform, a tool from Rough Paths theory that efficiently captures higher-order temporal interactions across modalities without supervision needed. The computed Signature features are finally incorporated as high dimensional features into a LASSO-regularized Cox model to estimate individualized risk scores. The performance of our novel MultiSigBERT pipeline is illustrated on the analysis of a real-world oncology cohort from the Léon Bérard Center, comprising over 120,000 medical reports and structured records from more than 2,500 patients. The model achieves a concordance index of 0.743 (sd 0.029) on an independent test set, demonstrating the benefit of jointly modeling multimodal temporal dynamics together with patient-level geometric structure for survival prediction.

ELICITED: EHR-grounded Longitudinal Interactive Conversations for Information-seeking Triage Evaluation and Decision-making

Emergency-department (ED) triage requires clinicians to rapidly identify patients who need immediate attention, determine who can safely wait, and prioritize limited clinical resources. At presentation, however, information may be limited to a chief complaint and initial vital signs. Clinically important details, including symptom onset and progression, associated symptoms, medical history, and medication use, are often obtained through focused conversation. Effective triage therefore requires clinicians to identify information gaps, ask appropriate follow-up questions, and update their assessment as new evidence becomes available. Most existing ED benchmarks evaluate acuity prediction from a fixed clinical snapshot. Although this formulation measures predictive performance after patient information has been assembled, it does not capture the interactive process through which triage-relevant evidence is elicited and interpreted. Existing medical dialogue datasets support the study of clinical communication, but dialogue statements are not always linked to temporally ordered events in the electronic health record (EHR). We introduce EHR2Dial-Triage, an agentic conversation-generation framework and benchmark grounded in MIMIC-IV-ED. The framework constructs triage conversations under explicit role-based and temporal information boundaries. Each accepted patient disclosure is linked to its supporting EHR event and the first dialogue turn at which it becomes available. EHR2Dial-Triage enables controlled evaluation of information elicitation, evidence use, five-level Emergency Severity Index prediction, and patient-facing communication across models and patient personas. It provides a structured setting for studying conversational triage as a dynamic process of clinical information acquisition, reasoning, and communication.

CliniCARE-Bench: Clinical Calibrated Audit of Medical Reasoning in EHR

Large language models perform strongly on medical knowledge benchmarks, but reliable clinical deployment requires agents to conduct defensible investigations over heterogeneous, longitudinal records: determining what evidence is needed, retrieving and reconciling structured and free-text data, grounding conclusions in verifiable evidence, and deferring cases that cannot be resolved reliably. We introduce CliniCARE-Bench (Clinical Calibrated Audit of Medical Reasoning in EHR), a benchmark for retrospective clinical audit: 25 clinician-validated scenarios instantiated as 750 patient-specific cases over real-patient-derived MIMIC-IV data. Systems investigate each case through a governed, logged tool environment for record retrieval, computation, and policy access, and return one of four verdicts---Yes, No, Indeterminate: Lack of Data, or Indeterminate: Medically Ambiguous---the last two separating missing evidence from residual medical ambiguity. Beyond verdict accuracy, we score patient-evidence and policy grounding, process adherence, calibrated abstention, reliability, and efficiency against case-level reference verdicts produced by independent multi-model adjudication and calibrated against Clinical Board review. Every retrieval, computation, and report is replayable, so the investigation trace is inspectable and scorable. To our knowledge, CliniCARE-Bench is the first deployment-oriented clinical-agent benchmark to jointly evaluate real longitudinal EHR investigation, claim-level evidence grounding, governing-policy use, process adherence, and calibrated abstention within a common patient-level adjudication framework. Across 16 agentic systems, four-way accuracy spans 65.3-76.1%, but raw accuracy overstates investigation quality. Defect-free accuracy, which credits a verdict only when correct and free of prohibited shortcuts, is 4.8-14.8 points lower and reorders the leaderboard.

