clinical informatics teams

Abstract: Purpose: Retrieval-augmented generation (RAG) can introduce electrocardiogram (ECG) criteria that lack patient-specific measurement support. This study evaluates the reliability of retrieved diagnostic criteria in AI-generated ECG reports. Methods: We analyzed 1,083 human-validated PTB-XL patient records using a library of 47 criteria cards, including 33 without numeric verification rules. Language models generated structured reports with and without retrieval. Criterion applicability was evaluated using Marquette 12SL measurements, with independent assessment using Uni-G and comparison against expert-validated diagnostic labels. Results: Keyword retrieval introduced untestable or measurement-disconfirmed criteria in 46.8% of GPT-4.1-mini reports. A deterministic verification rule withdrew 647 criterion applications, including 639 without numeric checks, while preserving 268 of 269 applications independently supported by Uni-G. Restricting retrieval to 14 testable criteria reduced the initial unsupported-criterion rate to 13.8%. Under matched instructions and an identical output schema, retrieval increased unsupported-criterion reports from 17.4% to 31.1%, while hypertrophy recall remained unchanged at 62.6%. Conclusion: These findings identify a fundamental limitation of retrieval-based clinical report generation: retrieved criteria do not necessarily provide valid patient-specific evidence. Measurement-based verification can reduce unsupported criterion applications, but diagnostic validity requires independent assessment.

Abstract: Conversational interfaces may make explainable AI (XAI) more accessible to users without machine learning expertise, but their benefits over dashboards remain insufficiently characterised in healthcare. Existing systems have typically been evaluated in isolation, leaving unclear whether conversational interaction improves interpretability beyond the underlying explanation methods. We report a within-subjects user study comparing the Explainability Assistant, an LLM function-calling conversational XAI system, with a traditional dashboard for explaining a heart disease classification model trained on the Cleveland Heart Disease dataset. Both interfaces expose the same Decision Tree classifier and post-hoc explanation methods: SHAP feature attribution, DiCE counterfactuals, and what-if analysis. This design supports comparison of interaction modalities while holding the model and explanation methods constant. Five participants with healthcare backgrounds, from medical students to practising clinicians and public health researchers, completed parallel task blocks on both interfaces; three participated in follow-up interviews. Task accuracy, Likert ratings, free-text questionnaire responses, and interviews revealed complementary strengths and weaknesses rather than a clear preference for either modality. The assistant offered easier entry and patient-specific explanations, while the dashboard supported simultaneous inspection of global and local information. All three interview participants recommended integrating conversational and dashboard elements within a single clinical workflow.

Abstract: Histopathology and computed tomography (CT) provide complementary views of renal cancer. We connect these modalities through bidirectional cross-attention between 16 histology prototypes and up to 32 kidney-centered CT tokens from frozen foundation models. In 210 TCGA-KIRC patients with 46 disease-specific survival (DSS) events, 5-fold evaluation yielded a C-index of $0.760\pm0.081$ and 3-year AUROC of 0.773 (95\% CI 0.678--0.860), the highest averages among evaluated unimodal and fusion baselines. External testing in 180 CPTAC-CCRCC patients yielded DSS C-index of 0.629 with CT withheld. Attribution analysis linked predictions to image regions while exposing acquisition artifacts. These findings support further study of cross-scale fusion and independent multimodal validation.

Abstract: Clinical trial prescreening requires distinguishing unmet conditions from insufficient evidence in patient records. Given patient records, criterion questions, and predefined answer options, we retrospectively compared JEV, a non-generative decision model returning native option probabilities, with schema-constrained Qwen Flash across 2,048 test patient-condition pairs from TrialGPT and question-answer datasets derived from MIMIC-III and MIMIC-IV, all evaluated under strict Zero Data Retention (ZDR) policies to ensure clinical data privacy. Both models assessed conditions individually or in batches sharing the same patient context, with performance measured against reference labels. In batch mode, JEV and Qwen achieved similar macro-F1 scores on TrialGPT (0.652 vs. 0.660) and MIMIC-IV (0.807 vs. 0.814), whereas JEV substantially outperformed Qwen on MIMIC-III (0.768 vs. 0.534; $Δ$ = +0.234, 95% CI: 0.187-0.281). This advantage largely reflected higher recall for conditions labeled as having insufficient information (56.3% vs. 9.9%). Across all three datasets, JEV also had lower observed median job latency (1.18-1.40 vs. 2.80-8.90 s) and 53%-74% lower estimated cost per condition. These findings position JEV as an initial assessment component that provides criterion-level judgments and flags potential information gaps for review. JEV's observed errors in interpreting clinical evidence underscore the need to verify its outputs against patient records before they inform eligibility decisions.

