Improving Health Literacy through Lay Summarization of Radiological Reports: An Evaluation of BioNER and Retrieval-Augmented Generation

Radiology reports are written primarily for clinicians, and their specialized terminology often makes them difficult for patients to interpret. As a result, many patients turn to publicly available Large Language Models (LLMs) to help explain their reports, despite well-documented risks of factual inaccuracies and hallucinations. Automated lay-summary generation has emerged as a promising alternative, yet the effectiveness of retrieval-enhanced and clinically informed approaches for radiology-specific communication remains underexplored. This study investigates the extent to which Retrieval-Augmented Generation (RAG) and Named Entity Recognition (NER) improve the quality, factual consistency, and readability of automatically generated lay summaries compared with standard LLM-based generation. We develop a framework combining NER-based extraction of clinically relevant findings with a RAG mechanism for contextual grounding, evaluated across few-shot and fine-tuned variants of two models (Qwen, BioBART). Results show that NER consistently improves readability and overall quality, while RAG alone offers no benefit and can introduce hallucinations from irrelevant retrieved terms. Combining RAG with NER degrades performance in few-shot settings but improves readability when fine-tuned. Fine-tuned BioBART with NER achieves the best overall performance, highlighting entity-aware extraction as the primary driver of improved patient-friendly summaries.

Homo-RAG: Homology-Guided Retrieval-Augmented Generation for Cross-Species Gene Function Prediction

The functional annotation of genes in non-model organisms remains a significant challenge in computational biology, with 20-70% of sequenced genes lacking characterized functions. Traditional homology-based methods are often costly and strongly dependent on high sequence similarity. This study presents Homo-RAG, a framework for large language model-based gene function prediction that integrates homology-guided multi-hop retrieval with evidence-aware ranking. The framework exploits biological relationships between zebrafish and human orthologs to guide evidence acquisition from ZFIN, UniProt, and PubMed through hybrid dense and lexical retrieval. An Evidence Confidence Score (ECS) integrates semantic relevance, entity matching, orthology information, source reliability, and literature association signals to refine the ranking of retrieved evidence. Extensive evaluation across 150 queries and 7,200 retrieved documents shows that evidence weighting parameter of lambda=0.50 improves NDCG@10 to 0.9879 and MRR to 0.99, while retrieving relevant evidence for 99.33% of queries. Furthermore, 80% of the retrieved documents are query-exclusive, indicating that evidence quality complements rather than replaces retrieval relevance. These findings establish Homo-RAG as a practical and robust framework for reliable, evidence-grounded gene function prediction in understudied organisms. The study addresses important limitations of conventional annotation pipelines while identifying opportunities for future improvements in evidence features and attribution mechanisms.

Generating Biomedical Fact-Checking Reports with RL-Enhanced Agentic Search

Automated fact-checking is essential for ensuring the reliability of public health information, yet the biomedical domain poses unique challenges. Validating biomedical claims requires rigorous interpretation of scientific literature, assessment of retrieved evidence, and comprehensive justification toward the conclusion. Although Large Language Models (LLMs) enhanced by Retrieval-Augmented Generation (RAG) and agentic search perform automated fact-checking in a retrieve-then-verify paradigm, current methods still output isolated prediction labels, lacking explanatory depth and offers limited utility for human understanding. To bridge this gap, we introduce an LLM-based agent named BioCheck Agent that generates structured biomedical fact-checking reports with agentic search. Rather than merely outputting supported or refuted labels, our agent synthesizes final conclusions with retrieved evidence and rigorous analysis. To ensure domain-specific accuracy, BioCheck Agent exclusively searches high-quality scientific literature in PubMed, utilizing advanced Boolean search operators. Recognizing that direct prompting often results in hallucinations and low-quality reports, especially for lightweight open-source models, we further propose the Evidence-Grounded Group Relative Policy Optimization (EG-GRPO) to perform reinforcement learning on BioCheck Agent with a task-specific reward that incentivizes advanced search behavior and high-quality evidence retrieval while penalizing hallucinations. Our experimental results show that compared to the base model Qwen3.5-4B, BioCheck Agent with EG-GRPO improves label prediction accuracy on SciFact by 9.95%. Furthermore, it achieves a 3.7% higher evidence quality score and a 19.63% lower evidence hallucination rate, demonstrating its ability to generate biomedical fact-checking reports with improved accuracy and quality.