A Comparative Study of Feature Selection Methods for EHR Diagnosis Codes in Opioid Use Disorder Prediction

Feature selection is a critical step in electronic health record (EHR)-based predictive modeling, where input variables are often high-dimensional, sparse, noisy, and redundant. Large feature sets not only increase computational burden and overfitting risk, but also make model interpretation difficult, leading to limited usefulness in clinical settings. In this study, we focus on diagnosis-related features and compare five feature selection paradigms for opioid use disorder (OUD) prediction: recurrence enrichment, NTK-motivated early gradient sensitivity, LightGBM-SHAP, Elastic Net, and large language model (LLM)-guided semantic selection. We use a unified preprocessing and evaluation framework and assess each method by downstream predictive performance, resampling stability, and representation of infrequent diagnosis codes. Our results demonstrate that performance improves with larger feature budgets with diminishing returns beyond a moderate size. NTK sensitivity provides the best overall balance of accuracy and stability, and LLM-guided selection contributes complementary clinically meaningful signals despite lower standalone performance.

Characterizing Treatment-Context Medication Evidence Across Clinic Notes and Structured EHR Medication History

Clinic notes and structured electronic health record (EHR) medication history often contain different medication information. Same-visit disagreement between these sources may result from note-side normalization errors, differences in terminology or timing, or actual differences in documentation. We developed a note-grounded approach that uses large language model (LLM) assisted reference construction, targeted and random human review, deterministic medication normalization, and semantic and temporal comparisons with structured medication history. We evaluated all normalization results on a patient-level held-out test set to limit adaptation to the study cohort. On 5,403 held-out mention rows, exact canonical agreement improved from 0.7226 with surface-exact matching to 0.8429 after lexical cleanup and curated alias mapping. In a random audit of previously unaudited rows, canonical-label agreement was 0.9210 among evaluable valid medication mentions, whereas treatment-action attribution was lower at 0.5326. In the full-cohort characterization analysis, only 16.44% of note-derived rows had same-visit exact overlap with structured medication history, but 55.17% had same-visit semantic overlap, 90.34% had same-visit or +/-30-day overlap, and only 3.97% remained in the strict no-structured-overlap bucket under broad project-level mapping. An ontology-backed sensitivity analysis further showed that held-out strict Observational Medical Outcomes Partnership (OMOP)-backed no-overlap fell from 43.99% to 36.68% after a development-derived alias supplement. These results show that note-to-structured-medication mismatch can arise from normalization errors, differences in terminology, and differences in documentation timing.

xMICD: Explainable Representation of Multiple ICD Codes

Electronic Health Records (EHRs) are widely used for clinical risk prediction using machine learning. International Classification of Diseases (ICD) codes provide structured information about patient diagnoses, but representing them effectively remains challenging. Existing approaches often face a trade-off between predictive performance and interpretability: grouping-based representations are interpretable but may lose information, while embedding-based representations achieve strong predictive performance but are difficult to interpret. We propose Explainable Representation of Multiple ICD Codes (xMICD), a method for constructing low-dimensional patient representations from sets of ICD codes. xMICD combines clinically meaningful diagnostic groupings with similarity in a pre-trained ICD embedding space. Instead of using binary group membership, the method assigns codes to groups via similarity-based relative assignments, yielding features that reflect how closely a patient's diagnoses align with each clinical group. Experiments on large-scale EHR datasets demonstrate that xMICD achieves predictive performance comparable to embedding-based representations such as ICD2Vec across multiple clinical prediction tasks. At the same time, the resulting features remain clinically interpretable because each dimension corresponds to a recognizable diagnostic group. xMICD therefore provides a practical way to integrate embedding-based semantic relationships into interpretable clinical feature spaces for machine learning models.

