Toward a universal foundation model for graph-structured data

Graphs are a central representation in biomedical research, capturing molecular interaction networks, gene regulatory circuits, cell--cell communication maps, and knowledge graphs. Despite their importance, currently there is not a broadly reusable foundation model available for graph analysis comparable to those that have transformed language and vision. Existing graph neural networks are typically trained on a single dataset and learn representations specific only to that graph's node features, topology, and label space, limiting their ability to transfer across domains. This lack of generalization is particularly problematic in biology and medicine, where networks vary substantially across cohorts, assays, and institutions. Here we introduce a graph foundation model designed to learn transferable structural representations that are not specific to specific node identities or feature schemes. Our approach leverages feature-agnostic graph properties, including degree statistics, centrality measures, community structure indicators, and diffusion-based signatures, and encodes them as structural prompts. These prompts are integrated with a message-passing backbone to embed diverse graphs into a shared representation space. The model is pretrained once on heterogeneous graphs and subsequently reused on unseen datasets with minimal adaptation. Across multiple benchmarks, our pretrained model matches or exceeds strong supervised baselines while demonstrating superior zero-shot and few-shot generalization on held-out graphs. On the SagePPI benchmark, supervised fine-tuning of the pretrained backbone achieves a mean ROC-AUC of 95.5%, a gain of 21.8% over the best supervised message-passing baseline. The proposed technique thus provides a unique approach toward reusable, foundation-scale models for graph-structured data in biomedical and network science applications.

Towards a Medical AI Scientist

Autonomous systems that generate scientific hypotheses, conduct experiments, and draft manuscripts have recently emerged as a promising paradigm for accelerating discovery. However, existing AI Scientists remain largely domain-agnostic, limiting their applicability to clinical medicine, where research is required to be grounded in medical evidence with specialized data modalities. In this work, we introduce Medical AI Scientist, the first autonomous research framework tailored to clinical autonomous research. It enables clinically grounded ideation by transforming extensively surveyed literature into actionable evidence through clinician-engineer co-reasoning mechanism, which improves the traceability of generated research ideas. It further facilitates evidence-grounded manuscript drafting guided by structured medical compositional conventions and ethical policies. The framework operates under 3 research modes, namely paper-based reproduction, literature-inspired innovation, and task-driven exploration, each corresponding to a distinct level of automated scientific inquiry with progressively increasing autonomy. Comprehensive evaluations by both large language models and human experts demonstrate that the ideas generated by the Medical AI Scientist are of substantially higher quality than those produced by commercial LLMs across 171 cases, 19 clinical tasks, and 6 data modalities. Meanwhile, our system achieves strong alignment between the proposed method and its implementation, while also demonstrating significantly higher success rates in executable experiments. Double-blind evaluations by human experts and the Stanford Agentic Reviewer suggest that the generated manuscripts approach MICCAI-level quality, while consistently surpassing those from ISBI and BIBM. The proposed Medical AI Scientist highlights the potential of leveraging AI for autonomous scientific discovery in healthcare.

Cerebra: A Multidisciplinary AI Board for Multimodal Dementia Characterization and Risk Assessment

Modern clinical practice increasingly depends on reasoning over heterogeneous, evolving, and incomplete patient data. Although recent advances in multimodal foundation models have improved performance on various clinical tasks, most existing models remain static, opaque, and poorly aligned with real-world clinical workflows. We present Cerebra, an interactive multi-agent AI team that coordinates specialized agents for EHR, clinical notes, and medical imaging analysis. These outputs are synthesized into a clinician-facing dashboard that combines visual analytics with a conversational interface, enabling clinicians to interrogate predictions and contextualize risk at the point of care. Cerebra supports privacy-preserving deployment by operating on structured representations and remains robust when modalities are incomplete. We evaluated Cerebra using a massive multi-institutional dataset spanning 3 million patients from four independent healthcare systems. Cerebra consistently outperformed both state-of-the-art single-modality models and large multimodal language model baselines. In dementia risk prediction, it achieved AUROCs up to 0.80, compared with 0.74 for the strongest single-modality model and 0.68 for language model baselines. For dementia diagnosis, it achieved an AUROC of 0.86, and for survival prediction, a C-index of 0.81. In a reader study with experienced physicians, Cerebra significantly improved expert performance, increasing accuracy by 17.5 percentage points in prospective dementia risk estimation. These results demonstrate Cerebra's potential for interpretable, robust decision support in clinical care.