Abstract: Purpose: To describe an evidence-aware retrieval evaluation protocol for a clinical retrieval-augmented generation (RAG) system over breast lesion management literature, addressing the dependence of retrieval scores on annotation coverage. Methods: An 18-document corpus and an 18-query development benchmark, with one Yes/No or WH-question per document, were used. Retrieval combined dense embeddings, BM25, and cross-encoder reranking. Chunk sizes of 128 to 1024 tokens, overlaps of 0 to 20%, and four retriever configurations were evaluated. Relevance was defined by evidence spans mapped to all containing chunks, treating overlapping chunks with equivalent evidence as relevant. Retrieval was evaluated using R-Precision, Recall@K, MRR, and nDCG@K. Separately, generation was assessed on a 512-token index at K=1 to 5 using DeepEval claim-level metrics, with deepseek-v4-pro as the LLM judge, and BLEU/ROUGE metrics. Results: The selected hybrid retriever, using 384-token chunks and 20% overlap, retrieved accepted evidence in the top three results for 17 of 18 queries. Recall@3, R-Precision, MRR@3, and nDCG@3 each reached 0.94. Ground-truth curation increased evidence spans from 25 to 37 and accepted chunk targets from 36 to 51 without changing retrieval rankings. Conclusion: Cross-encoder reranking achieved the highest retrieval scores. Expanded relevance annotations increased recognized evidence without changing rankings, highlighting annotation sensitivity. The small development set and retrieval-informed curation require independent validation, including radiologist assessment of evidence sufficiency.

Abstract: Early detection of cognitive decline in older adults remains challenging due to the resource demands of standard neuropsychological assessments. Chatbot-based Intelligent Cognitive Assistants (ICAs) provide a scalable alternative by eliciting open-ended responses rich in linguistic, semantic, and autobiographical cues. This study evaluates whether ICA question-answer (Q/A) interviews with older adults can screen for participant-reported perceived cognitive decline and related cognitive, functional, and personality outcomes. We compare traditional machine learning, frozen transformer embeddings, fine-tuned transformers, and large language model (LLM) reasoning strategies across Global Q/A, Single Q/A confidence averaging, and Aggregated Q/A pipelines. Among text-based methods, Gemini 3.1 Flash Lite (1-example-per-class, Aggregated Q/A) achieved the highest held-out test performance (0.742 accuracy, 0.739 balanced accuracy, 0.728 macro-F1). Given the small test set (n = 31), these results are interpreted descriptively. Frozen clinical transformer embeddings with a random forest head led non-LLM text methods, whereas fine-tuned models showed limited generalization. Models utilizing structured questionnaires, cognitive tasks, and personality traits outperformed text-based models in classification. Continuous regression analyses revealed modest predictive signals for AD8, FAQ, IQCODE, neuroticism, and conscientiousness. Exploratory prompt-level analyses identified both direct symptom-related and indirect autobiographical questions with strong test metrics, though sample sizes varied across prompts. These findings indicate that ICA chatbot interviews capture meaningful signals of perceived cognitive decline, supporting scalable screening research. Larger, clinically diverse cohorts with validated clinical outcomes are needed for clinical translation.

Abstract: Automatic radiology report generation (RRG) aims to translate medical images into diagnostic text, reducing radiologists' workload and standardizing clinical documentation. Nonetheless, existing approaches mainly focus on single-timepoint analysis and fail to capture temporal disease evolution across longitudinal examinations. While recent longitudinal RRG (LRRG) approaches incorporate historical data, they often combine images from different time points within a single representation space, leading to blurred semantics and inconsistent temporal reasoning. In this work, we propose a Temporal Decoupling with Iterative Mutual-Refinement Model (TIM), a two-stage framework that explicitly decouples spatial pathology from temporal progression and iteratively refines reports through mutual feedback. Stage I performs temporal-decoupled representation learning, separating temporal evolution patterns from disease-specific features and generating radiology reports for both prior and current studies. Stage II introduces a mutual report refinement mechanism that identifies diagnostic inconsistencies within prior reports and iteratively rectifies both prior and current reports through error-sensitive feedback. Experiments on the Longitudinal-MIMIC dataset demonstrate that TIM surpasses existing single-image and longitudinal baselines, achieving new state-of-the-art performance across both language and clinical metrics. Code is available at https://github.com/yihengd/TIM.