UIC-AIHealth4All at ArchEHR-QA 2026: Answer-First Evidence Grounding for Clinical Question Answering

We describe the UIC-AIHealth4All system for ArchEHR-QA 2026, a shared task on grounded question answering from electronic health records. We participated in Subtasks 2 (evidence identification), 3 (answer generation), and 4 (answer-evidence alignment). For Subtasks 2 and 3, we propose an answer-first pipeline in which the model generates candidate answers citing specific note sentences before classifying the full evidence set, exploiting the asymmetry between judging relevance in the abstract versus relative to a generated answer. For Subtask 4, we apply self-consistency voting over five independent model calls, retaining links by vote threshold. Our pipeline ranked third on evidence identification (Strict Micro F1 62.90), ninth on answer generation (Overall 31.90), and fifth on answer-evidence alignment (F1 79.81). A post-hoc linguistic analysis of 45 stylistic features reveals that model outputs remain 3.2 Flesch-Kincaid grade levels harder to read than clinician-authored references despite matching their word and sentence counts, suggesting readability warrants explicit optimization in clinical NLP systems. Code and prompts are available at https://github.com/mo-arvan/archehr-qa-2026-uic-aihealth4all.

Evidence-Grounded AI for Musculoskeletal Care

Musculoskeletal diseases are among the leading causes of disability worldwide and create the greatest global need for rehabilitation. Because recovery, remodelling and degeneration often unfold over months to years, musculoskeletal care requires longitudinal management that repeatedly integrates evolving patient evidence, external medical knowledge and stage-specific functional goals. In routine practice, this evidence is fragmented across visits, departments and hospital systems, limiting individualized, evidence-based care. Here we report OrthoPilot, a clinical artificial intelligence system powered by a large language model that integrates hospital data streams with authoritative external knowledge for continuous musculoskeletal management. OrthoPilot autonomously retrieves real-time imaging, laboratory, pathology and order data and converts evolving patient states into evidence-based decisions from admission diagnosis to rehabilitation planning. We established a specialist-validated benchmark from real-world electronic health records spanning 1,000 disease codes. In a reader study across the complete care pathway, OrthoPilot was compared with 81 orthopaedic physicians and surpassed experts with 25 years of experience in diagnostic reasoning, clinical decision-making and management planning. It also outperformed all evaluated intelligent systems across 60 external clinical centres. In a prospective study of 1,870 complex cases, OrthoPilot increased full-chain management success by 10.6%. During an 8-month randomised deployment involving 8,240 inpatients, it increased cumulative cases per bed by 9.7% and improved patient-reported access to health information. These results move clinical AI from predicting isolated events toward executing longitudinal management across complete musculoskeletal care pathways.

Multimodal Routing for Interpretable, Robust, and Auditable Clinical Prediction

Electronic health record (EHR) data are inherently multimodal, and leveraging multiple modalities can improve predictive performance. However, most existing approaches rely on deep fusion, which obscures how individual modalities contribute to predictions and limits the interpretability of multimodal reasoning. We propose an explicit multimodal routing framework for clinical prediction that enables interpretable, robust, and auditable reasoning across three EHR modalities: structured longitudinal variables (L), clinical notes (N), and chest X-rays (I). Our model constructs discrete unimodal, directional bimodal, and trimodal routes to capture both individual modality signals and asymmetric cross-modal interactions. To audit multimodal reasoning and assess robustness, we introduce inference-time route masking, which simulates missing modalities and reweights the remaining routes without retraining. We analyze changes in performance and routing weights under these scenarios to understand model decision-making. We evaluate our framework on multi-label phenotype prediction (K = 25) and binary ICU mortality prediction using trimodal patient stays from MIMIC-IV, revealing systematic differences in modality reliance across clinical condition groups. Overall, our framework offers a transparent, auditable, and practical approach to multimodal clinical prediction, providing interpretability, robustness, and insights into how different data sources drive model decisions.

LongMedBench: Benchmarking Medical Agents for Long-Horizon Clinical Decision-Making

In this work, we introduce LongMedBench, a real-world EHR-based benchmark for long-horizon clinical decision-making. Prior evaluations of LLM-based medical agents have largely emphasized short-context knowledge QA and tool use. However, real-world medical care is inherently longitudinal, and clinicians must aggregate evidence across repeated visits, tests, and evolving treatments. Therefore, long-horizon interaction is essential for realistic assessment. LongMedBench is constructed via a reproducible pipeline that integrates MIMIC-IV admission records and clinical notes into time-series event streams and long-context memory datasets, enabling long-horizon, multi-session interactions between agents and a clinical environment. It comprises 335 patients, with 19.72 inpatient visits per patient on average and 44.91 medical events per visit. Guided by the long-horizon decision process, we propose an evaluation taxonomy with three suites: fact-based QA, temporal reasoning, and long-horizon decision-making. This taxonomy measures how agents understand and leverage historical patient information over extended horizons. Our experiments show that while recent LLMs can make good use of explicit timestamps, they have challenges in implicit time inference; The RAG and agent memory system can improve the performance of information retrieval tasks, but the performance of decision-making tasks is highly dependent on the model's immediate context.

