Medical
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DrugReason: Dynamic Multi-View Reasoning over Knowledge Graph and Language Evidence for Drug Repurposing
2026-09-06 18:54:26Zijie Liu, Hongxuan Li, Zhen Tan, Jinhao Duan, Baixiang Huang, Zunpeng Liu, Kai Shu, Tianlong ChenAbstract
Drug repurposing aims to identify new therapeutic uses for existing compounds and, compared with de novo drug discovery, offers a faster and more cost-effective path to clinical translation. However, the space of candidate drug-disease pairs is enormous and their underlying relationships often depend on complex multi-hop biological mechanisms, making it difficult to reliably predict which pairs represent true therapeutic relationships. Existing approaches tackle this from two directions: knowledge graph-based methods organize curated biomedical evidence into structured relational networks for grounded multi-hop reasoning, while LLM-based methods leverage pretrained knowledge to generate flexible mechanistic rationales. Yet neither is sufficient alone - KGs are confined to observed graph structure while LLMs lack factual grounding and risk hallucination. To address this gap, we propose DrugReason, a multi-view reasoning framework that integrates grounded KG reasoning with LLM-generated mechanistic inference for drug repurposing. DrugReason adaptively routes diverse reasoning paths to specialized experts conditioned on the query context, while a cross-expert distillation objective enables knowledge sharing without sacrificing expert specialization. Experiments on PharmaDB, DDInter, and DrugBank show that DrugReason improves average performance over strong single-view reasoning baselines and achieves competitive or superior results compared with graph-based alternatives, while providing interpretable routing-based predictions.
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https://arxiv.org/abs/2609.06779
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What Matters, When? Diagnosing and Improving Conditional Visual Grounding in Visuomotor Imitation Policies
2026-09-04 17:27:35Vivek Chavan, Pengtao Xie, Yahuan Shi, Oliver Heimann, Kevin Haninger, J\"org Kr\"ugerAbstract
Visuomotor imitation policies can achieve high performance under in-distribution visual conditions yet fail when visually similar objects or receptacles are introduced. We study this behavior as a problem of conditional visual grounding: the visual target required for successful control changes with the manipulation phase and, in more complex tasks, with the observed task state. Using Action Chunking with Transformers (ACT), we systematically introduce distractor objects and receptacles with controlled color and shape similarity and localize failures to picking and placement. We find that distractor sensitivity is specific to both the type of visual similarity and the manipulation stage. Guided by this diagnosis, we evaluate distractor augmentation, phase-dependent attention regularization, and appearance-based visual prompting as complementary interventions for improving target selection while preserving spatial information required for control. These interventions substantially improve robustness in simulation and on a physical UR3e. We further examine the same failure pattern in a pretrained vision-language-action policy on a state-conditioned instrument-handling task, where the observed state of a medical instrument determines the correct destination. Together, the results show that visual distractors can cause incorrect object or destination selection even when the underlying manipulation skill remains intact, and that explicitly improving target selection can substantially recover performance across distinct visuomotor policy-learning regimes.
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https://arxiv.org/abs/2609.05376
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Real-World Multi-Modal and Longitudinal Lung Cancer Dataset
2026-09-04 14:35:10Rita Cordeiro Mendes, Maria Rita Fonseca Verdelho, Carlos Santiago, Catarina BarataAbstract
Multi-modal learning has demonstrated strong potential in medical applications by integrating heterogeneous data sources such as medical imaging, clinical records, and genomics to improve predictive performance and support clinical decision-making. However, advances in this area are often constrained by two key challenges: the limited availability of well-curated, ready-to-use datasets that accurately reflect real-world conditions, where medical data are frequently collected inconsistently and are often incomplete; and the inherent difficulty of integrating heterogeneous data modalities. In this work, we introduce a newly curated multi-center, multi-modal, and longitudinal dataset designed to support the evaluation of a wide range of learning pipelines under realistic conditions. The dataset comprises a total of 1,365 lung cancer patients and has three imaging modalities (whole-slide images, CT scans, and PET scans), structured clinical data, transcriptomic, and longitudinal follow-up and treatment information. For each imaging modality the dataset contains more than one instance. Moreover, the dataset exhibits substantial and non-uniform missingness across modalities, making it well-suited for studying robust multi-modal fusion strategies. We further provide both uni-modal and multi-modal benchmarks on the task of 12-month overall survival prediction, disease-specific survival, as well as longitudinal benchmark of hazard prediction under severe missing data. Our results show that, despite high levels of missingness, integrating complementary modalities consistently improves predictive performance over uni-modal approaches, highlighting the value of multi-modal fusion in realistic clinical settings. The dataset and benchmark code are available at this https URL.
