SDE-Driven Spatio-Temporal Hypergraph Neural Networks for Irregular Longitudinal fMRI Connectome Modeling in Alzheimer's Disease

Longitudinal neuroimaging is essential for modeling disease progression in Alzheimer's disease (AD), yet irregular sampling and missing visits pose substantial challenges for learning reliable temporal representations. To address this challenge, we propose SDE-HGNN, a stochastic differential equation (SDE)-driven spatio-temporal hypergraph neural network for irregular longitudinal fMRI connectome modeling. The framework first employs an SDE-based reconstruction module to recover continuous latent trajectories from irregular observations. Based on these reconstructed representations, dynamic hypergraphs are constructed to capture higher-order interactions among brain regions over time. To further model temporal evolution, hypergraph convolution parameters evolve through SDE-controlled recurrent dynamics conditioned on inter-scan intervals, enabling disease-stage-adaptive connectivity modeling. We also incorporate a sparsity-based importance learning mechanism to identify salient brain regions and discriminative connectivity patterns. Extensive experiments on the OASIS-3 and ADNI cohorts demonstrate consistent improvements over state-of-the-art graph and hypergraph baselines in AD progression prediction. The source code is available at https://anonymous.4open.science/r/SDE-HGNN-017F.

Joint Imaging-ROI Representation Learning via Cross-View Contrastive Alignment for Brain Disorder Classification

Brain imaging classification is commonly approached from two perspectives: modeling the full image volume to capture global anatomical context, or constructing ROI-based graphs to encode localized and topological interactions. Although both representations have demonstrated independent efficacy, their relative contributions and potential complementarity remain insufficiently understood. Existing fusion approaches are typically task-specific and do not enable controlled evaluation of each representation under consistent training settings. To address this gap, we propose a unified cross-view contrastive framework for joint imaging-ROI representation learning. Our method learns subject-level global (imaging) and local (ROI-graph) embeddings and aligns them in a shared latent space using a bidirectional contrastive objective, encouraging representations from the same subject to converge while separating those from different subjects. This alignment produces comparable embeddings suitable for downstream fusion and enables systematic evaluation of imaging-only, ROI-only, and joint configurations within a unified training protocol. Extensive experiments on the ADHD-200 and ABIDE datasets demonstrate that joint learning consistently improves classification performance over either branch alone across multiple backbone choices. Moreover, interpretability analyses reveal that imaging-based and ROI-based branches emphasize distinct yet complementary discriminative patterns, explaining the observed performance gains. These findings provide principled evidence that explicitly integrating global volumetric and ROI-level representations is a promising direction for neuroimaging-based brain disorder classification. The source code is available at https://anonymous.4open.science/r/imaging-roi-contrastive-152C/.

Adaptive Clinical-Aware Latent Diffusion for Multimodal Brain Image Generation and Missing Modality Imputation

Multimodal neuroimaging provides complementary insights for Alzheimer's disease diagnosis, yet clinical datasets frequently suffer from missing modalities. We propose ACADiff, a framework that synthesizes missing brain imaging modalities through adaptive clinical-aware diffusion. ACADiff learns mappings between incomplete multimodal observations and target modalities by progressively denoising latent representations while attending to available imaging data and clinical metadata. The framework employs adaptive fusion that dynamically reconfigures based on input availability, coupled with semantic clinical guidance via GPT-4o-encoded prompts. Three specialized generators enable bidirectional synthesis among sMRI, FDG-PET, and AV45-PET. Evaluated on ADNI subjects, ACADiff achieves superior generation quality and maintains robust diagnostic performance even under extreme 80\% missing scenarios, outperforming all existing baselines. To promote reproducibility, code is available at https://github.com/rongzhou7/ACADiff

MedGPT-oss: Training a General-Purpose Vision-Language Model for Biomedicine

Biomedical multimodal assistants have the potential to unify radiology, pathology, and clinical-text reasoning, yet a critical deployment gap remains: top-performing systems are either closed-source or computationally prohibitive, precluding the on-premises deployment required for patient privacy and PHI compliance. We introduce MEDGPT-OSS, an open-weight, 20B-parameter generalist vision-language model designed to facilitate open research in clinical AI. Rather than relying on architectural complexity, MEDGPT-OSS pairs the GPT-oss language backbone with a visual front-end via a optimized, three-stage training curriculum. By progressively domain-adapting these modules through rigorous data curation and long-context multimodal alignment, we demonstrate that a 20B model can bridge the capacity gap. It successfully outperforms larger open medical models on out-of-distribution (OOD) multimodal reasoning and complex text-only clinical tasks. By unifying diverse modalities under a single instruction-following interface, MEDGPT-OSS maintains a parameter-efficient footprint fully compatible with commodity GPUs. We release the complete training recipe, open-weight checkpoints, and a rigorous evaluation harness to serve as a verifiable foundation for privacy-preserving, institution-specific clinical AI research.

