Self-Supervised Pre-Training

Self-supervised speech models learn effective representations of spoken language, which have been shown to reflect various aspects of linguistic structure. But when does such structure emerge in model training? We study the encoding of a wide range of linguistic structures, across layers and intermediate checkpoints of six Wav2Vec2 and HuBERT models trained on spoken Dutch. We find that different levels of linguistic structure show notably distinct layerwise patterns as well as learning trajectories, which can partially be explained by differences in their degree of abstraction from the acoustic signal and the timescale at which information from the input is integrated. Moreover, we find that the level at which pre-training objectives are defined strongly affects both the layerwise organization and the learning trajectories of linguistic structures, with greater parallelism induced by higher-order prediction tasks (i.e. iteratively refined pseudo-labels).

Volumetric CT imaging is essential for clinical diagnosis, yet annotating 3D volumes is expensive and time-consuming, motivating self-supervised learning (SSL) from unlabeled data. However, applying SSL to 3D CT remains challenging due to the high memory cost of full-volume transformers and the anisotropic spatial structure of CT data, which is not well captured by conventional masking strategies. We propose NEMESIS, a masked autoencoder (MAE) framework that operates on local 128x128x128 superpatches, enabling memory-efficient training while preserving anatomical detail. NEMESIS introduces three key components: (i) noise-enhanced reconstruction as a pretext task, (ii) Masked Anatomical Transformer Blocks (MATB) that perform dual-masking through parallel plane-wise and axis-wise token removal, and (iii) NEMESIS Tokens (NT) for cross-scale context aggregation. On the BTCV multi-organ classification benchmark, NEMESIS with a frozen backbone and a linear classifier achieves a mean AUROC of 0.9633, surpassing fully fine-tuned SuPreM (0.9493) and VoCo (0.9387). Under a low-label regime with only 10% of available annotations, it retains an AUROC of 0.9075, demonstrating strong label efficiency. Furthermore, the superpatch-based design reduces computational cost to 31.0 GFLOPs per forward pass, compared to 985.8 GFLOPs for the full-volume baseline, providing a scalable and robust foundation for 3D medical imaging.

Reservoir simulation workflows face a fundamental data asymmetry: input parameter fields (geostatistical permeability realizations, porosity distributions) are free to generate in arbitrary quantities, yet existing neural operator surrogates require large corpora of expensive labeled simulation trajectories and cannot exploit this unlabeled structure. We introduce PI-JEPA (Physics-Informed Joint Embedding Predictive Architecture), a surrogate pretraining framework that trains without any completed PDE solves, using masked latent prediction on unlabeled parameter fields under per-sub-operator PDE residual regularization. The predictor bank is structurally aligned with the Lie--Trotter operator-splitting decomposition of the governing equations, dedicating a separate physics-constrained latent module to each sub-process (pressure, saturation transport, reaction), enabling fine-tuning with as few as 100 labeled simulation runs. On single-phase Darcy flow, PI-JEPA achieves $1.9\times$ lower error than FNO and $2.4\times$ lower error than DeepONet at $N_\ell{=}100$, with 24% improvement over supervised-only training at $N_\ell{=}500$, demonstrating that label-free surrogate pretraining substantially reduces the simulation budget required for multiphysics surrogate deployment.

Training deep learning models for three-dimensional (3D) medical imaging, such as Computed Tomography (CT), is fundamentally challenged by the scarcity of labeled data. While pre-training on natural images is common, it results in a significant domain shift, limiting performance. Self-Supervised Learning (SSL) on unlabeled medical data has emerged as a powerful solution, but prominent frameworks often fail to exploit the inherent 3D nature of CT scans. These methods typically process 3D scans as a collection of independent 2D slices, an approach that fundamentally discards critical axial coherence and the 3D structural context. To address this limitation, we propose the autoencoder for enhanced self-supervised medical image learning(MAESIL), a novel self-supervised learning framework designed to capture 3D structural information efficiently. The core innovation is the 'superpatch', a 3D chunk-based input unit that balances 3D context preservation with computational efficiency. Our framework partitions the volume into superpatches and employs a 3D masked autoencoder strategy with a dual-masking strategy to learn comprehensive spatial representations. We validated our approach on three diverse large-scale public CT datasets. Our experimental results show that MAESIL demonstrates significant improvements over existing methods such as AE, VAE and VQ-VAE in key reconstruction metrics such as PSNR and SSIM. This establishes MAESIL as a robust and practical pre-training solution for 3D medical imaging tasks.