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https://arxiv.org/abs/2609.05202
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Measuring the Novelty of Biomedical Papers Using the Latent Distances between Knowledge Units
2026-09-04 14:14:26Yi Zhao, Heng Zhang, Yuzhuo Wang, Wenqing Wu, Tong Bao, Chengzhi ZhangAbstract
Measuring the novelty of scientific papers is a central concern in research evaluation and scientometrics. From a recombination perspective, prior studies have largely focused on the co-occurrence of knowledge units to assess the novelty of scientific papers. However, these studies often overlook other relationships between knowledge units. This narrow view may result in inaccurate or incomplete evaluations of novelty for scientific papers. To fill this gap, this study introduces a comprehensive novelty measurement that incorporates three types of relationships between knowledge units: network, semantic, and hierarchical. These relationships are used to quantify the latent distances among knowledge units. Using a dataset of 142,036 articles published in PLoS ONE and a validation dataset from the H1 Connect platform, our results demonstrate that (1) each relationship type captures distinct latent distances between MeSH terms; (2) compared to the widely used indicators proposed by Uzzi et al. (2013), our measures show stronger alignment with peer judgements; and (3) combining all three distance metrics yields more effective identification of novel papers than using any single perspective alone.
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https://arxiv.org/abs/2609.05175
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SMILE: Self-Explainable Multimodal Information Bottleneck for Medical Diagnosis
2026-09-04 14:13:24Yuqing Yang, Alexander Schmatz, Zhaozhao Ma, Changkyu Choi, Robert Jenssen, Shujian YuAbstract
Explainability is increasingly seen as a crucial requirement in AI-based medical diagnosis, particularly in safety-critical clinical decision-making. Most existing explainability methods in healthcare operate in a post-hoc manner and are predominantly designed for unimodal data, which limits their applicability in increasingly prevalent multimodal diagnostic settings. This paper addresses the problem of self-explainable multimodal diagnosis by formulating it within the information bottleneck (IB) framework. We propose a unified learning paradigm that jointly optimizes predictive performance and modality-specific explainability by identifying the most informative elements inside each modality that contribute to diagnostic decisions. To enable tractable and stable optimization, we employ a matrix-based Renyi's $\alpha$-order entropy functional under the assumption of sufficiently expressive encoders. Extensive experiments on representative medical datasets spanning heterogeneous modalities demonstrate that the proposed method consistently achieves strong diagnostic performance, including an absolute accuracy improvement of 9.1 percentage points on the iCTCF dataset. Moreover, the learned explanations provide transparent and modality-aware insights into feature relevance, thereby improving both the explainability and generalization.
