ICML 2026 Papers

We study the problem of training self-supervised foundation models for functional MRI. Our main contributions are: (1) we introduce a new model family (CortexMAE) trained using the masked autoencoder framework on 2.1K hours of open fMRI data, and (2) we release the first open evaluation suite (Brainmarks) for fMRI foundation models. Our core innovation is simple: we adapt the Vision Transformer to fMRI by first converting each 3D fMRI volume to a 2D map using a cortical flat map projection. We directly compare flat maps to both parcellation and volume-based representations. While each has its advantages, flat maps generally perform best. We perform the first systematic scaling analysis for fMRI and observe strict power law scaling, albeit with limits. Finally, we use Brainmarks to do controlled benchmark comparisons. On subject-level trait prediction, we report a challenging null result: no single model achieves clear state-of-the-art performance. Moreover, all models struggle to outperform a simple functional connectivity baseline. On cognitive state decoding, we observe more robust performance, and in this setting our CortexMAE family outperforms prior models by a large margin. Code, models, and datasets are available at https://github.com/MedARC-AI/CortexMAE and https://github.com/MedARC-AI/Brainmarks.

Medical foundation models (MFMs) aim to learn universal representations from multimodal medical images that can generalize effectively to diverse downstream clinical tasks. However, most existing MFMs suffer from information ambiguity that blends multimodal representations in a single embedding space, leading to the degradation of modality specificity and diversity. In this paper, we propose M-IDoL, a self-supervised ***M***FM that introduces ***I***nformation ***D***ecomposition for multim***o***dal representation ***L***earning via two objectives: i) maximizing inter-modality entropy by dispersing multimodal representations into separable Mixture-of-Experts (MoE) subspaces to achieve representation specificity across modalities; and ii) minimizing intra-modality uncertainty by performing fine-grained semantic discrimination within each MoE subspace to enrich representation diversity per modality. By pre-training on 1.15 million medical images, M-IDoL i) delivers superior generalization across 21 downstream clinical tasks, outperforming 20 foundation models on five imaging modalities (e.g., X-ray, fundus, OCT, dermoscopy and pathology), and ii) learns modality-specific and diverse representations, showing clearer separation of feature clusters across modalities and finer-grained feature discrimination within each modality.

Learning meaningful representations from medical time series (MedTS), such as ECG or EEG signals, is a critical challenge. These signals are often high-dimensional, variable-length, and rife with noise. Existing self-supervised approaches, such as Masked Autoencoders (MAEs), are highly effective for pre-training general-purpose encoders. However, they do not explicitly learn compact, fixed-size, or semantically interpretable latent representations, typically relying on heuristic aggregation strategies such as global average pooling or a designated [CLS] token. We propose a novel framework that compresses a variable-length MedTS into a fixed-size set of $k$ latent Fingerprint Tokens. Our architecture employs a cross-attention bottleneck to generate these tokens and is trained with a dual-objective function. The first objective is a reconstruction loss, which ensures the tokens are \textit{sufficient statistics} for the original data. The second, a diversity penalty based on the Total Coding Rate (TCR), explicitly minimizes the redundancy between tokens, encouraging them to become statistically \textit{disentangled} representations. We present the theoretical justification for our method, framing it as a novel \textbf{Disentangled Rate-Distortion} problem. This approach produces a low-dimensional, interpretable, and sample-efficient representation, where each token is encouraged to capture an independent factor of variation, paving the way for more robust digital biomarkers.

Plug-and-Play diffusion prior (PnPDP) frameworks have emerged as a powerful paradigm for solving imaging inverse problems by treating pretrained generative models as modular priors. However, we identify a critical flaw in prevailing PnP solvers (e.g., based on HQS or Proximal Gradient): they function as *memoryless operators*, updating estimates solely based on instantaneous gradients. This lack of historical tracking inevitably leads to non-vanishing *steady-state bias*, where the reconstruction fails to strictly satisfy physical measurements under heavy corruption. To resolve this, we propose **Dual-Coupled PnP Diffusion (DC-PnPDP)**, which restores the classical *dual variable* to provide integral feedback, progressively enforce agreement between the data-consistency and prior. However, this rigorous geometric coupling introduces a secondary challenge: the accumulated dual residuals exhibit spectrally colored, structured artifacts that violate the Additive White Gaussian Noise (AWGN) assumption of diffusion priors, causing severe hallucinations. To bridge this gap, we introduce **Spectral Homogenization (SH)**, a frequency-domain adaptation mechanism that modulates these structured residuals into statistically compliant *pseudo-AWGN* inputs. This effectively aligns the solver's rigorous optimization trajectory with the denoiser's valid statistical manifold. Extensive experiments on CT and MRI reconstruction demonstrate that our approach resolves the bias-hallucination trade-off, achieving state-of-the-art fidelity with significantly accelerated convergence. The code is available at https://github.com/duchenhe/DC-PnPDP.

Group fairness can ensure equitable performance across different demographic subgroups for medical image analysis. However, the current fine-tuned foundation models (FMs) exhibit significant subgroup disparity. One-shot federated learning (OFL) can potentially mitigate this by leveraging cross-institutional data diversity within a single communication round. However, heterogeneous distributions across medical institutions may cause OFL local models to diverge severely, resulting in parameter conflicts that amplify disparity upon aggregation. To address these challenges, we propose Fair-FedMOE, a group-fair OFL framework for medical FMs. During local training, Fairness-aware Expert Routing leverages learnable prototypes to route samples to group-specific experts, enabling subgroup-specialized learning to capture group-specific features without inter-group interference. During model aggregation, Prototype-guided Differential Aggregation computes personalized weights based on prototype similarity and applies differentiated aggregation strategies to filter conflicting updates. We propose RES-AUC, a Rawlsian justice-inspired metric based on worst-group performance that remains stable as groups increase. Extensive experiments on retinal and chest X-ray datasets with multiple FMs demonstrate consistent fairness gains without sacrificing accuracy.