Primary ICD Category Prediction using LLM-based Probing

Objective: ICD codes are central to reimbursement, research, and population health surveillance, yet automated coding systems often struggle to integrate diagnostic signals from both clinical narratives and structured electronic health record (EHR) variables. We evaluated whether frozen medical large language model (LLM) representations can serve as a shared embedding space for multimodal primary diagnosis category prediction. Materials and Methods: We constructed a MIMIC-IV cohort of 13,645 admissions from the 10 most frequent primary ICD-10 codes, consolidated into seven categories. Structured variables were serialized into clinical narratives and combined with leakage-pruned discharge notes. Using a frozen MedFound-Llama3-8B-finetuned backbone, we extracted hidden states from five transformer layers and trained linear probes for structured-only, unstructured-only, and combined inputs, comparing against XGBoost and information-matched PLM-ICD baselines and evaluating MIMIC-III adaptation with a compact bottleneck adapter. Results: The combined probe performed best on MIMIC-IV (87.69% strict; 91.45% medical accuracy), exceeding both single-modality probes and baselines. The structured-only probe outperformed its standard baseline by 6.19 points in medical accuracy. Diagnostic information became increasingly linearly separable in deeper layers, and a 2M-parameter adapter restored cross-dataset transfer to MIMIC-III using only 5% of target labels. Discussion: LLM embeddings can unify structured and narrative EHR information for multimodal diagnosis prediction, supporting efficient reuse of clinical representations across modalities and datasets through a small representation-level module. Conclusion: Multimodal probing of frozen medical LLM representations provides a practical approach for studying EHR modalities and adapting clinical representations across datasets.

Improving Patient Subtyping on Longitudinal Data using Representations from Mamba-based Architecture

Effective sub-typing (also known as grouping or clustering) of patients using their electronic health record (EHR) data can greatly inform precision medicine efforts. However, subtyping temporal EHR datasets is known to be challenging due to inherent EHR issues, including complexity and irregularity. In this study, we propose a self-supervised Mamba-based model that learns effective EHR representations and enables enhanced patient subtyping. We evaluate the proposed model on public and private real-world EHR datasets to classify the data based on the available labels and subtype patients based on the representations learned from the model. Through an extensive set of experiments, we demonstrate that our model's design choices lead to better performance compared to competitive baseline models for prediction. Moreover, we evaluate several clustering techniques to demonstrate that our findings offer valuable insights into subtyping patients based on temporal records from EHR models\footnote{Our implementations are available at https://github.com/healthylaife/triplet_mamba.

Are LLMs Ready to Assist Physicians? PhysAssistBench for Interactive Doctor-Patient-EHR Assistance

The most plausible near-term role of medical LLMs is to assist rather than replace physicians, yet current evaluations often test isolated capabilities: clinical knowledge, EHR system interaction, or patient communication. Physician assistance instead requires coordinating these capabilities within the same interaction, where physicians issue underspecified requests, patients describe symptoms ambiguously, and EHR systems demand precise tool use. We introduce PhysAssistBench, a benchmark for interactive doctor-patient-EHR assistance. Built from real MIMIC-IV cases, PhysAssistBench uses a scalable pipeline to construct agentic patients: interactive, record-grounded agents that turn static EHR records into multi-turn clinical scenarios while preserving clinical factuality. PhysAssistBench provides a curated bilingual evaluation set of 1,296 manually reviewed and physician-validated turns. Experiments with leading LLMs show that current models remain unreliable in this setting, which exposes a key bottleneck for clinical LLMs: reliable assistance requires coordination across knowledge, communication, and systems, not isolated gains in any of them.