Teaching LLMs How ICU Physicians Approach Clinical Reasoning Through OMOP-Aligned Retrieval Improves Reasoning Across Clinical Domains

Clinical decision-making relies on identifying relevant patient information to guide diagnosis and treatment, a challenge that is especially difficult in the data-dense and rapidly changing intensive care unit (ICU). Large language models (LLMs) could support this task. However, existing applications and datasets mostly emphasize surface-level retrieval or factual recall rather than the inductive and deductive reasoning clinicians practice to select and reason over decision-relevant evidence. We hypothesized that training LLMs on expert ICU reasoning could yield clinical reasoning skills that generalize beyond critical care. Here we introduce ICU-REACT, a reasoning dataset developed with 19 clinicians through a clinician-in-the-loop framework to teach LLMs to perform information retrieval and context-aware clinical reasoning in the ICU. Using ICU-REACT, we fine-tuned Clin-REACT models spanning 8B-70B parameters and three model families. Across five clinical reasoning benchmarks, Clin-REACT consistently outperformed its backbone models and open-source general-purpose and medical LLMs. Gains extended to different tasks including script concordance tests, and downstream diagnosis and treatment tasks. These findings suggest that expert reasoning supervision in critical care can improve broader clinical reasoning, although prospective evaluation is needed before real-world clinical use.

Development and Feasibility Evaluation of an Edge AI as Medical Device System for Breast Cancer Multidisciplinary Team Meetings

Breast Cancer Multidisciplinary Team (MDT) meetings manage increasingly complex cases under considerable time pressure, and documentation requirements can reduce clinical efficiency and decision quality. Existing AI based MDT workflows rely on cloud-based processing, limiting their use because patient discussions contain identifiable information. We developed a fully on-device AI pipeline using open-source Automatic Speech Recognition (ASR) and Large Language Models (LLMs) that transcribes breast cancer MDT discussions, structures clinical information, and generates treatment recommendations using retrieval-augmented generation (RAG) grounded in National Institute for Health and Care Excellence (NICE) guidance. The pipeline runs on a single NVIDIA Jetson AGX Orin, ensuring that patient audio, transcripts, and outputs remain within institutional infrastructure. Evaluation included two recorded simulated MDT discussions, ten clinically validated synthetic discussions, and 1,270 acoustically augmented recordings. Optimisation of Whisper large-v3 reduced word error rate by 20.7% and 24.4% on the recorded discussions and achieved performance within 0.58% WER and 1.58% word information lost of a commercial clinical ASR benchmark on augmented audio. MedGemma-RAG identified 2.3 times more MDT-concordant interventions than a proprietary cloud comparator (p = 0.020), with no significant difference in overall accuracy. Stakeholders identified automated documentation, treatment recommendation support, and case triage as the most credible near-term applications while highlighting workflow integration, governance, and clinician trust as key implementation challenges. These findings demonstrate the feasibility of privacy-preserving, fully on-device AI for MDT documentation and guideline-informed decision support, providing a foundation for prospective clinical evaluation.

An integrated diffusion-weighted imaging processing and interpretation platform for MR-guided radiotherapy

Background: Magnetic resonance imaging-guided linear accelerators (MR-Linacs) allow diffusion-weighted imaging (DWI) to be acquired at every treatment fraction, but converting these low-signal-to-noise-ratio acquisitions into clinical decisions requires both reliable quantitative processing and an interpretation that reconciles a scattered and often contradictory literature. Purpose: To describe and evaluate an integrated, web-based platform that carries raw MR-Linac DWI to a structured, literature-grounded clinical interpretation, and to assess its retrieval-augmented generation (RAG) interpretation module by independent expert rating. Methods: The platform couples a deep-learning processing pipeline, comprising distortion correction, denoising, and intravoxel incoherent motion (IVIM)/apparent diffusion coefficient (ADC) fitting, with longitudinal region-of-interest analysis and a RAG interpretation agent. The agent reasons over a two-layer knowledge base of curated publications (a structured catalog index plus line-indexed full text), delegates arithmetic to deterministic tools, and is designed to trace each statement to a source document, section, and line range. One medical physicist and one physician independently rated the agent's reports for nine longitudinal glioblastoma cases on a 1-5 scale across three metrics: clinical-reasoning soundness, literature-citation quality, and overall clinical utility. Results: Across 54 ratings, the pooled mean was 4.65 +/- 0.80, with 93% of ratings >= 4; metric means were 4.6 (reasoning), 4.5 (citation), and 4.8 (utility), and raters agreed within one point on 85% of paired ratings. Conclusions: A single platform can integrate MR-Linac DWI post-processing with traceable, expert-evaluated clinical interpretation, while highlighting the safeguards needed to verify LLM-generated reasoning in radiation oncology.

From Generalist to Specialist: A Context-Fusion Framework for Endoscopic Polyp Reporting with a Frozen VLM

