Asma Ben Abacha

Wen-wai Yim, Yujuan Fu, Asma Ben Abacha et al.

Recent advances in dermatological image analysis have been driven by large-scale annotated datasets; however, most existing benchmarks focus on dermatoscopic images and lack patient-authored queries and clinical context, limiting their applicability to patient-centered care. To address this gap, we introduce DermaVQA-DAS, an extension of the DermaVQA dataset that supports two complementary tasks: closed-ended question answering (QA) and dermatological lesion segmentation. Central to this work is the Dermatology Assessment Schema (DAS), a novel expert-developed framework that systematically captures clinically meaningful dermatological features in a structured and standardized form. DAS comprises 36 high-level and 27 fine-grained assessment questions, with multiple-choice options in English and Chinese. Leveraging DAS, we provide expert-annotated datasets for both closed QA and segmentation and benchmark state-of-the-art multimodal models. For segmentation, we evaluate multiple prompting strategies and show that prompt design impacts performance: the default prompt achieves the best results under Mean-of-Max and Mean-of-Mean evaluation aggregation schemes, while an augmented prompt incorporating both patient query title and content yields the highest performance under majority-vote-based microscore evaluation, achieving a Jaccard index of 0.395 and a Dice score of 0.566 with BiomedParse. For closed-ended QA, overall performance is strong across models, with average accuracies ranging from 0.729 to 0.798; o3 achieves the best overall accuracy (0.798), closely followed by GPT-4.1 (0.796), while Gemini-1.5-Pro shows competitive performance within the Gemini family (0.783). We publicly release DermaVQA-DAS, the DAS schema, and evaluation protocols to support and accelerate future research in patient-centered dermatological vision-language modeling (https://osf.io/72rp3).

Jean-Philippe Corbeil, Asma Ben Abacha, Jerome Tremblay et al.

Clinical documentation increasingly uses automatic speech recognition and summarization, yet converting conversations into actionable medical orders for Electronic Health Records remains unexplored. A solution to this problem can significantly reduce the documentation burden of clinicians and directly impact downstream patient care. We introduce the MEDIQA-OE 2025 shared task, the first challenge on extracting medical orders from doctor-patient conversations. Six teams participated in the shared task and experimented with a broad range of approaches, and both closed- and open-weight large language models (LLMs). In this paper, we describe the MEDIQA-OE task, dataset, final leaderboard ranking, and participants' solutions.

Jean-Philippe Corbeil, Asma Ben Abacha, George Michalopoulos et al. · microsoft-research

Large language models (LLMs) such as GPT-4o and o1 have demonstrated strong performance on clinical natural language processing (NLP) tasks across multiple medical benchmarks. Nonetheless, two high-impact NLP tasks - structured tabular reporting from nurse dictations and medical order extraction from doctor-patient consultations - remain underexplored due to data scarcity and sensitivity, despite active industry efforts. Practical solutions to these real-world clinical tasks can significantly reduce the documentation burden on healthcare providers, allowing greater focus on patient care. In this paper, we investigate these two challenging tasks using private and open-source clinical datasets, evaluating the performance of both open- and closed-weight LLMs, and analyzing their respective strengths and limitations. Furthermore, we propose an agentic pipeline for generating realistic, non-sensitive nurse dictations, enabling structured extraction of clinical observations. To support further research in both areas, we release SYNUR and SIMORD, the first open-source datasets for nurse observation extraction and medical order extraction.

Jean-Philippe Corbeil, Amin Dada, Jean-Michel Attendu et al.

High computation costs and latency of large language models such as GPT-4 have limited their deployment in clinical settings. Small language models (SLMs) offer a cost-effective alternative, but their limited capacity requires biomedical domain adaptation, which remains challenging. An additional bottleneck is the unavailability and high sensitivity of clinical data. To address these challenges, we propose a novel framework for adapting SLMs into high-performing clinical models. We introduce the MediPhi collection of 3.8B-parameter SLMs developed with our novel framework: pre-instruction tuning of experts on relevant medical and clinical corpora (PMC, Medical Guideline, MedWiki, etc.), model merging, and clinical-tasks alignment. To cover most clinical tasks, we extended the CLUE benchmark to CLUE+, doubling its size. Our expert models deliver relative improvements on this benchmark over the base model without any task-specific fine-tuning: 64.3% on medical entities, 49.5% on radiology reports, and 44% on ICD-10 coding (outperforming GPT-4-0125 by 14%). We unify the expert models into MediPhi via model merging, preserving gains across benchmarks. Furthermore, we built the MediFlow collection, a synthetic dataset of 2.5 million high-quality instructions on 14 medical NLP tasks, 98 fine-grained document types, and JSON format support. Alignment of MediPhi using supervised fine-tuning and direct preference optimization achieves further gains of 18.9% on average.