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https://arxiv.org/abs/2609.05174
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A Hybrid Predictive Ensemble of Machine Learning and Deep Neural Networks for Early Cardiovascular Disease Risk Assessment
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This study introduces an intelligent framework that integrates machine learning and deep neural network ensemble techniques for early detection and prognosis of cardiovascular diseases. The system utilizes real-time physiological data collected from Internet of Medical Things (IoMT) devices, including ECG sensors, heart rate monitors, and blood pressure trackers. To ensure the accuracy and reliability of input data, preprocessing steps such as noise reduction, normalization, and missing value imputation are employed. The most significant health indicators are identified through effective feature selection methods and then processed using optimized classifiers such as Support Vector Machines (SVM), Random Forests, and eXtreme Gradient Boosting (XGBoost), which are combined in an ensemble architecture to improve diagnostic precision. The framework demonstrates remarkable performance in predicting cardiovascular disease risk, achieving higher accuracy, reduced false positives, and enhanced consistency compared to conventional methods. It is designed on a cloud-based infrastructure that ensures scalability and real-time processing for continuous patient monitoring. Experimental evaluation on real-world cardiovascular datasets confirms the framework's efficiency in early-stage risk assessment and clinical decision support. The results highlight the potential of combining traditional machine learning and deep learning paradigms to achieve proactive healthcare management and improve patient outcomes.
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https://arxiv.org/abs/2609.05146
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Cross-dataset transportability of pediatric chest X-ray deep learning across three countries: discrimination, calibration, operating-point failure, and limited-label recovery
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Background and Objective: External evaluation of medical-imaging AI is often collapsed into discrimination. We evaluated a computational protocol that separately tests discrimination, probability calibration, fixed operatingpoint transport, shortcut-associated signal, and limited-label recoverability for pediatric pneumonia classification across datasets from three countries. Methods: After exact-duplicate removal, 5,824 Guangzhou radiographs supported leakage-controlled source development and internal testing. A frozen three-seed DenseNet121 dual-view ensemble was evaluated zero-shot on BDCXR-3257 from Bangladesh (n = 3, 257) and an untouched harmonized VinDr-PCXR/PediCXR test cohort from Vietnam (n = 1, 077). Matched seed-42 variants tested architectural robustness. Secondary BDCXR analyses used a fixed 651-image adaptation pool and 2,606-image hold-out; 163, 326, and 651 labels represented 5%, 10%, and 20% of complete BDCXR. Results: Internal AUROC was 0.976 with 95.1% sensitivity. BDCXR and VinDr-PCXR AUROC were 0.798 and 0.742, while frozen-threshold sensitivity fell to 6.2% and 0%. Source-to-BDCXR AUROC degradation occurred for a full-image baseline (0.961 to 0.749), ungated dual-view model (0.977 to 0.766), and gated MixStyle model (0.966 to 0.789). With 163 BDCXR labels, Platt recalibration preserved AUROC while increasing held-out sensitivity to 88.3%, but specificity was 47.9% and the alert rate was 78.5%. Two hundred repeated 163-label fits confirmed sensitivity recovery but substantial specificity variability. Conclusions: Cross-dataset shifts across countries affected ranking, probability alignment, and source-defined decision behavior differently. Transport studies should evaluate these components separately and quantify the operational burden of apparent recovery.
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https://arxiv.org/abs/2609.05140
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Constructing and Evaluating Clinical Reasoning Trajectories for Medical Agent
2026-09-04 12:44:10Yunqi Zhu, Wensheng Zhang, Xuebing YangAbstract
Evaluation of medical artificial intelligence agents remains predominantly answer-centric, assessing only the correctness of final outputs while overlooking the quality of intermediate reasoning. In clinical settings, however, a correct answer reached through fabricated evidence or incoherent logic is as dangerous as an incorrect one. We propose MedTraj, a framework that treats reasoning trajectories as critical objects for construction, evaluation, and optimization. The pipeline generates structured multi-step reasoning chains from medical reasoning sources. Each trajectory is then parsed into clinical observations, evidence, numbered reasoning steps, and a final conclusion, and scored across five quality dimensions: coherence, evidence support, hallucination, completeness, and traceability. Controlled error injection introduces targeted faults into otherwise correct trajectories to establish causal links between specific reasoning failures and measurable quality degradation. Building on this, step-level filtering based on marginal contribution identifies which individual reasoning steps drive or undermine trajectory quality. Finally, quality-weighted context learning feeds trajectory evaluations back into the model at inference time, allowing it to learn from both strong and weak reasoning demonstrations. Experiments across CareQA, PubMedQA, and CECMed demonstrate that trajectory context consistently improves reasoning coherence, with gains of +0.029 to +0.041 over a zero-shot baseline. On CECMed, quality-weighted context nearly doubles the correctness over the zero-shot baseline while cutting the hallucination ratio by 87%. Marginal-contribution analysis further shows that a small minority of reasoning steps carry most of the quality signal, and that extending chains beyond four steps yields diminishing returns.