Vision-based Deep Learning Analysis of Unordered Biomedical Tabular Datasets via Optimal Spatial Cartography

Tabular data are central to biomedical research, from liquid biopsy and bulk and single-cell transcriptomics to electronic health records and phenotypic profiling. Unlike images or sequences, however, tabular datasets lack intrinsic spatial organization: features are treated as unordered dimensions, and their relationships must be inferred implicitly by the model. This limits the ability of vision architectures to exploit local structure and higher-order feature interactions in non-spatial biomedical data. Here we introduce Dynamic Feature Mapping (Dynomap), an end-to-end deep learning framework that learns a task-optimized spatial topology of features directly from data. Dynomap jointly optimizes feature placement and prediction through a fully differentiable rendering mechanism, without relying on heuristics, predefined groupings, or external priors. By transforming high-dimensional tabular vectors into learned feature maps, Dynomap enables vision-based models to operate effectively on unordered biomedical inputs. Across multiple clinical and biological datasets, Dynomap consistently outperformed classical machine learning, modern deep tabular models, and existing vector-to-image approaches. In liquid biopsy data, Dynomap organized clinically relevant gene signatures into coherent spatial patterns and improved multiclass cancer subtype prediction accuracy by up to 18%. In a Parkinson disease voice dataset, it clustered disease-associated acoustic descriptors and improved accuracy by up to 8%. Similar gains and interpretable feature organization were observed in additional biomedical datasets. These results establish Dynomap as a general strategy for bridging tabular and vision-based deep learning and for uncovering structured, clinically relevant patterns in high-dimensional biomedical data.

A Multidisciplinary AI Board for Multimodal Dementia Characterization and Risk Assessment

Modern clinical practice increasingly depends on reasoning over heterogeneous, evolving, and incomplete patient data. Although recent advances in multimodal foundation models have improved performance on various clinical tasks, most existing models remain static, opaque, and poorly aligned with real-world clinical workflows. We present Cerebra, an interactive multi-agent AI team that coordinates specialized agents for EHR, clinical notes, and medical imaging analysis. These outputs are synthesized into a clinician-facing dashboard that combines visual analytics with a conversational interface, enabling clinicians to interrogate predictions and contextualize risk at the point of care. Cerebra supports privacy-preserving deployment by operating on structured representations and remains robust when modalities are incomplete. We evaluated Cerebra using a massive multi-institutional dataset spanning 3 million patients from four independent healthcare systems. Cerebra consistently outperformed both state-of-the-art single-modality models and large multimodal language model baselines. In dementia risk prediction, it achieved AUROCs up to 0.80, compared with 0.74 for the strongest single-modality model and 0.68 for language model baselines. For dementia diagnosis, it achieved an AUROC of 0.86, and for survival prediction, a C-index of 0.81. In a reader study with experienced physicians, Cerebra significantly improved expert performance, increasing accuracy by 17.5 percentage points in prospective dementia risk estimation. These results demonstrate Cerebra's potential for interpretable, robust decision support in clinical care.

Suppressing Prior-Comparison Hallucinations in Radiology Report Generation via Semantically Decoupled Latent Steering

Automated radiology report generation using vision-language models (VLMs) is limited by the risk of prior-comparison hallucination, where the model generates historical findings unsupported by the current study. We address this challenge with a training-free, inference-time control framework termed Semantically Decoupled Latent Steering (SDLS). Unlike generic activation steering, which often suffers from semantic entanglement, our approach constructs a semantic-free intervention vector via large language model (LLM)-driven semantic decomposition followed by $QR$-based orthogonalization. This orthogonalization step is critical. It leverages geometric constraints to filter out the clinical semantics often entangled in standard principal component analysis (PCA) directions, ensuring that the steering vector targets only the ``historical comparison" axis. We validate our method on the BiomedGPT foundation model, demonstrating that it overcomes the trade-off between hallucination suppression and clinical accuracy. Extensive experiments on MIMIC-CXR, and zero-shot transfer evaluation on CheXpert Plus and IU-Xray, demonstrate the robustness of our approach. Quantitative evaluations on MIMIC-CXR show that our approach significantly reduces the probability of historical hallucinations (FilBERT score decreases from 0.2373 to 0.1889) and improves clinical label fidelity (CheXpert macro-F1 increases from 0.2242 to 0.3208). Supplementary evaluations confirm that the structural integrity of the clinical narrative is maintained.

