Electroencephalography (EEG) decoding models often generalize poorly across datasets and subjects due to domain shifts in acquisition protocols and individual neurophysiology. We propose EEG-PRIME, a two-stage EEG foundation model for cross-dataset multi-task decoding. EEG-PRIME combines masked pretraining with prototype-aligned instruction tuning to enable instruction-aware and subject-invariant decoding across diverse BCI paradigms. During pretraining, an EEG encoder learns transferable representations through masked reconstruction with frequency-cutoff spectral augmentation. During instruction tuning, EEG-PRIME incorporates task-semantic, dataset-specific, and subject-invariant conditioning. The resulting conditioning signal modulates the Q-Former through Layer-wise Query Modulation, while frozen text embeddings of class labels serve as prototypes for cosine-similarity-based prediction across heterogeneous label spaces. Experiments on sixteen datasets covering motor imagery, emotion recognition, ADHD detection, covert speech, and mental workload show consistent improvements over state-of-the-art baselines and prior EEG foundation models under cross-subject settings. On two additional held-out datasets, EEG-PRIME achieves balanced accuracy comparable to within-session calibration models without target-domain optimization, calibration, or linear probing, demonstrating promising zero-shot transfer capability.
Question answering (QA) over irregular clinical time series (ICTS) plays a pivotal role in a wide range of healthcare applications. Although recent multimodal time-series large language models (LLMs) have shown considerable promise in general-purpose time-series QA, they remain poorly equipped to model the sparsity, asynchrony, and irregular sampling patterns of clinical observations. To fill this gap, we propose ClinPRISM, a cost-effective multimodal LLM reasoning framework for question answering over ICTS data. First, we devise an irregularity-aware multi-scale encoder to capture sparse clinical evidence at diverse temporal scales. Then, we propose a temporal evidence distiller to integrate representations across these scales and compress them into a small number of LLM-compatible tokens. Moreover, we introduce a progressive alignment strategy that sequentially aligns the irregular trajectories with the LLM's textual embedding space. To facilitate training, we construct 30,000 clinical time series paired with multi-scale descriptions, together with 41,000 instruction-tuning instances spanning 11 tasks. Using a 4-billion-parameter LLM backbone, ClinPRISM achieves state-of-the-art performance on the held-out evaluation benchmark while using only 16 time-series tokens and achieving an average inference latency of 0.15 seconds per question.
Shinhwan Kang, Soo Yong Lee, Jaewon Kim +2cs.IR cs.LG
AI-based medication recommendation systems have attracted substantial attention due to their potential to enhance patient safety and therapeutic outcomes. Despite the clinical importance of accurately recommending rarely prescribed medications (rare-meds), we observe that most existing methods show significantly lower predictive performance for rare-meds. We attribute this issue to two intrinsic limitations: (a) the inherent scarcity of data for rare-meds and (b) limited consideration of co-recommended medications. To address these limitations, we propose GenRxR, a novel framework based on large language models (LLMs). GenRxR leverages the medical knowledge and clinical reasoning capability of LLMs to generate counterfactual medical data, mitigating the data scarcity issue for rare-meds. It also integrates an LLM into the medication recommendation process to model relationships among co-recommended medications. To further enhance the clinical reasoning, we introduce an instruction tuning step that aligns the LLM's capability with the recommendation task, enabling better handling of clinical context, including rare-meds cases. In our experiments, we show that GenRxR outperforms 14 (including 5 LLM-based) baselines in most cases. Specifically, it achieves up to 30.9% higher predictive performance for rare-meds than the strongest baseline.
While Multimodal Large Language Models (MLLMs) have demonstrated remarkable success in 2D medical image understanding, their extension to 3D volumetric imaging remains hindered by prohibitive annotation costs and dataset opacity. Current data formats, predominantly consisting of rigid Visual Question Answering (VQA) pairs or unstructured final clinical reports, typically fail to capture explicit clinical reasoning. To address this limitation, we introduce a large-scale structured reasoning dataset constructed via a novel slice-wise data synthesis paradigm. Inspired by the genuine diagnostic workflow of radiologists, this paradigm models visual cognition by decomposing the complex 3D reading process, translating global clinical priors into fine-grained, per-slice observations that are subsequently synthesized into an interpretable Chain-of-Thought (CoT). Crucially, this synthesized reasoning framework enforces essential clinical principles: sequential spatial tracking, multi-slice spatial awareness for artifact mitigation, and differential exclusion. To validate this approach, we instruction-tune a standard 2D-pretrained MLLM baseline using the synthesized data to enhance its volumetric comprehension. Comprehensive evaluations across multiple 3D medical benchmarks demonstrate that our method yields significant performance improvements over the 2D baseline. Furthermore, the resulting model exhibits robust spatial reasoning capabilities and rivals resource-intensive native 3D architectures, effectively bridging the performance gap. Ultimately, this data-centric strategy unlocks deep volumetric understanding and highly interpretable clinical logic without requiring computationally expensive 3D-specific pre-training. The complete repository, including datasets and training workflows, is publicly available at https://github.com/2020420145009/hounsfield.
Existing facial expression quality assessment (FEQA) methods typically produce only a severity score, without explicitly communicating the observable facial motion evidence that supports the prediction. This limits interpretability and makes it difficult to inspect the basis of model outputs in Parkinson's disease assessment. To address this gap, we propose TraMP-LLaMA, a unified multimodal framework that jointly predicts severity scores and generates structured textual reports from facial motion cues. The framework integrates RGB appearance and landmark trajectory cues, and adopts a decoupled instruction-tuning strategy to reduce task interference between severity prediction and language generation. To support this task, we further extend the PFED5 dataset with expert-guided textual motion descriptions and construct PFED5-plus. Experiments on PFED5-plus show that TraMP-LLaMA outperforms competitive video-language baselines in report generation and achieves the best severity prediction performance among the compared methods under joint multi-expression training, improving Spearman's rank correlation by at least 4.39 percent over all competing methods. The text annotations and code are available at https://github.com/shuchaoduan/TraMP-LLaMA.