Reliable endoscopic polyp reporting requires integrating quantitative lesion sizing, standardized Paris classification, and clinically meaningful morphological description within a single record. General-purpose vision-language models (VLMs) offer a unified interface for image understanding and report generation. Existing specialization strategies, however, typically rely on task-specific models or model-weight adaptation, leaving unresolved how to introduce reliable specialist knowledge while preserving both this unified interface and the VLM's pretrained capabilities. We introduce a context-fusion framework that specializes a frozen general-purpose VLM through both implicit instruction context and explicit transduction context without modifying its pretrained weights. Specifically, a self-supervised polyp encoder retrieves related image-report pairs as explicit, query-specific evidence, while learned continuous specialist tokens provide implicit instruction context shared across cases. Experiments were conducted on 2,056 expert-annotated public endoscopic images. We compared the framework with general-purpose VLMs, task-specific predictors, and weight-adaptation methods to assess specialist performance, unified reporting, and adaptation efficiency. Across numerical, categorical, and report-generation metrics, the proposed framework substantially improved direct frozen-VLM inference and achieved the strongest overall performance among the evaluated methods. It added trainable parameters equal to only 0.006% of the frozen VLM's parameter count. When the top-1 retrieved case carried the correct target category, our framework corrected 70.5% of the errors made by a weight-adaptation baseline. These findings support the context-fusion framework as a lightweight and effective strategy for specialist adaptation of a frozen VLM.

RAG-Audio: Retrieval-Augmented Generation for Faithful Brain-to-Audio Reconstruction

Brain-to-audio reconstruction is limited by \emph{prior domination}: when a pretrained generator is conditioned on a weak neural signal, it produces realistic but stimulus-inaccurate audio. We introduce RAG-Audio, which decodes fMRI into a semantic audio embedding, retrieves a matching real-audio exemplar, and initializes the frozen generator's sampling trajectory from that exemplar while retaining the decoded embedding as conditioning. On Brain2Music, RAG-Audio improves 10-way stimulus identification from $0.14$--$0.18$ for direct generation, near the $0.10$ chance level, to $0.40$--$0.43$, comparable to retrieval. It also reduces Fréchet Audio Distance by roughly an order of magnitude, from $13.49$ to $1.25$ for AudioLDM. RAG-Audio approaches nearest-neighbor retrieval in identification while remaining generative; its higher FAD is expected because retrieval directly replays real audio. An autoregressive negative control, which lacks an initializable latent trajectory, shows no comparable gain, attributing the improvement to trajectory initialization. These results suggest that retrieval-guided initialization can mitigate prior domination in brain-to-audio generation.

An Agentic Generative Large Language Model for Treatment Planning of Colorectal Cancer

Treatment planning in precision oncology requires synthesizing heterogeneous patient information with rapidly evolving clinical guidelines to ensure guideline-concordant care. While large language models (LLMs) show promise in many diagnostic tasks, their adoption for high-stakes treatment planning is hindered by complex reasoning, adherence to timely clinical guidelines, and safety concerns. In this study, we present GatorOnco, an agentic LLM for colorectal cancer (CRC) treatment planning. GatorOnco is developed using a total of 282 billion tokens of biomedical text, including healthcare system-scale clinical text comprising 166 billion tokens from UF Health. We implemented a domain-adaptation method that integrates pre-training, model merging, a two-stage post-training approach, and agent-based reinforcement learning. An agentic retrieval-augmented generation (RAG) approach dynamically integrates time-sensitive clinical guidelines into the reasoning process. In a blind, randomized clinical evaluation conducted by five UF Health oncologists, GatorOnco significantly outperformed open-source LLMs (P < 0.01) and achieved expert-level performance comparable to UF Health oncologists. Compared with expert oncologists, GatorOnco received significantly higher ratings for readability (4.46 vs. 4.19, P < 0.01) and completeness (3.91 vs. 3.52, P < 0.01), while showing statistically comparable performance in correctness (4.09 vs. 4.11, P = 0.921), currency (4.04 vs. 3.98, P = 0.478), and safety (4.22 vs. 4.22, P = 0.999). These findings demonstrate that integrating agentic reasoning with large-scale domain adaptation can help bridge the gap for generative AI in high-stakes cancer treatment planning.

When Retrieval Helps and Distracts: Evaluating Evidence-Generating LLMs for Biomedical Claim Verification

Biomedical fact-checking systems must do more than predict whether a claim is supported, contradicted, or unaddressed: they should also produce evidence that is faithful, complete, and useful for verification. We study this evidence-generation setting on CARE-XAI, a unified benchmark spanning five biomedical and health fact-checking sources. We compare base instruction LLMs, PubMed retrieval-augmented LLMs, fine-tuned LLMs, label-only LLMs, and biomedical encoder classifiers under a shared evaluation protocol. Biomedical classifiers remain strongest for verdict-only prediction, while fine-tuned LLMs are the strongest evidence-generating systems. PubMed retrieval is mixed: it helps PubMed-aligned sources such as PubMedQA and SciFact, but can distract models on broader public-health claims. We introduce Bio-GRACE, a gold-reference-normalized diagnostic for measuring whether retrieved evidence recovers the decision benefit of reference evidence. Bio-GRACE shows that retrieval utility is source-dependent, motivates selective retrieval, and exposes why retrieval recall and lexical evidence overlap are insufficient for biomedical fact-checking.