Network traffic classification using self-supervised pre-training models based on Masked Autoencoders (MAE) has demonstrated a huge potential. However, existing methods are confined to isolated byte-level reconstruction of individual flows, lacking adequate perception of the multi-granularity contextual relationship in traffic. To address this limitation, we propose Mean MAE (MMAE), a teacher-student MAE paradigm with flow mixing strategy for building encrypted traffic pre-training model. MMAE employs a self-distillation mechanism for teacher-student interaction, where the teacher provides unmasked flow-level semantic supervision to advance the student from local byte reconstruction to multi-granularity comprehension. To break the information bottleneck in individual flows, we introduce a dynamic Flow Mixing (FlowMix) strategy to replace traditional random masking mechanism. By constructing challenging cross-flow mixed samples with interferences, it compels the model to learn discriminative representations from distorted tokens. Furthermore, we design a Packet-importance aware Mask Predictor (PMP) equipped with an attention bias mechanism that leverages packet-level side-channel statistics to dynamically mask tokens with high semantic density. Numerous experiments on a number of datasets covering encrypted applications, malware, and attack traffic demonstrate that MMAE achieves state-of-the-art performance. The code is available at https://github.com/lx6c78/MMAE

The approximation and convergence properties of implicit neural representations (INRs) are known to be highly sensitive to parameter initialization strategies. While several data-driven initialization methods demonstrate significant improvements over standard random sampling, the reasons for their success -- specifically, whether they encode classical statistical signal priors or more complex features -- remain poorly understood. In this study, we explore this phenomenon through a series of experimental analyses leveraging noise pretraining. We pretrain INRs on diverse noise classes (e.g., Gaussian, Dead Leaves, Spectral) and measure their ability to both fit unseen signals and encode priors for an inverse imaging task (denoising). Our analyses on image and video data reveal a surprising finding: simply pretraining on unstructured noise (Uniform, Gaussian) dramatically improves signal fitting capacity compared to all other baselines. However, unstructured noise also yields poor deep image priors for denoising. In contrast, we also find that noise with the classic $1/|f^α|$ spectral structure of natural images achieves an excellent balance of signal fitting and inverse imaging capabilities, performing on par with the best data-driven initialization methods. This finding enables more efficient INR training in applications lacking sufficient prior domain-specific data. For more details, visit project page at https://kushalvyas.github.io/noisepretraining.html

Self-supervised pre-training, where large corpora of unlabeled data are used to learn representations for downstream fine-tuning, has become a cornerstone of modern machine learning. While a growing body of theoretical work has begun to analyze this paradigm, existing bounds leave open the question of how sharp the current rates are, and whether they accurately capture the complex interaction between pre-training and fine-tuning. In this paper, we address this gap by developing an asymptotic theory of pre-training via two-stage M-estimation. A key challenge is that the pre-training estimator is often identifiable only up to a group symmetry, a feature common in representation learning that requires careful treatment. We address this issue using tools from Riemannian geometry to study the intrinsic parameters of the pre-training representation, which we link with the downstream predictor through a notion of orbit-invariance, precisely characterizing the limiting distribution of the downstream test risk. We apply our main result to several case studies, including spectral pre-training, factor models, and Gaussian mixture models, and obtain substantial improvements in problem-specific factors over prior art when applicable.