AIPatient Arena: EHR-grounded evaluation of large language models in end-to-end clinical consultation workflows

Large language models (LLMs) are increasingly considered for use in clinical consultation tasks, yet most medical evaluations remain static, single-turn, or narrowly outcome-based, limiting their ability to reflect the sequential, uncertain, and interactive nature of real-world care. Here, we propose AIPatient Arena, an EHRs-grounded evaluation framework for assessing the clinical utility of LLMs across eight dimensions of clinical competence. The framework integrates EHR data into patient-specific knowledge graphs, enabling multi-turn physician-patient interactions. We applied AIPatient Arena on a primary cohort of 437 patients and two out-of-distribution validation cohorts of 119 and 67 patients. We observe that LLMs performed well in medical interview questioning skills (QS; mean scores, 4.43-4.99/5), ethical and professional conduct (ET; 4.38-4.93/5), and clarity and transparency of clinical explanations (EX; 3.80-4.72/5). Performance was moderate in information integration (II; 3.19-4.21/5) and medication safety and justification (MS; 3.13-3.78/5), but persistent weaknesses were observed in handling of ambiguous patient responses (HR; 2.57-3.32/5), information coverage (IC; 2.08-3.02/5), and diagnostic accuracy and reasoning (Dx; 2.63-3.55/5). Process-based evaluation revealed recurrent interaction failures, including repetitive questioning, omission of past medical history, and inadequate handling of uncertainty. Richer conversational context improved diagnostic reasoning but yielded limited gains in treatment planning. These findings indicate that final-answer accuracy alone is insufficient for evaluating clinical readiness and highlight the importance of assessing how models gather, interpret, and communicate information throughout a consultation. AIPatient Arena provides an EHR-grounded framework for workflow-oriented pre-deployment evaluation of medical LLMs.

CAP: Towards PPG Universal Representation Learning with Patient-level Supervision

Photoplethysmography (PPG) plays a central role in wearable health monitoring and clinical decision support. Yet existing approaches to universal PPG representation learning largely focus on signal-level objectives and often overlook patient-level health context, which limits generalization to complex clinical tasks and heterogeneous cohorts. To address this gap, we construct a large-scale paired PPG-EHR multimodal dataset by distilling fragmented medical histories and clinical records into cohesive, patient-level electronic health records (EHR). Building on this resource, we propose Clinical Anchored Pretraining for PPG (CAP). During pretraining, CAP performs cross-modal contrastive alignment that anchors PPG representations to patient-level clinical semantics, guiding the encoder beyond waveform fitting toward modeling consistency in a patient's overall physiological state. During downstream adaptation, the pretrained PPG encoder provides clinically grounded representations that strengthen inductive bias and improve robustness and transferability. Experiments demonstrate that CAP consistently outperforms strong baselines on four diverse downstream tasks. CAP achieves a particularly large gain on respiratory rate prediction (up to +87.6% relative improvement over the state-of-the-art baseline) and delivers an average relative +26.7% across all tasks. We further enhance the interpretability of our approach through comprehensive analyses, including ablations and multiple complementary visualizations of the learned representations. The code for our experiments is available at: https://github.com/gody123gody/CAP .

Curation of a Cardiology Interface Terminology for Highlighting Electronic Health Records using Machine Learning

Electronic health record (EHR) notes are dense medical documents containing large amounts of information, often filled with complex medical jargon. Highlighting all details in EHRs helps reduce the likelihood of missing crucial information by drawing attention to key content. This study proposes the design of a Cardiology Interface Terminology (CIT) to accurately highlight all details in EHR notes of cardiology patients. We introduce an innovative Machine Learning (ML) technique for the design of CIT. The ML technique requires training data. Manual preparation of such training data is time-consuming and expensive. The process of the CIT design includes three phases. In the first two phases, we innovatively derive a training data CIT to be used by the third phase, ML technique. We start by designing an initial CIT, composed of several components: the cardiology-related sub-hierarchies of SNOMED, other SNOMED concepts mined from EHRs of build set, and necessary components of terms e.g., medical abbreviations and medications. Utilizing an iterative process, fine-grained phrases containing initial CIT concepts are extracted from build set as CIT concept candidates. The candidate concepts are semi-automatically reviewed before being added to CIT, yielding the training data CIT, TCIT. In the third phase, a ML model is trained with TCIT to identify candidates fitting to be concepts in the CIT. This model is used to extract further concepts from build set, yielding the final CIT. The final CIT is then used to highlight the test set and evaluate the extent to which it captures details in an unseen EHR dataset. For this purpose, four evaluation metrics, coverage, breadth, completeness, and conciseness are used. The highlighted test set has a coverage of 74.21%, with a breadth of 1.68. For 20 random notes in test set, the average completeness is 98.2% and average conciseness is 84.2%.