Large language models improve physician accuracy but lead to false reliance

Retrieval-augmented large language models (LLMs) promise source-linked clinical support, but their value depends on whether displayed evidence guides rather than distorts physician reliance. We developed CORA, an agentic retrieval-augmented LLM, to investigate how source-linked assistance affects physician decision-making. CORA maintained benchmark performance and achieved larger gains on cases published after the models' training-data cutoffs. In a study of 46 physicians, accuracy increased from 70.8% unaided to 82.6% with CORA. Supporting citations predicted correct answers (87.7% vs 65.5%), but citations created an important asymmetry: perceived support increased adoption of correct advice from 34% to 76.9% but when an incorrect LLM answer appeared citation-supported, physician resistance to it fell from 92% to 34.8%. These findings show that source-linked LLM assistance can improve physician accuracy while introducing a grounding-dependent safety risk.

MA-RAG: Multi-Agent Retrieval-Augmented Generation for Query-Driven Summarization of Longitudinal Parkinson's Disease Assessments

Accurate interpretation of single-visit and longitudinal clinical assessments for Parkinson's disease is time-consuming and often depends on specialist expertise. Although large language models (LLMs) can generate natural language summaries, they frequently lack domain-specific clinical grounding and struggle to produce factually correct and temporally consistent responses for structured longitudinal assessment data. To address these limitations, we propose MA-RAG, a query-driven multi-agent retrieval-augmented generation framework that decomposes clinical reasoning into domain-specialized agents, combines structured fact extraction, and synthesizes clinically grounded summaries through a final verification stage. The framework supports four clinical analysis tasks: single-session, trajectory, comparison, and cohort summarization. We evaluate MA-RAG using objective metrics, namely Fact Precision, Hallucination Rate, Temporal Fidelity, and Semantic Similarity, together with subjective evaluations conducted by clinical experts. Compared to Traditional, RAG-only, and Single-agent RAG baselines, MA-RAG substantially improves factual correctness, achieving up to a 122% relative increase in Fact Precision (from 0.436 to 0.990) and reducing the Hallucination Rate by up to 98% (from 0.564 to 0.010), while consistently receiving top ratings from clinical experts for organization and clinical usefulness. These results demonstrate that domain-specialized multi-agent reasoning enables reliable query-driven summarization of structured longitudinal clinical assessment data.

RAG-HAR+: Towards Cost-Efficient LLM-Based Human Activity Recognition for Edge Deployment

Human Activity Recognition (HAR) from wearable sensors supports applications in healthcare, rehabilitation, fitness tracking, and smart environments. Yet, existing deep learning approaches require dataset-specific training, large labeled corpora, and repeated adaptation to new sensor settings or activity taxonomies. Retrieval-Augmented Generation for Human Activity Recognition (RAG-HAR) addresses this by framing HAR as a training-free, retrieval-augmented task, in which statistical descriptions of sensor windows are used to retrieve similar labeled examples that guide LLM-based classification. We introduce RAG-HAR+, a retrieval-first and cost-optimized extension that strengthens retrieval while reducing dependence on LLM-based inference. RAG-HAR+ uses an offline Retrieval Designer Agent to design dataset-specific feature groups from a diverse pool of motion descriptors, enabling sensor windows to be compared using features better aligned with dataset-specific activity patterns. During inference, RAG-HAR+ uses majority voting over retrieved neighbors for samples with strong retrieval evidence and defers only uncertain cases to an LLM-based Ambiguity Resolver Agent. Across six HAR benchmarks, RAG-HAR+ maintains competitive or improved performance while reducing LLM usage, token consumption, and inference time. We further extend the RAG-HAR mobile prototype to demonstrate the practical feasibility of retrieval-first, LLM-assisted HAR in mobile sensing scenarios.

Grounded in Consensus, In Step With Emerging Science: A Consensus-Anchored Multi-Corpus Clinical Chatbot for Long COVID

Long COVID (LC) poses a challenge for clinical decision support because relevant evidence is distributed across sources with different update cycles, evidentiary roles, and levels of clinical maturity. We present a clinician-facing chatbot that organizes four sources within a retrieval-augmented workflow: expert-curated consensus guidance, current PubMed literature, registered interventional trials, and evidence from living systematic reviews. Consensus guidance is always included to frame responses, while the remaining sources are retrieved in parallel when selected by the user. In an exploratory automated evaluation on 50 clinician-facing questions, our chatbot showed comparable mean ratings to OpenEvidence, with numerically higher scores and lower score variability in an LLM-judged comparison.