Protein-peptide interactions are central to cellular regulation and peptide-based drug discovery, yet existing computational methods mainly focus on interaction classification, binding-site prediction, or peptide binder generation. These formulations provide limited insight into the physicochemical mechanisms that determine how a peptide binds to a protein. In this work, we introduce \textbf{PepLLM}, an instruction-tuned framework for structured protein-peptide interface understanding. Given protein-peptide sequences, PepLLM generates a machine-readable JSON annotation describing multiple interface properties, including peptide burial state, hydrogen-bond density, salt-bridge presence, hotspot residues, hydrophobicity, and electrostatic complementarity. To support this task, we construct a new protein-peptide interface dataset by integrating structural interface analysis, solvent-accessible surface area computation, hydrophobic burial estimation, electrostatic potential calculation, and redundancy-aware data splitting. PepLLM connects a pretrained ESM encoder with a LLaMA decoder through a nonlinear modality adapter. The adapted ESM residue embeddings are injected into the LLaMA prompt as continuous soft tokens via placeholder-token replacement, enabling the decoder to generate structured interface annotations under instruction tuning. By moving beyond single-label prediction toward multi-property and mechanism-aware generation, PepLLM establishes a new task and modeling paradigm for interpretable protein-peptide interface analysis.
Voice-based screening offers a scalable and non-invasive way to assess neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD), but their staging remains challenging due to the difficulty of integrating heterogeneous data. This paper presents NeurMLLM, an efficient multimodal generative framework for neurodegenerative disease staging. NeurMLLM first encodes the spectrograms and Mel-frequency cepstral coefficients of audio data with vision transformers and projects their representations into the embedding space of a large language model (LLM), where they are concatenated with transcript and demographic instruction tokens as a single unified sequence. The LLM is then instruction-tuned via Low-Rank Adaptation using task prompts to autoregressively predict a constrained label token, enabling a generative classification. By evaluating on the Bridge2AI-Voice dataset for fine-grained staging of AD and PD, we observe that NeurMLLM achieves strong performance, consistently outperforming classical machine learning methods and existing LLM-based approaches. The results show the high potential of multimodal LLMs in neurodegenerative disease staging, improving staging accuracy and supporting accessible deployment.
We study whether grounded reasoning supervision from abundant 2D medical images can improve 3D medical VQA when both input types are aligned through a common reasoning interface. We introduce UniReason-Med, a single-checkpoint framework that processes either a 2D image or a slice-serialized 3D volume at inference time, generating interleaved textual reasoning and localized visual evidence through shared box syntax, region-token injection, and a common grounded reasoning policy. To train this interface, we construct UniMed-CoT, a 220K instruction-tuning dataset with interleaved textual reasoning and grounded visual evidence, including 170K 2D and 50K 3D samples. Through supervised fine-tuning followed by outcome-level reinforcement learning, UniReason-Med learns to generate grounded reasoning traces without IoU/Dice-based localization rewards during RL. Data-mixture and component ablations show that joint 2D+3D grounded supervision substantially improves 3D reasoning over 3D-only training, while grounding and region-token injection consistently benefit both 2D and 3D tasks. These results suggest that a shared grounded reasoning interface can transfer reasoning structure from 2D images to slice-serialized volumetric medical understanding. The code and data are publicly available at https://github.com/IQuestLab/unireason-med.
Breast cancer remains a leading cause of cancer-related mortality among women. Its clinical management requires multimodal reasoning across a clinical workflow that spans \textit{screening}, \textit{diagnosis} and \textit{treatment planning}, where each stage involves distinct imaging modalities, task objectives, and reasoning patterns. However, constrained by data scarcity and model versatility, existing medical MLLMs are typically evaluated on isolated modalities or narrow task families, limiting their ability to support workflow-level clinical reasoning. In this work, we first introduce \textbf{BreastStage}, a workflow-aligned breast imaging instruction corpus comprising 1.86M instruction-following pairs curated from 17 sub-datasets across 5 imaging modalities and 136 task templates. Its held-out split, \textbf{BreastStage-Bench}, provides a comprehensive benchmark for evaluating multimodal reasoning across the breast cancer care continuum. Building on this corpus, we propose \textbf{BreastGPT}, a unified MLLM equipped with a dual-branch visual encoder and concept-preserving token compression to bridge the scale gap between standard radiology and gigapixel pathology. On BreastStage-Bench, BreastGPT achieves 75.66\% closed-ended accuracy and 89.92\% open-ended score, outperforming both general-purpose and medical-specific MLLMs across clinical stages and task formats. These results suggest that workflow-aligned data and cross-scale visual modeling are critical for clinically grounded medical MLLMs. All data, code, and model checkpoints are released at https://yangyy-liu.github.io/BreastGPT.io.
Darya Shlyk, Stefano Montanelli, Lawrence Huntercs.CL cs.AI cs.IR
Despite recent progress, Biomedical Entity Linking (BEL) with large language models (LLMs) remains computationally inefficient and challenging to deploy in practical settings. In this work, we demonstrate that instruction-tuning of open-source generative models can offer an effective solution when applied at the re-ranking stage of the BEL pipeline. We propose a set-wise instruction-tuning formulation that enables fast and accurate candidate selection. Our method demonstrates strong performance on multiple BEL benchmarks, yielding significant improvements in linking accuracy (3%-24%) while reducing inference time compared to the state-of-the-art. We integrate our generative re-ranker into BeLink, a modular, end-to-end system designed for practical real-world BEL applications.