Trajectory-Aware Clinical Risk Prediction via Severity-Grounded Knowledge Graphs and Retrieval-Augmented Generation

While Electronic Health Records (EHRs) offer a wealth of clinical data, effectively augmenting a patient's records with heterogeneous external knowledge to predict the patient's clinical risk remains a significant challenge. Existing methods fail to capture disease severity, treatment responses, and nuanced clinical progression, due to data sparsity and the underutilization of unstructured clinical notes. To address these challenges, we propose TRACER (a trajectory-aware and clinically grounded prediction framework) that (1) constructs a medical knowledge graph enriched with severity information from medical literature, (2) retrieves clinically relevant, severity-weighted paths of a patient's progression from the knowledge graph, (3) extracts clinically relevant events from unstructured clinical notes, and (4) augments patient context with similar peer cases. Experiments on the MIMIC-III and MIMIC-IV datasets demonstrate large gains over state-of-the-art baselines, with up to 28.5% increase in Macro F1 score for the mortality prediction task, and 19.7% increase for the readmission prediction task.

ClinEnv: An Interactive Multi-Stage Long Horizon EHR Environment for Agents

Clinical practice is not the selection of an answer from enumerated options: a physician gathers heterogeneous information incrementally and commits to sequential, irreversible decisions under uncertainty. Static benchmarks cannot probe and existing interactive medical benchmarks each compromise on at least one of them. We present ClinEnv, an interactive benchmark that evaluates LLMs as attending physicians over real inpatient admissions under a paradigm we term Longitudinal Inpatient Simulation. Each case is automatically constructed into an ordered sequence of decision stages; at every stage the model must actively query four specialized agents before committing to medications, procedures, and diagnoses. ClinEnv scores both what the model decides, through deterministic ontology-grounded matching, and how it gathers information. Across seven models, the strongest reaches only 0.31 decision F1, and outcome quality is sharply decoupled from process quality. Difficulty concentrates in management decisions and later stages, where models recover discharge diagnoses far more reliably than management actions (0.51 vs. 0.17 F1) and continue to issue redundant queries as cases progress. ClinEnv makes this information-acquisition gap, invisible to outcome-only evaluation, directly measurable.

ChronoMedicalWorld: A Medical World Model for Learning Patient Trajectories from Longitudinal Care Data

Long-horizon clinical simulation -- predicting how a patient's physiology evolves over years under specified interventions -- is central to chronic-disease care, yet existing electronic health record (EHR) models are predominantly discriminative, and general-purpose large language models drift under repeated interventions. We propose the \textbf{ChronoMedicalWorld Model (CMWM)}, an action-conditioned latent world-model framework for learning patient trajectories from longitudinal care data. CMWM couples a joint-embedding state encoder with a wide action encoder that admits both structured intervention indicators and free-text communication embeddings, and trains a recurrent latent transition module under a six-term objective: next-observation supervision, next-latent prediction, SIGReg latent regularisation, and three physiology-aware shape priors (slope, continuity, large-jump penalty). A closed-loop rollout-prefix protocol matches training to deployment, so the model is optimised against the same multi-step error it exhibits at inference. As a concrete case study, we instantiate CMWM for annual estimated glomerular filtration rate (eGFR) trajectory forecasting in chronic kidney disease (CKD). On a 2{,}232-patient nephrology cohort, the CKD instantiation achieves a dynamic-50\% history rollout test mean absolute error (MAE) of 7.384 and root-mean-square error (RMSE) of 10.256, against 7.964 and 11.069 for a tuned GPT-5.5 structured-prompting baseline ($-7.28\%$ MAE, $-7.35\%$ RMSE), with the gain dominated by the dialogue portion of patient--health-coach communication. The framework is not CKD-specific: its architecture, loss design, and training protocol apply to any chronic condition that can be cast as periodic clinical state interleaved with structured and conversational interventions.

