PaSTel: Anchoring Histology in Spatial Transcriptomics via Multi-Scale Hierarchical Bio-Prior Contrastive Pretraining

Spatial transcriptomics (ST) links tissue morphology with molecular programs, motivating multimodal pretraining methods that align histology images with gene expression. However, existing approaches suffer from two key limitations: spatially informative gene selection is often dominated by ubiquitous housekeeping genes, leading to weakly discriminative representations, and independent spot-patch alignment fails to capture spatial dependencies that are critical for tissue organization. To address these challenges, we introduce PaSTel, a hierarchical multimodal pretraining framework that integrates biological priors at three levels. At the spot level, TF-IDF reweighting is used to identify spatially informative genes; at the functional level, curated KEGG pathways serve as anchors for encoding global biological semantics; and at the regional level, spatial clustering aggregates neighboring spots to model meso-scale tissue structure. Across multiple downstream tasks, PaSTel consistently outperforms existing vision and vision-omics encoders, demonstrating that incorporating multiscale biological priors yields more informative and transferable representations for spatial transcriptomics.

SLED: Scalable Location Encoding via Distillation

The plethora of readily available geospatial data offers exciting opportunities to learn high quality representations of the planet, but the sheer size of the Earth Observations (EO), differing modalities, and different sensor types pose significant challenges in doing so. Location encoders have emerged as an efficient way of compressing EOs into location-specific embeddings. However, current state-of-the-art location encoders rely on computationally expensive CLIP-style frameworks that require large batch sizes in the 16K--32K range, suffer from false negative samples, and scale poorly with additional modalities. We introduce the Scalable Location Encoder via Distillation (SLED), a distillation-based location encoder that uses geospatial location as a binding modality to pretrain location encoders with any modality of geospatial data. The resulting location encoder framework is lightweight, modular, and can flexibly incorporate multiple modes, while eliminating the need for spatiotemporal coregistration of samples. SLED is performant with batch sizes as small as 128, enabling pretraining at a fraction of the runtime and compute costs of current state-of-the-art models. We demonstrate our approach by pretraining unimodal and multimodal SLED models on Sentinel-1, Sentinel-2, and Landsat imagery. We show that both unimodal and multimodal SLED models keep pace with or outperform existing approaches on a diverse set of 19 human-centric benchmark tasks and explore the benefits of using additional modes in pretraining.

Towards Physics of Multimodal Pretraining: Knowledge Flow, Modality Synergy, Early Unification, and Recipes

Vision offers a critical axis for advancing foundation models, driving a shift towards natively unified multimodal pretraining. Despite this momentum, the design space and the fundamental mechanisms of how modalities interact during unified training remain underexplored. We provide empirical clarity through a systematic exploration of multimodal pretraining. Our controlled experiments on both synthetic and large-scale real-world datasets yield four key insights into the physics of multimodal pretraining: (i) Knowledge Flow: We disentangle how language, visual understanding, and visual generation transfer knowledge across modalities, revealing distinct patterns of influence and asymmetry; (ii) Synergy vs. Competition: We show that data "complexity" largely determines whether modalities are synergistic, identify architectural choices that promote synergy: such as shared attention and normalization with modality-specific feed-forward layers, and find that these behaviors generalize across different visual tokenizer designs; (iii) Early Unification: Unifying modalities from the very early stages and training them jointly is shown to be more effective than late alignment or sequential training. This process uncovers a vision laziness phenomenon, where delayed integration leads models to rely on language priors; (iv) Recipes: We derive efficient pretraining recipes that achieve strong generative performance using only 5% of the compute budget. These core findings are subsequently validated at scale by training multiple 13.5B MoE models on 2T tokens. We hope this study provides a principled foundation for understanding and scaling multimodal pretraining.

ReMiX-MAE: Learning Missing-Channel Cross-Modal Representations from RGB-Only Clinical Facial Videos for Sympathetic-Mediated Pain Assessment

Automated pain assessment in real clinics is limited by scarce clinically grounded facial video data with weak labels (often sequence-level self-report) and by the fact that pain cues can be subtle or near-neutral in RGB, while thermal and depth signals are informative yet impractical to deploy routinely. To address these challenges, we propose ReMiX-MAE (Reconstructing Missing Channel Cross-Modal Masked Autoencoder), a self-supervised multimodal masked pretraining framework that learns transferable facial representations from synchronized RGB, thermal, and depth videos and explicitly trains robustness to missing modalities, enabling RGB-only deployment. To fill the gap of clinically grounded facial pain data with video-level self-report and longitudinal treatment trajectories, we collect the Sympathetic Mediated Pain (SMP) dataset with paired pre- and post-recordings across multiple visits. Under RGB-only deployment, we evaluate ReMiX-MAE using both direct feature extraction and pseudo-multimodal features decoded from RGB. ReMiX-MAE consistently outperforms an RGB-only masked autoencoder baseline on SMP, with pseudo-multimodal features providing additional gains in the challenging five-class setting. Across external datasets, ReMiX-MAE further shows more robust and label-efficient transfer than RGB-only baselines, highlighting its advantage in data-limited clinical settings.