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https://arxiv.org/abs/2609.05090
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A Structured Debate-Mixture-of-Agents Framework for Complex Clinical Diagnostic Decision Support
2026-09-04 12:28:31Chang Xia, Leilei Ouyang, Huimin Wang, Yong Zhao, Kang LiAbstract
Large language models (LLMs) show potential for medical tasks, but their single-turn question-answer format does not reflect how clinical diagnosis is performed in practice. As a result, they remain limited in complex diagnostic settings. We developed Debate-Mixture-of-Agents (DMoA), a novel multi-agent framework that structures role-based interaction to support iterative diagnostic reasoning. Base models and DMoA were evaluated on 297 rare disease cases and 1,719 challenging cases. Across both datasets, DMoA improved most likely diagnosis accuracy by 10.21 percentage points and safety rate by 11.36 percentage points over GPT-4o baseline. Ablation experiments showed that the gains were not simply due to the use of more models or longer outputs, but also reflected the contribution of the structured workflow. Further analyses examined how framework design, base model choice, and token budget affected performance. DMoA performed better with a 4*2 structure, stronger base models, and a larger token budget. These findings demonstrate the potential of DMoA for clinical tasks and suggest further investigation of multi-agent frameworks.
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https://arxiv.org/abs/2609.05069
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Compositional Reward Models for Conditional Medical Image Generation
2026-09-04 11:46:25Aayush Kumar Tyagi, Prathosh A. P., MausamAbstract
Acquiring high quality annotated medical image data is critical for training deep learning models; however, annotation is expensive, time consuming, and requires domain expertise. Conditional diffusion models, such as ControlNet, offer an alternative by generating images conditioned on semantic masks and text. However, existing approaches fail to capture fine grained properties (e.g., intensity and texture), as well as semantic consistency expected by domain experts, limiting their effectiveness for downstream tasks. Recent attempts to address these issues using reinforcement learning fine-tuning remain limited due to the reliance on a single scalar reward, which conflates diverse failure modes and provides weak corrective signals. We propose PRISM, a Compositional Reward Model (CRM) framework for conditional medical image generation. Instead of assigning a single reward, we decompose image quality into verifier grounded stages, each evaluating a distinct aspect of correctness from fine to coarse properties, including low level attributes (intensity and texture), structural alignment with conditioning inputs, and high level semantic fidelity. These stage wise rewards are composed through a Hierarchical Constrained Propagation (HCP) mechanism that enforces a fine to coarse notion of correctness, ensuring that lower level deficiencies are resolved before higher level rewards are accrued, preventing easier objectives from masking critical failures. We evaluate PRISM across three datasets spanning diverse medical imaging tasks: PanNuke (multi-class cell segmentation), CeDeM (villi/crypt detection and measurement), and ISIC (skin lesion classification). Training downstream models with data generated by PRISM yields improvements over closest baselines, including a 2.3% increase in mDice on PanNuke, a 8.5% reduction in Mean Relative Error (MRE) on CeDeM, and increases ISIC F1 by 5.9%.