Joint Treatment Effect Estimation from Incomplete Healthcare Data: Temporal Causal Normalizing Flows with LLM-driven Evolutionary MNAR Imputation

Target trial emulation (TTE) enables causal questions to be studied with observational data when randomized controlled trials (RCTs) are infeasible. Yet treatment-effect methods often address causal estimation, missingness, and temporal structure separately, limiting their robustness in electronic health records (EHRs), where time-varying confounding and missing-not-at-random (MNAR) biomarkers can reach 50%--80%. We propose a two-stage pipeline for treatment effect estimation from incomplete longitudinal EHRs. First, CausalFlow-T, a directed acyclic graph (DAG)-constrained normalizing flow with long short-term memory (LSTM)-encoded patient history, performs exact invertible counterfactual inference, avoiding approximation errors from variational inference and separating confounding through explicit causal structure. Ablations on four synthetic and one semi-synthetic benchmark with known counterfactuals show that DAG constraints and exact inference address distinct failure modes: neither compensates for the other. Second, because CausalFlow-T requires completed inputs, we introduce an LLM-driven evolutionary imputer that proposes executable imputation operators rather than individual entries, and evaluate it with three large language model (LLM) backends, including two open-source models. Across 30%--80% MNAR missingness, this imputer achieves the best pooled rank over biomarker and causal metrics, leading in point-wise accuracy and temporal extrapolation while preserving average treatment effect (ATE) recovery as statistical baselines degrade. On Swiss primary-care EHRs from adults with type 2 diabetes initiating a GLP-1 receptor agonist or SGLT-2 inhibitor, the pipeline estimates a per-protocol weight-loss difference of -0.98 kg [95% CI -1.01, -0.96] favoring GLP-1 receptor agonists, consistent with randomized evidence and obtained from realistically incomplete real-world EHRs.

PhysicianBench: Evaluating LLM Agents in Real-World EHR Environments

We introduce PhysicianBench, a benchmark for evaluating LLM agents on physician tasks grounded in real clinical setting within electronic health record (EHR) environments. Existing medical agent benchmarks primarily focus on static knowledge recall, single-step atomic actions, or action intent without verifiable execution against the environment. As a result, they fail to capture the long-horizon, composite workflows that characterize real clinical systems. PhysicianBench comprises 100 long-horizon tasks adapted from real consultation cases between primary care and subspecialty physicians, with each task independently reviewed by a separate panel of physicians. Tasks are instantiated in an EHR environment with real patient records and accessed through the same standard APIs used by commercial EHR vendors. Tasks span 21 specialties (e.g., cardiology, endocrinology, oncology, psychiatry) and diverse workflow types (e.g., diagnosis interpretation, medication prescribing, treatment planning), requiring an average of 27 tool calls per task. Solving each task requires retrieving data across encounters, reasoning over heterogeneous clinical information, executing consequential clinical actions, and producing clinical documentation. Each task is decomposed into structured checkpoints (670 in total across the benchmark) capturing distinct stages of completion graded by task-specific scripts with execution-grounded verification. Across 13 proprietary and open-source LLM agents, the best-performing model achieves only 46% success rate (pass@1), while open-source models reach at most 19%, revealing a substantial gap between current agent capabilities and the demands of real-world clinical workflows. PhysicianBench provides a realistic and execution-grounded benchmark for measuring progress toward autonomous clinical agents.