Computational pathology needs whole-slide image (WSI) foundation models that transfer across diverse clinical tasks, yet current approaches remain largely slide-centric, often depend on private data and expensive paired-report supervision, and do not explicitly model relationships among multiple slides from the same patient. We present MOOZY, a patient-first pathology foundation model in which the patient case, not the individual slide, is the core unit of representation. MOOZY explicitly models dependencies across all slides from the same patient via a case transformer during pretraining, combining multi-stage self-supervision with scaled low-cost task supervision. In Stage 1, we pretrain a vision-only slide encoder on 77,134 public slide feature grids using masked self-distillation. In Stage 2, we align these representations with clinical semantics using a case transformer and multi-task supervision over 333 tasks from 56 public datasets, including 205 classification and 128 survival tasks across four endpoints. Across sixteen held-out tasks, MOOZY improves macro weighted F1, balanced accuracy, and macro weighted ROC-AUC relative to PRISM by +4.19%, +7.93%, and +6.95%, respectively. MOOZY is also parameter efficient with 85.77M parameters, 14$\times$ smaller than GigaPath. These results suggest that patient-level pretraining yields transferable embeddings, providing a path toward scalable patient-first histopathology foundation models.

While self-supervised learning (SSL) has revolutionized audio representation, the excessive parameterization and quadratic computational cost of standard Transformers limit their deployment on resource-constrained devices. To address this bottleneck, we propose HEAR (Human-inspired Efficient Audio Representation), a novel decoupled architecture. Inspired by the human cognitive ability to isolate local acoustic features from global context, HEAR splits the processing pipeline into two dedicated modules: an Acoustic Model for local feature extraction and a Task Model for global semantic integration. Coupled with an Acoustic Tokenizer trained via knowledge distillation, our approach enables robust Masked Audio Modeling (MAM). Extensive experiments demonstrate that HEAR requires only 15M parameters and 9.47 GFLOPs for inference, operating at a fraction of the computational cost of conventional foundation models (which typically require 85M-94M parameters). Despite this high efficiency, HEAR achieves highly competitive performance across diverse audio classification benchmarks. The code and pre-trained models are available at https://github.com/HarunoriKawano/HEAR

Since the introduction of Masked Autoencoders, various improvements to masking techniques have been explored. In this paper, we rethink masking strategies for audio representation learning using masked prediction-based self-supervised learning (SSL) on general audio spectrograms. While recent informed masking techniques have attracted attention, we observe that they incur substantial computational overhead. Motivated by this observation, we propose dispersion-weighted masking (DWM), a lightweight masking strategy that leverages the spectral sparsity inherent in the frequency structure of audio content. Our experiments show that inverse block masking, commonly used in recent SSL frameworks, improves audio event understanding performance while introducing a trade-off in generalization. The proposed DWM alleviates these limitations and computational complexity, leading to consistent performance improvements. This work provides practical guidance on masking strategy design for masked prediction-based audio representation learning.

Unified Multimodal Models (UMMs) are often constrained by the pre-training of their $\textbf{visual generation components}$, which typically relies on inefficient paradigms and scarce, high-quality text-image paired data. In this paper, we systematically analyze pre-training recipes for $\textbf{UMM visual generation}$ and identify these two issues as the major bottlenecks. To address them, we propose $\textbf{Image-Only Training for UMMs (IOMM)}$, a data-efficient two-stage training framework. The first stage pre-trains the visual generative component $\textbf{exclusively}$ using abundant unlabeled image-only data, thereby removing the dependency on paired data $\textbf{for this costly phase}$. The second stage fine-tunes the model using a mixture of unlabeled images and a small curated set of text-image pairs, leading to improved instruction alignment and generative quality. Extensive experiments show that IOMM not only improves training efficiency but also achieves state-of-the-art (SOTA) performance. For example, our IOMM-B (3.6B) model was trained from scratch using only $\sim \textbf{1050}$ H800 GPU hours (with the vast majority, $\textbf{1000}$ hours, dedicated to the efficient $\textbf{image-only pre-training stage}$). It achieves $\textbf{0.89}$ on GenEval and $\textbf{0.55}$ on WISE--surpassing strong baselines such as BAGEL-7B (0.82 & 0.55) and BLIP3-o-4B (0.84 & 0.50). Code is available https://github.com/LINs-lab/IOMM.