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https://arxiv.org/abs/2609.05028
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BIT.UA at BioASQ 14B: Modular Retrieval with pg_textsearch and Qdrant, and Agent-Based Answer Generation
2026-09-04 11:10:07Andr\'e Ribeiro, R\'uben Garrido, Alexander Christiansen, Richard A. A. Jonker, S\'ergio MatosAbstract
This paper describes the participation of the this http URL team from the University of Aveiro in the 14th edition of the BioASQ Task B challenge on biomedical question answering. Building on our previous submissions, we introduced a substantially refactored and modular codebase, and made significant changes to both the retrieval and generation components of the pipeline. For Phase~A document retrieval, we replaced the PyTerrier PISA index with PostgreSQL-based pg\_textsearch for BM25 retrieval and adopted Qdrant for dense embedding indexing, enabling more efficient storage and GPU-accelerated similarity search. We explored HyDE-based query expansion alongside a Context-1 retrieval strategy. A new reranker training pipeline was developed, incorporating dense retrieval for negative sampling. For Phases A+ and B answer generation, we introduced an LLM-as-a-judge framework and a novel agent quorum mechanism, where multiple agents with diverse prompts debate and iteratively converge on a consensus answer using adaptive document retention. We also participated in the snippets generation subtask for the first time. Our systems achieved competitive results across all batches, with Phase~A systems achieving MAP ranks of 5 (Batch~1,3). We discuss the impact of these architectural changes, lessons learned, and outline directions for future work including SPLADE and ColBERT integration. All code is openly available: this https URL.
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https://arxiv.org/abs/2609.04999
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MMTClinic: Multimodal, Multilingual Time Series Question Answering and Reasoning Benchmark for Clinical Domain
2026-09-04 07:59:19Sourav Malakar, Harshit Nigam, Akash Ghosh, Sriparna Saha, Amlan Chakrabarti, Saptarsi Goswami, Priti SinghAbstract
Time-series data in clinical settings is crucial for capturing dynamic changes in a patient's health over time, enabling timely diagnosis, personalized treatment, and early detection of critical events. However, the development of clinically reliable and linguistically inclusive medical AI systems remains a significant challenge, primarily due to the lack of multimodal, multilingual, and time-series-grounded benchmarks that reflect the complexity of real-world clinical scenarios. To fill this gap, we present MMTClinic, a benchmark designed to evaluate large language models (LLMs) on complex reasoning and question-answering tasks involving clinical time-series. MMTClinic combines text, medical images, and multivariate physiological signals and includes 30,000 QA pairs (15,000 multiple choice questions (MCQs) and 15,000 open-ended questions) across five languages: English, Hindi, Bengali, Marathi, and Tamil. These questions cover three important clinical tasks---mortality prediction, heart rate forecasting, and SOFA score estimation. We evaluate 13 state-of-the-art LLMs in zero-shot, few-shot, and chain-of-thought settings. Our evaluation reveals notable differences in model performance across tasks, languages, and modalities, highlighting current limitations in clinical reasoning capabilities. MMTClinic provides a valuable resource for advancing multilingual, multimodal, and time-series-aware medical AI research. The dataset will be made publicly available on successful acceptance of the work.
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https://arxiv.org/abs/2609.04842
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MedFlow: Class-Aware Multi-Scale Generation for Medical Time-Series Synthesis
2026-09-04 07:02:12Yanhao Huang, Shibo Feng, Wanjin Feng, Peilin Zhao, Chunyan MiaoAbstract
Synthetic medical time-series generation can alleviate data scarcity and support the development of reliable clinical prediction models. However, existing methods mainly focus on matching the overall distribution and temporal dynamics of real data, which does not necessarily ensure strong downstream utility on imbalanced medical datasets. Clinically informative patterns often occur at heterogeneous temporal scales, while rare minority-class characteristics can be obscured by dominant population patterns. To address these challenges, we propose MedFlow, a class-aware multi-scale flow matching framework for medical time-series synthesis. MedFlow employs a vector-quantized multi-scale tokenizer to represent medical sequences at complementary temporal resolutions, capturing both coarse clinical trends and fine-grained dynamics. We further introduce Token Marginal Guidance, which incorporates class-conditional token statistics directly into the flow matching process to steer generation toward class-specific regions of the learned tokens. This mechanism strengthens minority-class patterns, while preserving the global and tail distributions of real data. Experiments on four public datasets covering electronic health records, EEG, and ECG signals demonstrate that MedFlow consistently outperforms recent state-of-the-art diffusion-based baselines across downstream prediction tasks. On average, it improves AUPRC by 5.8%, reduces Context-FID by 88.6%, and achieves 3.8$\times$ higher sampling throughput.