MedJudgeRAG: Option-Wise Evidence Judgment with Dynamic Knowledge Graphs for Medical MCQA

In medical multiple-choice question answering (MCQA), Retrieval-Augmented Generation (RAG) can supplement the domain knowledge of language models (LMs). However, since vanilla RAG indiscriminately utilizes retrieved documents, it can degrade LM performance. To address this, we propose MedJudgeRAG. Our framework represents retrieved documents as a dynamic knowledge graph (KG) composed of entities and relations. For each option, the model judges an evidence verdict from the retrieved documents and the KG. Based on the verdict combination, the model determines a knowledge utilization strategy to reason toward the final answer. These capabilities are trained via supervised fine-tuning using structured reasoning traces generated by a teacher LM. The training employs a weighted cross-entropy loss that differentially weights the KG and reasoning segments. Experiments on two medical MCQA benchmarks demonstrate that MedJudgeRAG consistently outperforms both vanilla RAG and parametric baselines. Furthermore, ablation analysis reveals that the dynamic KG is more effective as graph-conditioned supervision at training time than as an explicit output at inference time. Our code is available at https://github.com/hyu-amllab/medjudgerag, and the generated reasoning traces are released at https://huggingface.co/datasets/youarethewon/medjudgerag.

MamaBench: Benchmarking LLM Robustness in Maternal and Child Health Diagnosis through Counterfactual Clinical Perturbation

Large language models achieve strong scores on medical benchmarks, yet these benchmarks evaluate each question in isolation, providing no measure of whether a system can distinguish clinically similar presentations requiring different interventions. We introduce MamaBench, the first counterfactual benchmark for maternal and paediatric AI: 434 expert-authored clinical narratives in 217 pairs across 371 pathologies, evaluated via the Bias Trap Rate (BTR), the conditional probability that a model fails the counterfactual given success on the base case. We propose Evidence-Anchored RAG (EA-RAG), a three-stage retrieval method that replaces aggregate similarity with an evidence coverage objective through clinical parameter extraction, coverage auditing, and contrastive sub-queries. Across eight configurations of four frontier LLMs, base accuracy overstates robust accuracy by 16-28 percentage points in every model. EA-RAG achieves 20.3% BTR and 65.0% robust accuracy on Claude Sonnet 4.6, a 5.5 percentage point BTR reduction without degrading base accuracy. The residual 20% BTR confirms that counterfactual robustness in clinical AI remains an open challenge. Keywords: counterfactual evaluation, clinical AI, maternal healthcare, retrieval-augmented generation, diagnostic robustness

MonteRET: AI Agent Enhancing Multimodal LLMs with Multi-granularity Knowledge Retrieval for Chest CT Report Generation

Automated chest CT report generation remains challenging because clinically faithful reporting requires both whole-volume understanding and accurate description of localized anatomical findings. Here we developed and retrospectively evaluated MonteRET, a region-aware retrieval-enhanced framework for generating chest CT findings sections. MonteRET integrates global CT features with region-level anatomical representations, retrieves clinically relevant knowledge using predicted medical conditions and region-level vision-language alignment, and refines initial reports through a knowledge-guided report rewriting agent. We trained our model on a public cohort with 24,128 CT scans from RadGenome-ChestCT. We evaluated MonteRET on the public RadGenome-ChestCT test set of 1,564 CT scans and an external cohort of 82 CT scans from NewYork-Presbyterian/Weill Cornell Medical Center. MonteRET improved report quality, semantic similarity, and clinical efficacy compared with a matched baseline and several state-of-the-art methods. Gains were most pronounced for recall, suggesting fewer omitted findings. Human expert evaluation by radiology residents also favored MonteRET.

Deceptive Grounding: Entity Attribution Failure in Clinical Retrieval-Augmented Generation

Retrieval-augmented generation evaluation checks whether model claims are factually grounded in retrieved documents. It does not check whether retrieved evidence is attributed to the correct entity. A clinical RAG response can pass every automated check (zero hallucinations, near-perfect faithfulness, real citations) while presenting drug Y's clinical evidence as evidence about queried drug X. We term this deceptive grounding (DG): a failure invisible to faithfulness, hallucination, and citation checks because every claim is sourced from a real document, about the wrong entity. Using a controlled factorial benchmark across 13 models, we find DG rates spanning 8-87% at peak adversarial conditions. Medical and biomedical fine-tuned models reach up to 86.7%; domain specialization amplifies the failure rather than mitigating it. A controlled ablation identifies the mechanism: removing entity-specific clinical evidence from retrieved documents eliminates entity-attribution failure entirely, shifting all failures to confabulation. The two failure modes respond to the same trigger, taking different paths. Production measurement across 740 drug-disease pairs finds 7.8% overall DG in a deployed RAG system, rising to 13.6% for recently approved drugs. Entity-attribution verification (checking that cited evidence applies to the queried entity) detects DG at 97.0% precision and 98.7% DG recall (IPW-adjusted human gold standard); no existing framework implements it.