Masked auto-encoders (MAE) and related approaches have shown promise for satellite imagery, but their application to synthetic aperture radar (SAR) remains limited due to challenges in semantic labeling and high noise levels. Building on our prior work with SAR-W-MixMAE, which adds SAR-specific intensity-weighted loss to standard MixMAE for pretraining, we also introduce SAR-W-SimMIM; a weighted variant of SimMIM applied to ALOS-2 single-channel SAR imagery. This method aims to reduce the impact of speckle and extreme intensity values during self-supervised pretraining. We evaluate its effect on semantic segmentation compared to our previous trial with SAR-W-MixMAE and random initialization, observing notable improvements. In addition, pretraining and fine-tuning models on satellite imagery pose unique challenges, particularly when developing region-specific models. Imbalanced land cover distributions such as dominant water, forest, or desert areas can introduce bias, affecting both pretraining and downstream tasks like land cover segmentation. To address this, we constructed a SAR dataset using ALOS-2 single-channel (HH polarization) imagery focused on the Japan region, marking the initial phase toward a national-scale foundation model. This dataset was used to pretrain a vision transformer-based autoencoder, with the resulting encoder fine-tuned for semantic segmentation using a task-specific decoder. Initial results demonstrate significant performance improvements compared to training from scratch with random initialization. In summary, this work provides a guide to process and prepare ALOS2 observations to create dataset so that it can be taken advantage of self-supervised pretraining of models and finetuning downstream tasks such as semantic segmentation.

Foundation models have transformed vision and language by learning general-purpose representations from large-scale unlabeled data, yet 3D medical imaging lacks analogous approaches. Existing self-supervised methods rely on low-level reconstruction or contrastive objectives that fail to capture the anatomical semantics critical for medical image analysis, limiting transfer to downstream tasks. We present MASS (MAsk-guided Self-Supervised learning), which treats in-context segmentation as the pretext task for learning general-purpose medical imaging representations. MASS's key insight is that automatically generated class-agnostic masks provide sufficient structural supervision for learning semantically rich representations. By training on thousands of diverse mask proposals spanning anatomical structures and pathological findings, MASS learns what semantically defines medical structures: the holistic combination of appearance, shape, spatial context, and anatomical relationships. We demonstrate effectiveness across data regimes: from small-scale pretraining on individual datasets (20-200 scans) to large-scale multi-modal pretraining on 5K CT, MRI, and PET volumes, all without annotations. MASS demonstrates: (i) few-shot segmentation on novel structures, (ii) matching full supervision with only 20-40% labeled data while outperforming self-supervised baselines by over 20 in Dice score in low-data regimes, and (iii) frozen-encoder classification on unseen pathologies that matches full supervised training with thousands of samples. Mask-guided self-supervised pretraining captures broadly generalizable knowledge, opening a path toward 3D medical imaging foundation models without expert annotations. Code is available: https://github.com/Stanford-AIMI/MASS.

Fine-tuning LLM-based text embedders via contrastive learning maps inputs and outputs into a new representational space, discarding the LLM's output semantics. We propose LLM2Vec-Gen, a self-supervised alternative that instead produces embeddings directly in the LLM's output space by learning to represent the model's potential response. Specifically, trainable special tokens are appended to the input and optimized to compress the LLM's own response into a fixed-length embedding, guided by an unsupervised embedding teacher and a reconstruction objective. Crucially, the LLM backbone remains frozen and training requires only unlabeled queries. LLM2Vec-Gen achieves state-of-the-art self-supervised performance on the Massive Text Embedding Benchmark (MTEB), improving by 8.8% over the unsupervised embedding teacher. Since the embeddings preserve the LLM's response-space semantics, they inherit capabilities such as safety alignment (up to 22.6% reduction in harmful content retrieval) and reasoning (up to 35.6% improvement on reasoning-intensive retrieval). Finally, the learned embeddings are also interpretable: they can be decoded back into text to reveal their semantic content. Our code, data, and pretrained models are publicly available at https://github.com/McGill-NLP/llm2vec-gen.