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https://arxiv.org/abs/2609.04804
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An Attention-Guided Global and Local Fusion Framework for Lesion-Focused Image Classification
2026-09-04 06:36:06Mst Shafia Tasnima, Md Samaun Elaheea, Tanjim Taharat Aurpab, Md Musfique AnwarAbstract
Lesion-focused image classification presents a core analytical challenge, as discriminative signals are often sparse, spatially dispersed, and easily obscured by background noise, while conventional convolutional neural networks (CNNs) process entire images uniformly and may dilute signal relevance. This study hypothesizes that adaptive fusion of global contextual information and lesion-focused local information can improve classification performance compared with using either representation independently. We propose a three-branch, attention-guided deep learning framework built on Densely Connected Convolutional Network-121 (DenseNet-121) to improve feature attribution, interpretability, and classification reliability. The architecture consists of a global branch that learns representations from full images, followed by Gradient-weighted Class Activation Mapping (Grad-CAM) to generate attention maps that highlight prediction-relevant regions and produce masked inputs, and a local branch enhanced with a Convolutional Block Attention Module (CBAM) to extract refined spatial and channel-wise features from these focused regions. An adaptive fusion branch integrates global and local representations by learning instance-specific weights, allowing dynamic prioritization between contextual and localized information. The framework is evaluated on a synthetic Spot Pattern Dataset (SSPD) and three benchmark datasets, including skin lesion, guava leaf, and grape leaf image datasets, where the fusion branch outperformed the individual global and local branches, reaching 97.75% accuracy on the skin lesion dataset and 99.64% on the guava leaf dataset. The results highlight the value of attention-guided architectures in healthcare analytics by improving model transparency, strengthening feature relevance, and supporting more reliable data-driven decision-making in medical image analysis.
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https://arxiv.org/abs/2609.04791
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CoMLP: Cooperatively-Gated MLPs for Fine-Grained Cross-Modal Information Fusion in Medical Image Segmentation
2026-09-04 06:18:44Mingyuan Meng, Shuchang Ye, Mingjian Li, Zhenyu Zhao, Jinman Kim, Lei BiAbstract
Multi-modal medical images and clinical reports provide complementary anatomical, functional, and semantic information for medical image segmentation. Effectively exploiting these heterogeneous sources requires fine-grained cross-modal information fusion that preserves subtle spatial details while capturing semantic dependencies across modalities. Existing fusion approaches frequently rely on cross-attention, whose computational burden increases rapidly with spatial resolution, making dense cross-modal interaction difficult on high-resolution feature maps, particularly for volumetric medical images. In this work, we propose CoMLP, a cooperatively-gated MLP module for fine-grained cross-modal information fusion in medical image segmentation. CoMLP models cross-modal dependencies through cooperative cross-gating, built upon complementary regional and dilated MLP interactions, to capture local and global cross-modal dependencies. We further develop a multi-source fusion architecture in which CoMLP performs both inter-image fusion across imaging modalities and vision-language fusion between visual features and textual reports, enabling heterogeneous information to be integrated without relying on dense cross-attention. Extensive experiments on five medical segmentation benchmarks, covering 2D/3D images, clinical reports, multiple imaging modalities, and diverse anatomical regions, demonstrate consistent improvements over state-of-the-art multi-modal and language-guided segmentation methods. Ablation studies further show that fine-grained interaction at high spatial resolutions and complementary local-global fusion are critical to the performance gains. These results demonstrate the potential of MLP-based interaction as an effective alternative for fine-grained cross-modal information fusion in medical image segmentation.