Medi-Gemma: A Hybrid Clinical Decision Support System Integrating Deterministic EMR Analytics and Retrieval-Augmented Generation

Deploying Large Language Models (LLMs) in high-stakes clinical settings remains limited by structural hallucinations, weak deterministic reasoning over tabular patient data, and omissions in vector retrieval. This paper presents the architecture and validation of Medi-Gemma, a Clinical Decision Support System (CDSS) for wound pathology triage and workflow automation. The platform introduces a decoupled framework that separates clinical perception from data orchestration while preserving traceable reasoning. Medi-Gemma uses a multi-stage pipeline coordinated by a centralized ClinicalOrchestrator. Data requests are handled without generative inference by a DataManager that cleans unstructured Electronic Medical Record (EMR) files through type coercion. Natural language queries are processed by a hierarchical IntentRouter, which routes requests to deterministic analytics paths executed by a PandasQueryEngine or to patient-specific reasoning managed by a ClinicalRAGEngine using a CPU-optimized vector store. A key contribution is the Ground Truth Injection Module, which intercepts patient-specific queries, extracts numeric identification tokens, queries the structured dataframe via Pandas, retrieves the latest validated clinical state, and embeds this snapshot as an overriding context block in the LLM prompt before generation. Safety compliance is enforced by a deterministic ProtocolManager that maps clinical terminology to fixed evidence-based risk pathways, while a SafetyVerifier phrase filter prevents output rule violations. Validation shows that this architecture eliminates semantic context drift, prevents database compilation crashes, and improves factual adherence to backend clinical repositories. These results support Medi-Gemma as a safer pattern for LLM-based clinical decision support where structured data fidelity, retrieval grounding, and deterministic safeguards are essential.

MMIR-TCM: Memory-Integrated Multimodal Inference and Retrieval for TCM Clinical Decision Support

Traditional Chinese Medicine (TCM) diagnosis, particularly through tongue inspection, faces persistent challenges in subjectivity and reproducibility. The application of multimodal artificial intelligence to TCM clinical tasks, such as syndrome differentiation and prescription generation, is significantly hampered by the semantic gap between visual tongue features and textual reasoning, as well as the lack of large-scale, standardized datasets. To address these challenges, we introduce MMIR-TCM, a novel framework that emulates the diagnostic process of TCM experts by integrating multimodal large language model(MLLM) with memory-augmented segmentation and retrieval-augmented generation (RAG). Employing a three-stage architecture, MMIR-TCM integrates a training-free Memory-SAM module for robust tongue extraction, a fine-tuned Qwen3-VL model for structured tongue diagnosis generation, and a Qwen3-based RAG component for evidence-grounded clinical decision support generation. The framework was developed and validated using MedTCM, a new large-scale multimodal dataset that we introduce specifically for advanced TCM research. To properly evaluate our framework's clinical accuracy, which existing metrics fail to capture, we also developed TDEU, a domain-specific evaluation metric incorporating semantic understanding and diagnostic importance. Our comprehensive experiments demonstrate that MMIR-TCM significantly outperforms leading models, including GPT-4o and Gemini 2.5 Flash.

ClinRAG-GRAPH: Clinical-prior Retrieval-Augmented Graph Model with Domain Adversarial Learning for Breast pCR Prediction

Neoadjuvant chemotherapy (NAC) response prediction is clinically important for treatment stratification in breast cancer. However, robust pre-treatment pathological complete response (pCR) prediction remains challenging due to insufficient cross-modal modeling, multicenter imaging heterogeneity, and weak evidence-grounded interpretability. We propose ClinRAG-GRAPH, a Clinically informed Retrieval-Augmented Generation Graph framework, for pre-treatment pCR prediction from DCE-MRI, structured clinical variables, and biopsy-derived pathological biomarkers. ClinRAG-GRAPH constructs an intra-patient clinical-prior graph and applies a prior-guided relation-aware graph convolutional network for structured multimodal representation learning. To improve cross-center robustness, we introduce a dual-branch domain-adversarial learning strategy to suppress protocol-related MRI bias while preserving pCR-relevant features. To enhance interpretability, we further incorporate large language model (LLM)-driven subgraph RAG module that retrieves clinically analogous historical cases and integrates retrieved evidence for pCR inference. We assemble a large-scale multicenter NAC breast cancer cohort for extensive validation, drawing from two public sources and three in-house centers.Results show that ClinRAG-GRAPH achieves AUCs of 0.815 on the internal test set and 0.774/0.712 on two external test sets, demonstrating robust pre-treatment pCR prediction across centers. The code is available at the anonymized https://github.com/miccai26-1181/ClinRAG-GRAPH.

MAM-AI: An On-Device Medical Retrieval-Augmented Generation System for Nurses and Midwives in Zanzibar