Redefining the Down-Sampling Scheme of U-Net for Precision Biomedical Image Segmentation

U-Net architectures have been instrumental in advancing biomedical image segmentation (BIS) but often struggle with capturing long-range information. One reason is the conventional down-sampling techniques that prioritize computational efficiency at the expense of information retention. This paper introduces a simple but effective strategy, we call it Stair Pooling, which moderates the pace of down-sampling and reduces information loss by leveraging a sequence of concatenated small and narrow pooling operations in varied orientations. Specifically, our method modifies the reduction in dimensionality within each 2D pooling step from $\frac{1}{4}$ to $\frac{1}{2}$. This approach can also be adapted for 3D pooling to preserve even more information. Such preservation aids the U-Net in more effectively reconstructing spatial details during the up-sampling phase, thereby enhancing its ability to capture long-range information and improving segmentation accuracy. Extensive experiments on three BIS benchmarks demonstrate that the proposed Stair Pooling can increase both 2D and 3D U-Net performance by an average of 3.8\% in Dice scores. Moreover, we leverage the transfer entropy to select the optimal down-sampling paths and quantitatively show how the proposed Stair Pooling reduces the information loss.

Uncovering spatial tissue domains and cell types in spatial omics through cross-scale profiling of cellular and genomic interactions

Cellular identity and function are linked to both their intrinsic genomic makeup and extrinsic spatial context within the tissue microenvironment. Spatial transcriptomics (ST) offers an unprecedented opportunity to study this, providing in situ gene expression profiles at single-cell resolution and illuminating the spatial and functional organization of cells within tissues. However, a significant hurdle remains: ST data is inherently noisy, large, and structurally complex. This complexity makes it intractable for existing computational methods to effectively capture the interplay between spatial interactions and intrinsic genomic relationships, thus limiting our ability to discern critical biological patterns. Here, we present CellScape, a deep learning framework designed to overcome these limitations for high-performance ST data analysis and pattern discovery. CellScape jointly models cellular interactions in tissue space and genomic relationships among cells, producing comprehensive representations that seamlessly integrate spatial signals with underlying gene regulatory mechanisms. This technique uncovers biologically informative patterns that improve spatial domain segmentation and supports comprehensive spatial cellular analyses across diverse transcriptomics datasets, offering an accurate and versatile framework for deep analysis and interpretation of ST data.w

Reshaping Action Error Distributions for Reliable Vision-Language-Action Models

In robotic manipulation, vision-language-action (VLA) models have emerged as a promising paradigm for learning generalizable and scalable robot policies. Most existing VLA frameworks rely on standard supervised objectives, typically cross-entropy for discrete actions and mean squared error (MSE) for continuous action regression, which impose strong pointwise constraints on individual predictions. In this work, we focus on continuous-action VLA models and move beyond conventional MSE-based regression by reshaping action error distributions during training. Drawing on information-theoretic principles, we introduce Minimum Error Entropy (MEE) into modern VLA architectures and propose a trajectory-level MEE objective, together with two weighted variants, combined with MSE for continuous-action VLA training. We evaluate our approaches across standard, few-shot, and noisy settings on multiple representative VLA architectures, using simulation benchmarks such as LIBERO and SimplerEnv as well as real-world robotic manipulation tasks. Experimental results demonstrate consistent improvements in success rates and robustness across these settings. Under imbalanced data regimes, the gains persist within a well-characterized operating range, while incurring negligible additional training cost and no impact on inference efficiency. We further provide theoretical analyses that explain why MEE-based supervision is effective and characterize its practical range. Project Page: https://cognition2actionlab.github.io/VLA-TMEE.github.io/

Latent Reasoning VLA: Latent Thinking and Prediction for Vision-Language-Action Models

Vision-Language-Action (VLA) models benefit from chain-of-thought (CoT) reasoning, but existing approaches incur high inference overhead and rely on discrete reasoning representations that mismatch continuous perception and control. We propose Latent Reasoning VLA (\textbf{LaRA-VLA}), a unified VLA framework that internalizes multi-modal CoT reasoning into continuous latent representations for embodied action. LaRA-VLA performs unified reasoning and prediction in latent space, eliminating explicit CoT generation at inference time and enabling efficient, action-oriented control. To realize latent embodied reasoning, we introduce a curriculum-based training paradigm that progressively transitions from explicit textual and visual CoT supervision to latent reasoning, and finally adapts latent reasoning dynamics to condition action generation. We construct two structured CoT datasets and evaluate LaRA-VLA on both simulation benchmarks and long-horizon real-robot manipulation tasks. Experimental results show that LaRA-VLA consistently outperforms state-of-the-art VLA methods while reducing inference latency by up to 90\% compared to explicit CoT-based approaches, demonstrating latent reasoning as an effective and efficient paradigm for real-time embodied control. Project Page: \href{https://loveju1y.github.io/Latent-Reasoning-VLA/}{LaRA-VLA Website}.