Abstract: Patients admitted to pediatric ICU and cardiac ICU often require intensive perioperative support and frequent chest radiography to monitor support devices, extravascular lung water, and body-wall edema. Radiographic interpretation and analysis is often difficult due to superimposed anatomic and iatrogenic structures that obscure clinically relevant signals. While deep learning can provide decision support, translation to pediatric radiographs is still limited by high device burden and scarcity of pediatric datasets with clinically grounded device annotations. To address this gap, we first introduce PediaDeviceSeg-1K, a curated dataset of 1,000 anterior-posterior radiographs of pediatric CICU patients with clinically grounded, fine-grained annotations of common ICU devices. To our best knowledge, this is the first publicly available pediatric CICU CXR resource with clinically grounded device annotations for device-focused benchmarking. Building on PediaDeviceSeg-1K, we further present PCXR-Copilot, a device-aware pipeline that outputs lung and device masks, optional device-suppressed views, and edema-related visualization maps and scalar indices. The full pipeline has been integrated and runs in real time within the TWIST platform at Boston Children's Hospital, demonstrating feasibility for real-world clinical deployment.

Abstract: Respiratory auscultation provides a low-cost means of assessing pulmonary function, yet transient crackles and sustained wheezes can be difficult to recognize in noisy clinical recordings. Conventional deep learning classifiers often operate as black boxes, offering limited insight into the temporal acoustic evidence supporting their predictions. We present RespFocus, a weakly supervised framework that uses multiple instance learning (MIL) to learn inspectable temporal evidence from cycle-level labels and integrate it into classification. We also introduce PedResp2026, a multicenter pediatric respiratory sound cohort collected in routine clinical environments with adjudicated cycle-level annotations. In classification experiments, RespFocus achieves four-class Scores of 69.55\% on public ICBHI 2017 and 72.91\% on PedResp2026. Evidence diagnostics and matched temporal interventions support the functional contribution of the learned evidence to model predictions. Together, these findings highlight RespFocus's potential as a tool for automated respiratory sound diagnosis.

Abstract: We evaluate whether AI agents can match the reported findings of published biomedical studies using public data. Existing evaluations do not consistently separate analysis from prior knowledge or retrieval of the published answer. We introduce BioStudyBench, a benchmark of 25 long-horizon analysis tasks drawn from studies first published between July and September 2026, after the developer-reported knowledge cutoffs of the models we evaluate, semi-automatically filtered down from 404,019 PubMed records. In each task, the agent receives a neutral research question but no data files, so it must find and download the relevant public data, search the literature through tools that return only records dated before its cutoff, and report findings through data analysis. To measure gains over prior knowledge, we run every task both with and without access to data and tools. Across eight models, access to data and tools raises the pass rate by 47 percentage points on average over the no-data baseline. Open-weight models across sizes trail closed-weight models, with the best open-weight model passing 81.3% of tasks against 94.7% for the best closed-weight model.

Abstract: Clinical decision-support outputs can lack an au- ditable link between patient observations, encoded knowledge, conclusions, and recommendations. We present the CKG Clinical Explanation Engine, a downstream layer for a frozen, training-free clinical knowledge-graph reasoner that converts patient inference states and disease knowledge into typed facts, explicit rule-application traces, provenance-linked conclusions, and policy-licensed recommendations. The design separates measurement availability, representation completeness, and disease-specific activation; consequently, observed zero-activation evience is not treated as missing and partial representation is distinct from unobserved evidence. Optional language generation is restricted to symbolically licensed content. Across five usable workbooks (6,720 patients; 20,160 patient-disease traces; 1,021,440 feature-evidence rows), IG-range validity and knowledge provenance were 100%, numerical cross-sheet fidelity was 100% (120,960/120,960), and exported logical/report trace completeness was 100% (20,160/20,160). Availability representation consistency was 99.7028% (1,018,404/1,021,440); all 3,036 disagreements were confined to three systematic feature-cohort patterns. The corpus contained 86,783 observed zero-activation and 139,949 observed partially represented instances. A separate seeded 25-patient end-to-end audit completed without execution failure and passed all pre-specified trace, licensing, provenance, and state-consistency checks. These results establish structural and implementation auditability, not clinical correctness or utility.