Modern imaging techniques heavily rely on Bayesian statistical models to address difficult image reconstruction and restoration tasks. This paper addresses the objective evaluation of such models in settings where ground truth is unavailable, with a focus on model selection and misspecification diagnosis. Existing unsupervised model evaluation methods are often unsuitable for computational imaging due to their high computational cost and incompatibility with modern image priors defined implicitly via machine learning models. We herein propose a general methodology for unsupervised model selection and misspecification detection in Bayesian imaging sciences, based on a novel combination of Bayesian cross-validation and data fission, a randomized measurement splitting technique. The approach is compatible with any Bayesian imaging sampler, including diffusion and plug-and-play samplers. We demonstrate the methodology through experiments involving various scoring rules and types of model misspecification, where we achieve excellent selection and detection accuracy with a low computational cost.

The characterization of histopathology with AI promises to assist clinical decision-making, but it is currently limited due to coarse-grained annotations that miss cellular identities. To overcome this gap, we bridge histopathological images, gene expression profiles, and natural-language descriptions using *SpatialWhisperer*, a trimodal contrastive learning model. Our training integrates community-scale datasets comprising spatially resolved gene expression profiles paired with histopathology images, as well as single-cell gene expression profiles with detailed annotations. The shared gene expression modality implies a transitive relationship between images and textual annotations, which our method leverages to enable accurate zero-shot cell type annotation directly from H&E images. *SpatialWhisperer* outperforms published baselines, achieving relative AUROC gains of up to 15.9% across three benchmarks spanning 19 tissues and 20 cell types. When training with data from all three modality pairs, we observe performance gains in low-data regimes. We formalize our approach and present a sufficient condition under which this transitive alignment is induced. Our work establishes *transitive representation learning* for fine-grained interpretation of histopathology images.

Self-supervised pre-training methods in medical imaging typically treat each individual as an isolated instance, learning representations through augmentation-based objectives or masked reconstruction. They often do not adequately capitalize on a key characteristic of physiological features: anatomical structures maintain consistent spatial relationships across individuals (instances), such as the thalamus being medial to the basal ganglia, regardless of variations in brain size, shape, or pathology. We propose leveraging this cross-instance topological consistency as a supervisory signal. The challenge arises from the inherent variability in medical imaging, which can differ significantly across instances and modalities. To tackle this, we focus on two alignment regimes. (i) Intra-instance: with pixel-level correspondences available, a cross-modal triplet objective explicitly preserves local neighborhood topology. (ii) Inter-instance: without such supervision, we derive pseudo-correspondences to control partial neighborhood alignment and prevent topology collapse across modalities. We validate our approach across 7 downstream multi-modal tasks, achieving average improvements of 1.1\% and 5.94\% in segmentation and classification tasks, respectively, and demonstrating significantly better robustness when modalities are missing at test time.

3D CT analysis spans a continuum from low-level perception to high-level clinical understanding. Existing 3D-oriented analysis methods adopt either isolated task-specific modeling or task-agnostic end-to-end paradigms to produce one-hop outputs, impeding the systematic accumulation of perceptual evidence for downstream reasoning. In parallel, recent multimodal large language models (MLLMs) exhibit improved visual perception and can integrate visual and textual information effectively, yet their predominantly 2D-oriented designs fundamentally limit their ability to perceive and analysis volumetric medical data. To bridge this gap, we propose 3DMedAgent, an unified agent that enables 2D MLLMs to perform general 3D CT analysis without 3D-specific fine-tuning. 3DMedAgent coordinates heterogeneous visual and textual tools through a flexible MLLM agent, progressively decomposing complex 3D analysis into tractable subtasks that transition from global to regional views, from 3D volumes to informative 2D slices, and from visual evidence to structured textual representations. Central to this design, 3DMedAgent maintains a long-term structured memory that aggregates intermediate tool outputs and supports query-adaptive, evidence-driven multi-step reasoning. We further introduce the DeepChestVQA benchmark for evaluating unified perception-to-understanding capabilities in 3D thoracic imaging. Experiments across over 40 tasks demonstrate that 3DMedAgent consistently outperforms general, medical, and 3D-specific MLLMs, highlighting a scalable path toward general-purpose 3D clinical assistants. Code and data are available \href{https://github.com/jinlab-imvr/3DMedAgent}{here}.

Reconstructing hyperspectral images from compressive measurements is challenging due to a fundamental mismatch between locally reliable observations and globally entangled structures induced by spectral dispersion. This study formalizes this issue as a local–global dissonance in representation learning for CASSI systems. To resolve it, we propose a Hierarchical Scale-Reconciling Architecture (HSRA) that enforces local sufficiency and global consistency in a principled, scale-aware manner. HSRA combines multi-kernel token mixing, latent window interactions, and hierarchical multi-granularity spatially shifted attention to progressively reconcile physical constraints across scales. Embedded into a deep unfolding framework as a physically grounded learned prior, Extensive experiments on benchmarks demonstrate that HSRA achieves consistent and significant improvements over state-of-the-art methods.