End-to-End Evaluation and Governance of an EHR-Embedded AI Agent for Clinicians

Clinical AI systems require not just point-in-time evaluation but continuous governance: the ongoing practice of monitoring, evaluating, iterating, and re-evaluating performance throughout deployment. We present an end-to-end framework of governance that integrates rubric validation, live deployment feedback, technical performance monitoring, and cost tracking, with controlled experimentation gating system changes before deployment. Applied to Hyperscribe, an EHR-embedded agent that converts ambient audio into structured chart updates, twenty clinicians authored 1,646 validated rubrics across 823 cases. Seven Hyperscribe versions were evaluated through controlled experiments, with median scores improving from 84% to 95%. Analysis of 107 live feedback entries over three months showed feedback composition shifting from 79% error reports and 14% positive observations to 30% errors and 45% positive observations as engineering interventions resolved failures. Median processing time per audio segment was 8.1 seconds with a 99.6% effective completion rate after retry mechanisms absorbed transient model errors. These results demonstrate that continuous, multi-channel governance of deployed clinical AI is both achievable and effective.

HealthNLP_Retrievers at ArchEHR-QA 2026: Cascaded LLM Pipeline for Grounded Clinical Question Answering

Patient portals now give individuals direct access to their electronic health records (EHRs), yet access alone does not ensure patients understand or act on the complex clinical information contained in these records. The ArchEHR-QA 2026 shared task addresses this challenge by focusing on grounded question answering over EHRs, and this paper presents the system developed by the HealthNLP_Retrievers team for this task. The proposed approach uses a multi-stage cascaded pipeline powered by the Gemini 2.5 Pro large language model to interpret patient-authored questions and retrieve relevant evidence from lengthy clinical notes. Our architecture comprises four integrated modules: (1) a few-shot query reformulation unit which summarizes verbose patient queries; (2) a heuristic-based evidence scorer which ranks clinical sentences to prioritize recall; (3) a grounded response generator which synthesizes professional-caliber answers restricted strictly to identified evidence; and (4) a high-precision many-to-many alignment framework which links generated answers to supporting clinical sentences. This cascaded approach achieved competitive results. Across the individual tracks, the system ranked 1st in question interpretation, 5th in answer generation, 7th in evidence identification, and 9th in answer-evidence alignment. These results show that integrating large language models within a structured multi-stage pipeline improves grounding, precision, and the professional quality of patient-oriented health communication. To support reproducibility, our source code is publicly available in our GitHub repository

Case-Specific Rubrics for Clinical AI Evaluation: Methodology, Validation, and LLM-Clinician Agreement Across 823 Encounters

Objective. Clinical AI documentation systems require evaluation methodologies that are clinically valid, economically viable, and sensitive to iterative changes. Methods requiring expert review per scoring instance are too slow and expensive for safe, iterative deployment. We present a case-specific, clinician-authored rubric methodology for clinical AI evaluation and examine whether LLM-generated rubrics can approximate clinician agreement. Materials and Methods. Twenty clinicians authored 1,646 rubrics for 823 clinical cases (736 real-world, 87 synthetic) across primary care, psychiatry, oncology, and behavioral health. Each rubric was validated by confirming that an LLM-based scoring agent consistently scored clinician-preferred outputs higher than rejected ones. Seven versions of an EHR-embedded AI agent for clinicians were evaluated across all cases. Results. Clinician-authored rubrics discriminated effectively between high- and low-quality outputs (median score gap: 82.9%) with high scoring stability (median range: 0.00%). Median scores improved from 84% to 95%. In later experiments, clinician-LLM ranking agreement (tau: 0.42-0.46) matched or exceeded clinician-clinician agreement (tau: 0.38-0.43), attributable to both ceiling compression and LLM rubric improvement. Discussion. This convergence supports incorporating LLM rubrics alongside clinician-authored ones. At roughly 1,000 times lower cost, LLM rubrics enable substantially greater evaluation coverage, while continued clinical authorship grounds evaluation in expert judgment. Ceiling compression poses a methodological challenge for future inter-rater agreement studies. Conclusion. Case-specific rubrics offer a path for clinical AI evaluation that preserves expert judgment while enabling automation at three orders lower cost. Clinician-authored rubrics establish the baseline against which LLM rubrics are validated.