Abstract: Biomedical large language model (LLM) evaluation requires auditable assessment of narrow, evolving, source-grounded subspecialty knowledge. Multiple sclerosis MRI (MS-MRI) provides a high-stakes textual-knowledge test case because correct reasoning requires current diagnostic criteria, standardized acquisition and reporting knowledge, longitudinal monitoring concepts, lesion morphology, and recognition of difficult mimics. We present MS-Exam-Gen, a reproducible framework for constructing and auditing a text-based multiple-choice question (MCQ) benchmark for MS-MRI knowledge; it does not evaluate direct MRI image interpretation. MS-Exam-Gen targets source-grounded criteria, protocols, reporting, and differential diagnosis. The framework combines expert-source indexing, exam-oriented topic induction, evidence-grounded MCQ generation, automated quality audits, a same-family consistency screen, and empirical calibration. From a 66-source corpus indexed into 4,289 retrieval chunks, the pipeline produced a locked 3,058-item candidate benchmark spanning 16 topics and 53 subtopics. Evaluation across 12 primary LLM endpoints yielded 36,696 item-level predictions and separated performance over a 42.8-percentage-point accuracy range (89.7% to 46.9%). Across these endpoints, 25.5% of items were missed by at least four. Post-generation audits showed that refreshed construction reduced measurable answer cues, while option-order testing showed that absolute MCQ scores remain position-sensitive. Generated construction labels remain metadata rather than validated psychometric categories. Because expert adjudication and full option-order counterbalancing remain future work, MS-Exam-Gen is not a clinically certified examination. It should be interpreted as an automatically filtered, source-grounded candidate benchmark and reproducible audit workflow for item-level and topic-specific LLM evaluation.

Abstract: Systematic reviews condense clinical trials into evidence tables, yet clinicians can interrogate these tables only through database queries, and many questions concern attributes that the table does not record, such as a drug's target class or a harmonised endpoint. Here we introduce FD-SCoPE, a language-model framework that answers both kinds of question, exposes the query, the selected trials and the derivation rule behind every answer, and learns from expert corrections. On an oncology evidence table of 159 immune checkpoint inhibitor trial records, FD-SCoPE completed all 140 clinician-style tasks (alternatives, 90.7-97.9%). For questions needing derived attributes it retrieved 99.3% of relevant trial records at a positive predictive value of 89.8% and outperformed four alternative approaches (derived-value F1 77.7% versus 64.8-73.4%). Corrections on 299 questions, simulated from reference answers, raised F1 on 1,201 unseen questions from 77.9% to 84.9%. Language models coupled with executable queries, verified programs and expert feedback can give clinicians auditable access to trial evidence.

Abstract: This paper presents an overview of the fourteenth edition of the BioASQ challenge, organized in the context of the Conference and Labs of the Evaluation Forum (CLEF) 2026. BioASQ is an international challenge series that supports progress in biomedical language processing tasks ranging from semantic indexing and information extraction to question answering and summarization. In 2026, BioASQ included six shared tasks: a) Task 14b on biomedical semantic question answering. b) Task Synergy14 on question answering for developing biomedical top- ics. c) Task MultiClinSum-2 on multilingual clinical summarization. d) Task BioNNE-R on extracting relations between nested named entities in Russian and English. e) Task ELCardioCC on clinical coding in cardiology. f) Task GutBrainIE on gut-brain interplay information extrac- tion. Across these six tasks, 87 distinct teams participated, submitting more than 1000 runs overall. As in previous editions, several submissions reached competitive performance, reflecting the continued progress of state-of-the-art methods across biomedical language processing tasks.