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https://arxiv.org/abs/2609.04781
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Model Retirement Creates Reproducibility Risk in Biomedical AI Publications
2026-09-04 04:00:54Nathan Wolfrath, Meghan Conroy, Thomas Kosten, Dave Bell, Bhabishya Neupane, Jonah Kindel, Anjishnu Banerjee, Priya Deshpande, Bradley Taylor, Anai N. KothariAbstract
Background. Large language models (LLMs) are being adopted in biomedical research at a rapid and accelerating pace, yet commercial services that host many widely used models operate under deprecation schedules that can complicate scientific reproducibility. Methods. We searched PubMed for original research articles from 2022 through March 2026 that applied a specific LLM to a biomedical task. An extraction agent identified model names from 61,077 article abstracts with human reviewers validating a subset for extraction accuracy. Extracted model names were normalized to canonical model identifiers. Lifecycle data (release date, retirement date, status) were compiled for the 50 most frequently used models. Results. We identified 8,931 paper-model mentions spanning 5,242 unique publications after restricting the analysis to the 50 most frequently used models. Among these mentions, 77.7% cited a commercial closed-weight model. Overall, 42% involved a model that was already retired by the time of official publication or is scheduled to retire within two years of publication. The median interval from publication to model retirement was 538 days. Conclusion. Many biomedical publications using LLMs are on a trajectory toward computational non-reproducibility after publication. Model deprecation should be treated as a core reporting and preservation issue for biomedical research.
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https://arxiv.org/abs/2609.04699
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Knowledge Graph-Augmented Ambient AI for Clinical Note Generation
2026-09-04 03:05:50Jakir Hossain, Yi-Fei Zhao, Hongjian Wang, Minmei Shih, Katie Leigh Mullen, Ahmad P. Tafti, Leming Zhou, Manoj Purohit, William Hogan, Jay Zeng, Elizabeth Skidmore, Yanshan WangAbstract
Ambient AI is increasingly adopted in healthcare to automatically generate clinical notes from patient-clinician conversations, with the potential to substantially reduce clinician documentation burden. However, generated notes may omit clinically relevant information discussed during the encounter, creating information gaps that can affect downstream care. Knowledge graphs (KGs) constructed from encounter transcripts can provide a structured representation of what was discussed and enable systematic identification of missing information from generated notes that are critical for patient care. In this study, we introduce Coverage-Directed Revision (CDR), a model-agnostic framework that constructs a KG from the encounter transcript, identifies medical concepts absent from an initially generated note, and directs large language models (LLMs) to restore the missing information without modifying the underlying note-generation system. We evaluate CDR on two datasets: 1) Pitt-Bench, a local dataset comprising rehabilitation sessions, and 2) ACI-Bench, a public dataset for benchmarking clinical note generation. We tested four underlying LLMs widely used in ambient AI systems. The results show that CDR consistently improves content recall across all evaluated conditions. Our study provides a practical approach for improving the completeness of ambient AI-generated clinical documentation.