Maternal and newborn mortality remain among the highest in sub-Saharan Africa, where midwifery care is often delivered by nurses who lack midwifery training to international standards, and consulting authoritative guidance at the point of care is hard: the guidelines are long and connectivity is intermittent. We present MAM-AI, a medical question-answering assistant for nurse-midwives in Zanzibar that runs entirely on a commodity Android device: a question is embedded (EmbeddingGemma, 300M) and matched against a curated corpus of 87 guideline documents (63,650 passages), then answered with citations by a 4B int4 generator (Gemma 4 E4B), fully offline, with no query leaving the device. We evaluate the exact deployed configuration with a layered methodology -- retriever, generator under oracle context, end-to-end, and latency -- scored by LLM judges validated against physician rubrics. The evaluation relocates the hard problem. On-device retrieval is essentially solved: the 300M embedder ranks third of seven retrievers and rivals cloud systems, so the passages the system needs are usually found. The small generator is what remains in doubt: adding retrieved context does not improve its answers, and at 4B it cannot be both helpful and safe at once -- of two same-size candidates, the more helpful one commits genuine dangerous errors, so we deploy the other, which is about twice as faithful to its sources (as faithful as a frontier model), and recover its helpfulness with a redesigned prompt that cuts deflection from 33% to 3%. Corpus quality is decisive for the same reason: where the corpus holds the right passage the answer is specific and actionable, and where it does not it goes vague. MAM-AI is a thoroughly evaluated, open-source research prototype, not a fielded product; the system, knowledge base, benchmarks, and evaluation harness are released.

mamabench and mamaretrieval: Benchmarks for Evaluating Medical Retrieval-Augmented Generation in Maternal, Neonatal, and Reproductive Health

Medical question-answering benchmarks rarely cover the maternal, neonatal, child, and reproductive-health questions a nurse-midwife asks, and, to our knowledge, no public chunk-level relevance benchmark exists for maternal-health guideline retrieval. We release two benchmarks that fill these gaps. mamabench is a scope-filtered QA set of 25,949 items assembled from seven existing expert-authored sources across multiple-choice, short-answer, and rubric-graded tracks; to help users calibrate the LLM judge that scores the rubric track, we re-scope HealthBench's physician-labelled meta-evaluation to the domain. mamaretrieval pairs 3,185 clinical queries with graded (0-6) relevance labels over a 63,650-chunk maternal-health guideline corpus, using a decomposed rubric that distinguishes a chunk that answers a query from one merely on its topic. Three decisions shape both: assemble and filter expert sources rather than author questions, grade relevance rather than binarise it, and measure and disclose the limits of the labels -- scope-classifier agreement, a frontier-judge check, and a pooling-completeness audit -- rather than treat them as an oracle. A companion paper uses the benchmarks to evaluate a deployed on-device assistant; both are released openly for research.

Hybrid-IR: Dual-Path Hybrid Retrieval with Iterative Reasoning for Complex Medical Question Answering

Large language models (LLMs) have shown promising performance across a wide range of biomedical applications, including medical question answering (QA), yet they remain prone to hallucinations and outdated knowledge. Although retrieval-augmented generation (RAG) can alleviate this issue by incorporating external documents, there still exist two fundamental limitations. First, medical knowledge is often fragmented across documents, while most RAG methods rely on a single retrieval path, which makes it challenging to jointly preserve fine-grained semantic information and structured global associations. Second, static retrieval strategies are typically insufficient to support deep reasoning that is important in complex medical QA. In this paper, we present a dual-path retrieval framework with an iterative retrieval-reasoning mechanism termed "Hybrid-IR" for complex medical QA. The proposed Hybrid-IR integrates graph-based retrieval for exploration of structured knowledge and dense retrieval for fine-grained semantic matching. Moreover, the reasoning trajectory can be progressively refined through an iterative retrieve-reason loop. Experiments on three widely used medical QA benchmarks demonstrate the effectiveness of our Hybrid-IR.

RASC+: Retrieval-Constrained LLM Adjudication for Clinical Value Set Authoring

Clinical value sets define the standardized terminology codes used in quality measurement, phenotyping, cohort construction, and clinical decision support. The recently introduced Retrieval-Augmented Set Completion (RASC) benchmark showed that direct zero-shot large language model (LLM) generation is poorly suited to this task: clinical code systems are large, version-controlled, and not reliably memorized by language models. We study a stage-wise alternative in which candidate-pool construction is optimized for recall and a constrained LLM adjudicator is optimized for candidate selection. On the full 3,744-value-set RASC test split, Qwen3-based retrieval with vocabulary-aware expansion and code-display rescue retrieval increases candidate-pool recall from the original RASC retrieval baseline of 0.553 to 0.730; on the held-out-publisher stratum, pool recall is 0.655. The higher-recall pool alone is not sufficient: applying the original SAPBert cross-encoder to this expanded pool gives full-test macro F1 of 0.287 and held-out-publisher macro F1 of 0.233. Replacing the stage-2 selector with blinded GPT-5 adjudication over the same pool increases full-test macro F1 to 0.549 and held-out-publisher macro F1 to 0.533. These results show that retrieval-constrained LLM adjudication can substantially improve value set completion while preserving the safety constraint that all returned codes must come from an auditable candidate pool.