Abstract: Multidisciplinary tumor boards integrate multimodal clinical observations and longitudinal patient histories through specialist discussions, yet benchmarks rarely capture these real-world trajectories. We introduce OpenTumorBoard, a benchmark with 611 patient cases and 19,157 discussion turns across ten specialist roles, transcribed from 12,534 minutes of publicly available tumor board recordings on YouTube. The benchmark evaluates two settings: SPECIALIST TURN, in which an LLM responds to a clinically significant question posed during a real discussion, and BOARD SIMULATION, in which it generates an entire back-and-forth discussion and reaches a consensus on therapy recommendations, surgical plans, next actions and clinical trial matching. Evaluation of 14 general-purpose frontier and medical LLMs reveals substantial limitations: the best models score 3.43 out of 5 in clinical equivalence to specialist answers and 2.78 out of 5 in alignment with recorded board conclusions. Supervised finetuning and reinforcement learning improve performance on a held-out test set, suggesting that real-world discussion trajectories can support model adaptation. Three M.D. experts review a subset of the benchmark, finding high information coverage and factuality of patient cases and strong fidelity of extracted consensus conclusions. We will release OpenTumorBoard and its automated curation pipeline to support the development and evaluation of LLMs for multidisciplinary, personalized cancer decision-making.

Abstract: Large language models (LLMs) have been widely adopted for clinical question answering (QA). Current systems can attach citations to their answers, but these often point to broad texts, leaving time-pressed clinicians unable to verify them efficiently. An alternative is to ensure that responses are verifiable by construction: providing fine-grained verbatim quotes from reference material that substantiate claims, so users can verify an answer without opening other documents. In this paper, we evaluate the ability of current models to perform this task end-to-end: from providing citations for every factual claim, to producing verbatim quotes, to ensuring that those quotes fully substantiate the claims. To do so, we build a standardized harness over four clinical practice guidelines and evaluate twelve LLMs on 222 synthetic clinical questions, measuring each of these stages separately. We find that most models can attach verbatim quotes to over 90% of their claims from prompting alone, apart from some lightweight models such as claude-haiku-4.5. Yet these quotes often fail to substantiate every detail of the claims they accompany. For instance, claude-opus-5 produces verbatim quotes for 98.0% of its claims, but fully substantiates only 37.1%. Our work provides insights into the current capability gap of LLMs in building verifiable clinical QA systems, along with artifacts for future research.

Abstract: Graph Retrieval-Augmented Generation (GraphRAG) can connect evidence distributed across a corpus graph, but most systems use largely shared exploration procedures across queries. This creates a structural mismatch: direct facts may need compact local neighborhoods, comparisons need balanced coverage of multiple targets, and mediated questions may require deeper paths through weakly related connectors. We present Mosaic, a training-free framework that formulates GraphRAG retrieval as a per-query control problem. An LLM analyzer converts query-specific evidence requirements into a bounded policy over seed selection, graph traversal, stopping, and evidence selection, while the corpus graph, indexes, scoring functions, grounding procedure, and answer generator remain shared. On GraphRAG-Bench, Mosaic achieves query-weighted Answer Correctness of 76.97 on Medical and 64.33 on Novel, improving over the strongest previously reported overall results by 5.13 and 4.43 points. On Medical, it reaches 95.1 Evidence Recall and 86.1 Context Relevancy. Controlled comparisons on an identical graph and generator show that no fixed narrow, medium, or wide policy is consistently optimal; Mosaic improves by 9.96 points over the strongest canonical fixed policy. Relative to Fixed Wide, it evaluates 81.9% fewer paths and retains 47.2% fewer evidence items. Transfer experiments on HotpotQA, MuSiQue, and 2WikiMultiHopQA further show that the policy interface can be applied without benchmark-specific retriever training.

Abstract: Large language models (LLMs) have demonstrated strong capabilities across diverse domains, showing considerable potential in medicine. However, their application in medical settings remains limited by the scarcity of visual question answering (VQA) datasets that capture clinical reasoning and explicit image-text alignment. Here, we leverage de-identified medical images and expert commentaries shared on clinician-oriented social media. By combining an advanced LLM with clinician-in-the-loop verification, we established a rigorous pipeline to construct ThoughtMed-1M, a long-form medical VQA dataset containing over one million VQA pairs and designed to capture structured clinical logic and medical image-text alignment. To demonstrate its utility, we developed a FOundational LLM Trained on ThoughtMed-1M (FOLTMed). FOLTMed achieved state-of-the-art performance across 42 medical VQA benchmark datasets, with a macro accuracy of 85.4%, and generated more clinically coherent responses on the ThoughtMed-1M test set. It outperformed state-of-the-art models by 3--5% across factuality and similarity metrics, highlighting a scalable paradigm for advancing research on clinically grounded multimodal LLMs.