Diffusion-Guided Pretraining for Brain Graph Foundation Models

With the growing interest in foundation models for brain signals, graph-based pretraining has emerged as a promising paradigm for learning transferable representations from connectome data. However, existing contrastive and masked autoencoder methods typically rely on naive random dropping or masking for augmentation, which is ill-suited for brain graphs and hypergraphs as it disrupts semantically meaningful connectivity patterns. Moreover, commonly used graph-level readout and reconstruction schemes fail to capture global structural information, limiting the robustness of learned representations. In this work, we propose a unified diffusion-based pretraining framework that addresses both limitations. First, diffusion is designed to guide structure-aware dropping and masking strategies, preserving brain graph semantics while maintaining effective pretraining diversity. Second, diffusion enables topology-aware graph-level readout and node-level global reconstruction by allowing graph embeddings and masked nodes to aggregate information from globally related regions. Extensive experiments across multiple neuroimaging datasets with over 25,000 subjects and 60,000 scans involving various mental disorders and brain atlases demonstrate consistent performance improvements.

Digital Twin AI: Opportunities and Challenges from Large Language Models to World Models

Digital twins, as precise digital representations of physical systems, have evolved from passive simulation tools into intelligent and autonomous entities through the integration of artificial intelligence technologies. This paper presents a unified four-stage framework that systematically characterizes AI integration across the digital twin lifecycle, spanning modeling, mirroring, intervention, and autonomous management. By synthesizing existing technologies and practices, we distill a unified four-stage framework that systematically characterizes how AI methodologies are embedded across the digital twin lifecycle: (1) modeling the physical twin through physics-based and physics-informed AI approaches, (2) mirroring the physical system into a digital twin with real-time synchronization, (3) intervening in the physical twin through predictive modeling, anomaly detection, and optimization strategies, and (4) achieving autonomous management through large language models, foundation models, and intelligent agents. We analyze the synergy between physics-based modeling and data-driven learning, highlighting the shift from traditional numerical solvers to physics-informed and foundation models for physical systems. Furthermore, we examine how generative AI technologies, including large language models and generative world models, transform digital twins into proactive and self-improving cognitive systems capable of reasoning, communication, and creative scenario generation. Through a cross-domain review spanning eleven application domains, including healthcare, aerospace, smart manufacturing, robotics, and smart cities, we identify common challenges related to scalability, explainability, and trustworthiness, and outline directions for responsible AI-driven digital twin systems.

R-GenIMA: Integrating Neuroimaging and Genetics with Interpretable Multimodal AI for Alzheimer's Disease Progression

Early detection of Alzheimer's disease (AD) requires models capable of integrating macro-scale neuroanatomical alterations with micro-scale genetic susceptibility, yet existing multimodal approaches struggle to align these heterogeneous signals. We introduce R-GenIMA, an interpretable multimodal large language model that couples a novel ROI-wise vision transformer with genetic prompting to jointly model structural MRI and single nucleotide polymorphisms (SNPs) variations. By representing each anatomically parcellated brain region as a visual token and encoding SNP profiles as structured text, the framework enables cross-modal attention that links regional atrophy patterns to underlying genetic factors. Applied to the ADNI cohort, R-GenIMA achieves state-of-the-art performance in four-way classification across normal cognition (NC), subjective memory concerns (SMC), mild cognitive impairment (MCI), and AD. Beyond predictive accuracy, the model yields biologically meaningful explanations by identifying stage-specific brain regions and gene signatures, as well as coherent ROI-Gene association patterns across the disease continuum. Attention-based attribution revealed genes consistently enriched for established GWAS-supported AD risk loci, including APOE, BIN1, CLU, and RBFOX1. Stage-resolved neuroanatomical signatures identified shared vulnerability hubs across disease stages alongside stage-specific patterns: striatal involvement in subjective decline, frontotemporal engagement during prodromal impairment, and consolidated multimodal network disruption in AD. These results demonstrate that interpretable multimodal AI can synthesize imaging and genetics to reveal mechanistic insights, providing a foundation for clinically deployable tools that enable earlier risk stratification and inform precision therapeutic strategies in Alzheimer's disease.