Configurable Clinical Information Extraction with Agentic RAG: What Works, What Breaks, and Why

Patient contexts span hundreds of heterogeneous documents and thousands of structured data points, yet the document-level metadata that AI systems need for retrieval and triage is absent or incomplete. Standard retrieval-augmented generation fails on this data, mishandling temporal reasoning, cross-document dependencies, and missing metadata. We deploy ACIE (Agentic Clinical Information Extraction) at University Medicine Essen: an on-premise agentic RAG pipeline that reasons over complete patient contexts and grounds every answer in source passages for clinician verification. We quantify the metadata gap, trace the architectural decisions it shaped, and evaluate extraction alongside an independent retrospective lymphoma registry study, in which nuclear-medicine physicians verify every extracted value against its cited sources. Across 7,326 judgments, clinicians accepted 96.5\% of extractions, with per-type acceptance ranging from 80\% to 99\%.

Designing Safety-Constrained LLM Systems for Public Health Information Access

We present the design and implementation of a safety constrained large language model (LLM) system for public health information access, focusing on maternal and child health (MCH) resource navigation. While LLM based systems offer flexible and natural interfaces for information retrieval, their deployment in healthcare contexts introduces risks related to safety, trust, and uncontrolled generation. This work explores practical design patterns for constraining LLM behavior in safety critical environments. We introduce a multi-layered architecture that integrates domain-restricted retrieval augmented generation (RAG), strict boundary enforcement to prevent medical advice, anonymous multiuser session management, and comprehensive audit logging for monitoring and compliance. A key aspect of the design is a controlled data pipeline that grounds all responses in curated public health resources, avoiding reliance on the model pretrained medical knowledge. We implement the system in a real world public health setting and conduct scenario-based validation across in scope, out of scope, and emergency queries. Results show consistent enforcement of safety constraints, reliable resource grounding, and stable system performance, with an average response time of 5.3 seconds. Beyond the specific application, we discuss design trade offs and lessons learned in balancing safety, usability, and system flexibility. Our findings provide practical guidance for deploying LLM based systems in healthcare and other domains where strict information boundaries and accountability are required.

MARD: Mirror-Augmented Reasoning Distillation for Mechanism-Level Drug-Drug Interaction Prediction

Mechanism-level drug-drug interaction (DDI) prediction requires identifying which enzyme or pharmacodynamic axis is implicated, in which direction, and with which evidence -- not merely whether two drugs interact. We introduce a reproducible mechanism-level DDI labelling and evaluation protocol with a structured 7-family/147-subtype taxonomy, leakage-safe cold-split protocols, and auditable reasoning metrics for evaluating pharmacological prediction beyond flat interaction classification. We propose a pipeline that produces a 7B reasoning MARD (Mirror-Augmented Reasoning Distillation), combining three training innovations: a single-token KL divergence on direction tag that ties the model's prediction, per-loss PRM-weighted DPO with programmatic hard negatives, and a leakage-safe mechanism-aware retrieval channel. Process-reward step labels are automatically verifiable against DrugBank-structured fields, requiring no human or LLM judges. On the April-2026 DrugBank release, our MARD-7B is the only system in a 32-system comparison whose accuracy survives drug-pair novelty, beating the best baseline by +13.9 pp and GPT-4o by +6.7 pp at ~1% of frontier API cost. Further analysis reveals an anti-memorisation signature where accuracy improves on rarely seen drugs, suggesting that gain comes from structured pharmacological reasoning rather than drug-frequency memorisation. We release corpus, DDI-PRM, retrieval index, and training code.

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.

ChronoMedKG: A Temporally-Grounded Biomedical Knowledge Graph and Benchmark for Clinical Reasoning

Biomedical knowledge graphs (KGs) treat disease associations as static facts, but temporal information is crucial for clinical reasoning, e.g., a symptom diagnostic of one disease at age 3 may imply a different disease at age 13. Existing KGs such as PrimeKG, Hetionet, and iKraph do not encode when a finding becomes clinically relevant over the course of a disease. This limits their usefulness for longitudinal clinical reasoning and retrieval augmentation. We introduce ChronoMedKG, a temporal biomedical knowledge graph that contains 460,497 evidence-linked triples (filtered from 13M raw extractions) covering 13,431 diseases. Each association is tied to temporal components like onset window or progression stage, which are backed by PMID-traceable evidence and a multi-signal credibility score. The graph is constructed through a disease-autonomous multi-agent pipeline in which multiple frontier LLMs independently extract knowledge from PubMed and PMC literature. Only those relations are kept that are supported by multi-model consensus, survive credibility filtering, as well as ontology alignment. ChronoMedKG scored 92.7% agreement against Orphadata and adds temporal grounding for 6,250 diseases absent from HPOA, Orphadata, and Phenopackets, including 1,657 Orphanet-coded rare diseases. We further introduce ChronoTQA, a benchmark of 3,341 questions across eight task types (six temporal plus two static controls), with a 12-question supplementary probe. Frontier LLMs lose roughly 30 points moving from static to temporal questions; ChronoMedKG retrieval rescues 47-65% of their long-tail failures, against 17-29% for HPOA-RAG. As such, ChronoMedKG provides a crucial temporal axis for retrieval-augmented clinical systems that was previously absent.