Does the Heart Show Your Pain? Tackling the X-ITE Pain Challenge with Self-Supervised ECG Representation Learning

Accurate recognition of pain using physiological signals remains a challenging problem due to pain's subjective nature and high inter-individual variability. In this study, we investigate self-supervised representation learning (SSL) methods applied to unimodal electrocardiogram (ECG), complemented by multimodal pretraining, including accelerometer (ACC) signals from the chest. We focus on classifying low versus medium pain levels on the X-ITE Pain dataset. Our results reveal that while ECG-based models show limited classification performance, multimodal pretraining improves learned representations by capturing cross-modal dependencies. Notably, we observe substantial inter-subject variability in model performance, suggesting that pain-related ECG patterns may be subject-specific. Visualizations indicate distinct subject-specific clustering but no clear separation by pain levels, highlighting the complexity of pain detection from ECG alone. We discuss limitations of unimodal input, label noise, and generalization across subjects and propose future directions. This work advances the understanding of physiological signal representation learning for pain recognition and sets the stage for more robust, clinically relevant wearable pain monitoring solutions.

Multimodal Pretraining for Generalizable EEG Representation Learning

Electroencephalography (EEG) models used for epilepsy are often limited to specific datasets and tasks. This limited approach can make it challenging to apply these models across different datasets or in various situations. However, recent studies in foundation models and self-supervised learning suggest that an adaptable EEG backbone could support a range of EEG related tasks. In this study, we have developed a multimodal EEG foundation model that combines a raw signal encoder based on the Mamba architecture, a Vision Transformer (ViT)-style encoder for time-frequency data, and a lightweight encoder for text, all within a shared embedding space. The pretraining process relies on several innovative techniques, such as masked modeling, cross-view contrastive alignment, and temporal consistency losses. These methods are designed to create rich, seizure-relevant representations without requiring labeled data. To assess the efficacy and generalization of our pretrained model, we fine-tuned it on the canonical CHB-MIT seizure detection benchmark and additional seizure detection datasets, and conducted extensive experiments comparing different model variants. On the standard CHB-MIT split, our best single model achieved an AUROC of 0.874, and an ensemble variant reached 0.878 AUROC, representing state-of-the-art performance on this benchmark. In addition to standard train-test splits, we evaluated performance under a leave-one-subject-out (LOSO) protocol, which is rarely reported in prior EEG seizure modeling work and highlights the difficulty of patient-independent seizure detection, with a mean LOSO balanced accuracy of 0.558 across 19 subjects. Across datasets and evaluation settings, our multimodal foundation model enabled robust seizure detection and straightforward adaptation to new seizure detection scenarios, while also supporting interpretable seizure localization.

Rosetta: Composable Native Multimodal Pretraining

Achieving true artificial general intelligence requires foundation models capable of integrating new modalities without forgetting prior knowledge. However, accommodating continuous generative objectives alongside discrete understanding tasks causes severe gradient conflicts. Existing architectures, including standard Mixture-of-Experts (MoE), are highly susceptible to representation overwriting. Even structurally partitioned paradigms like Mixture-of-Transformers (MoT) remain vulnerable to catastrophic forgetting, severely impeding multimodal scalability. In this work, we introduce Rosetta, a composable native multimodal pretraining framework designed for seamless and non-destructive modality expansion. Rosetta adopts a modular paradigm where core foundational knowledge is preserved within global shared experts, while modality-specific capabilities are distributed across plug-and-play experts. To guarantee non-destructive composition, we propose Momentum-Anchored Orthogonal Projection (MAOP). MAOP leverages the optimizer's momentum state as an implicit semantic anchor, selectively neutralizing conflicting gradient components from new modalities while preserving synergistic updates. Extensive evaluations demonstrate that, while standard MoE and MoT architectures suffer catastrophic forgetting of previously acquired knowledge, Rosetta robustly preserves established language and visual understanding. Furthermore, it delivers superior image generation and unlocks cross-modal synergy, paving the way for truly composable and unified multimodal foundation models. To facilitate further multimodal research, we release our code and checkpoints to the community. Project page at https://rosetta-lmm.github.io/.