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https://arxiv.org/abs/2609.22239
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Hakken: Predicting future discoveries to fill the gaps in today's knowledge
2026-09-03 21:28:36Tarek R. Besold, Uchenna Akujuobi, Pablo Sanchez, Alessandra Toniato, Kana Maruyama, Jihun Choi, Samy Badreddine, Frederick Gifford, Daniel Evans-Yamamoto, Sucheendra K. Palaniappan, Miquel Ferrer, Kae Nagano, Iris Rossell, Tom Joy, Hatem ElShazly, Chrysa Iliopoulou, Christoph Wehner, Thiviyan Thanapalasingam, Susana Nunes, Pedro G. Cotovio, Peter Wurman, Peter Stone, Hiroaki Kitano, Michael SprangerAbstract
We present Hakken, a domain-agnostic prediction and explanation system performing knowledge prediction, i.e., growing scientific knowledge by establishing novel relationships, ones that are not limited to the deductive hull of previous knowledge. Hakken uses a transformer-based prediction model built on temporal sequences of knowledge graphs extracted from vast bodies of research publications, fused with an LLM's semantic knowledge, to predict the presence and define the type of as-yet undocumented relationships between scientific concepts. It then calls a model-agnostic explanation framework to provide accompanying information for each prediction that allows scientists to evaluate the suggested new relationship. While general purpose, we demonstrate Hakken's practical capabilities by applying it to the biomedical domain. There, Hakken's prediction model establishes a new benchmark for time-aware multi-label relation prediction, and we show that the model's output stays coherent and informative over extended time spans in historic data. In addition, we scored 1.5 million above-confidence-threshold hypotheses related to aging, qualitatively validated batches of these predictions with biologists and progressed three of them for empirical validation in wet-lab. Two predictions with potentially significant impact in the context of drug discovery and repurposing were confirmed, introducing previously undocumented interactions between TP53 and BAMBI, and between RAF1 and TNF, to biomedical science.
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https://arxiv.org/abs/2609.04494
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REFINE: LLM Refinement over Budgeted Text-Attributed Graphs for Personalized Medical Concept Representation
2026-09-03 19:29:22Mohsen Nayebi Kerdabadi, Arya Hadizadeh Moghaddam, Dongjie Wang, Zijun YaoAbstract
Learning rich medical concept representations is essential for EHR prediction. Text-attributed knowledge graphs (TKGs) provide a natural foundation by organizing heterogeneous medical relations together with textual semantics. However, most existing encoders process concepts uniformly across patients, despite the fact that a code's meaning and predictive value depend on patient-specific clinical context and trajectory. Learning patient-personalized concept representations from TKGs introduces two key challenges: (1) deciding how much KG context to incorporate for each observed code, and (2) aligning semantic information with the patient-specific relational structure. We propose REFINE, a KG-aware budgeted LLM graph refinement framework for patient-personalized medical concept encoding. Starting from a global TKG, REFINE constructs patient-specific temporal graphs. A sequential reinforcement learning policy selects a personalized KG expansion budget for each observed code. The resulting patient graph is processed by a heterogeneous GNN to capture relation-aware structural dependencies, while a frozen LLM uses graph-aware soft prompts to semantically refine concept representations. Experiments on MIMIC-III and MIMIC-IV show that REFINE consistently improves diverse EHR backbones, outperforms strong baselines, and demonstrates robust gains across component ablation, KG selection, and data insufficiency.
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https://arxiv.org/abs/2609.04415
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MedProb: Probing Internal Representations of Vision-Language Models for Medical Question Answering
2026-09-03 18:04:36Erfan Nourbakhsh, Ke Yang, Anthony RiosAbstract
Medical visual question answering (Med-VQA) is often assumed to require medical fine-tuning, large models, or complex multi-agent pipelines. We revisit this assumption with \textbf{MedProb}, a lightweight probing framework that predicts multiple-choice Med-VQA answers from frozen VLM representations without free-text generation. Across PATH-VQA, SLAKE, and VQA-RAD, MedProb recovers substantially more answer-relevant signal than prompting and performs stronger than medical VLMs and agentic systems. Probing also reduces the apparent gap between small and large models compared to prompting, suggesting that smaller VLMs contain more recoverable Med-VQA signal than generation-based evaluation reveals. Across 14 matched general-purpose and medical VLM pairs, medical adaptation does not consistently improve this linear decodability. Finally, free-text generation exhibits an answer-position bias of up to 10 percentage points, whereas MedProb also has positional bias, however, it is impacted differently than prompting. Our main results target the multiple-choice/multiclass Med-VQA setting; we additionally show the probe can be extended to open-ended generation via a rejection-sampling scoring procedure.
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https://arxiv.org/abs/2609.04336
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