Conditional Neural ODE for Longitudinal Parkinson's Disease Progression Forecasting

Parkinson's disease (PD) shows heterogeneous, evolving brain-morphometry patterns. Modeling these longitudinal trajectories enables mechanistic insight, treatment development, and individualized 'digital-twin' forecasting. However, existing methods usually adopt recurrent neural networks and transformer architectures, which rely on discrete, regularly sampled data while struggling to handle irregular and sparse magnetic resonance imaging (MRI) in PD cohorts. Moreover, these methods have difficulty capturing individual heterogeneity including variations in disease onset, progression rate, and symptom severity, which is a hallmark of PD. To address these challenges, we propose CNODE (Conditional Neural ODE), a novel framework for continuous, individualized PD progression forecasting. The core of CNODE is to model morphological brain changes as continuous temporal processes using a neural ODE model. In addition, we jointly learn patient-specific initial time and progress speed to align individual trajectories into a shared progression trajectory. We validate CNODE on the Parkinson's Progression Markers Initiative (PPMI) dataset. Experimental results show that our method outperforms state-of-the-art baselines in forecasting longitudinal PD progression.

Towards a general-purpose foundation model for fMRI analysis

Functional Magnetic Resonance Imaging (fMRI) is essential for studying brain function and diagnosing neurological disorders, but current analysis methods face reproducibility and transferability issues due to complex pre-processing and task-specific models. We introduce NeuroSTORM (Neuroimaging Foundation Model with Spatial-Temporal Optimized Representation Modeling), a generalizable framework that directly learns from 4D fMRI volumes and enables efficient knowledge transfer across diverse applications. NeuroSTORM is pre-trained on 28.65 million fMRI frames (>9,000 hours) from over 50,000 subjects across multiple centers and ages 5 to 100. Using a Mamba backbone and a shifted scanning strategy, it efficiently processes full 4D volumes. We also propose a spatial-temporal optimized pre-training approach and task-specific prompt tuning to improve transferability. NeuroSTORM outperforms existing methods across five tasks: age/gender prediction, phenotype prediction, disease diagnosis, fMRI-to-image retrieval, and task-based fMRI classification. It demonstrates strong clinical utility on datasets from hospitals in the U.S., South Korea, and Australia, achieving top performance in disease diagnosis and cognitive phenotype prediction. NeuroSTORM provides a standardized, open-source foundation model to improve reproducibility and transferability in fMRI-based clinical research.

EfficientLLM: Efficiency in Large Language Models

Large Language Models (LLMs) have driven significant progress, yet their growing parameter counts and context windows incur prohibitive compute, energy, and monetary costs. We introduce EfficientLLM, a novel benchmark and the first comprehensive empirical study evaluating efficiency techniques for LLMs at scale. Conducted on a production-class cluster (48xGH200, 8xH200 GPUs), our study systematically explores three key axes: (1) architecture pretraining (efficient attention variants: MQA, GQA, MLA, NSA; sparse Mixture-of-Experts (MoE)), (2) fine-tuning (parameter-efficient methods: LoRA, RSLoRA, DoRA), and (3) inference (quantization methods: int4, float16). We define six fine-grained metrics (Memory Utilization, Compute Utilization, Latency, Throughput, Energy Consumption, Compression Rate) to capture hardware saturation, latency-throughput balance, and carbon cost. Evaluating over 100 model-technique pairs (0.5B-72B parameters), we derive three core insights: (i) Efficiency involves quantifiable trade-offs: no single method is universally optimal; e.g., MoE reduces FLOPs and improves accuracy but increases VRAM by 40%, while int4 quantization cuts memory/energy by up to 3.9x at a 3-5% accuracy drop. (ii) Optima are task- and scale-dependent: MQA offers optimal memory-latency trade-offs for constrained devices, MLA achieves lowest perplexity for quality-critical tasks, and RSLoRA surpasses LoRA efficiency only beyond 14B parameters. (iii) Techniques generalize across modalities: we extend evaluations to Large Vision Models (Stable Diffusion 3.5, Wan 2.1) and Vision-Language Models (Qwen2.5-VL), confirming effective transferability. By open-sourcing datasets, evaluation pipelines, and leaderboards, EfficientLLM provides essential guidance for researchers and engineers navigating the efficiency-performance landscape of next-generation foundation models.