Self-supervised masked modeling shows promise for encrypted traffic classification by masking and reconstructing raw bytes. Yet recent work reveals these methods fail to reduce reliance on labeled data despite costly pretraining: under frozen encoder evaluation, accuracy drops from greater than 0.9 to less than 0.47. We argue the root cause is inductive bias mismatch: flattening traffic into byte sequences destroys protocol-defined semantics. We identify three specific issues: 1) field unpredictability, random fields like ip.id are unlearnable yet treated as reconstruction targets; 2) embedding confusion, semantically distinct fields collapse into a unified embedding space; 3) metadata loss, capture-time metadata essential for temporal analysis is discarded. To address this, we propose a protocol-native paradigm that treats protocol-defined field semantics as architectural priors, reformulating the task to align with the data's intrinsic tabular modality rather than incrementally adapting sequence-based architectures. Instantiating this paradigm, we introduce FlowSem-MAE, a tabular masked autoencoder built on Flow Semantic Units (FSUs). It features predictability-guided filtering that focuses on learnable FSUs, FSU-specific embeddings to preserve field boundaries, and dual-axis attention to capture intra-packet and temporal patterns. FlowSem-MAE significantly outperforms state-of-the-art across datasets. With only half labeled data, it outperforms most existing methods trained on full data.

Pretraining and fine-tuning have emerged as a new paradigm in remote sensing image interpretation. Among them, Masked Autoencoder (MAE)-based pretraining stands out for its strong capability to learn general feature representations via reconstructing masked image regions. However, applying MAE to multispectral remote sensing images remains challenging due to complex backgrounds, indistinct targets, and the lack of semantic guidance during masking, which hinders the learning of underlying structures and meaningful spatial-spectral features. To address this, we propose a simple yet effective approach, Spectral Index-Guided MAE (SIGMAE), for multispectral image pretraining. The core idea is to incorporate domain-specific spectral indices as prior knowledge to guide dynamic token masking toward informative regions. SIGMAE introduces Semantic Saliency-Guided Dynamic Token Masking (SSDTM), a curriculum-style strategy that quantifies each patch's semantic richness and internal heterogeneity to adaptively select the most informative tokens during training. By prioritizing semantically salient regions and progressively increasing sample difficulty, SSDTM enhances spectrally rich and structurally aware representation learning, mitigates overfitting, and reduces redundant computation compared with random masking. Extensive experiments on five widely used datasets covering various downstream tasks, including scene classification, semantic segmentation, object extraction and change detection, demonstrate that SIGMAE outperforms other pretrained geospatial foundation models. Moreover, it exhibits strong spatial-spectral reconstruction capability, even with a 90% mask ratio, and improves complex target recognition under limited labeled data. The source codes and model weights will be released at https://github.com/zxk688/SIGMAE.

Self-supervised learning (SSL) has emerged as a powerful paradigm for Chest X-ray (CXR) analysis under limited annotations. Yet, existing SSL strategies remain suboptimal for medical imaging. Masked image modeling allocates substantial computation to reconstructing high-frequency background details with limited diagnostic value. Contrastive learning, on the other hand, often depends on aggressive augmentations that risk altering clinically meaningful structures. We introduce Semantic-Partitioned Contrastive Learning (S-PCL), an efficient pre-training framework tailored for CXR representation learning. Instead of reconstructing pixels or relying on heavy augmentations, S-PCL randomly partitions patch tokens from a single CXR into two non-overlapping semantic subsets. Each subset provides a complementary but incomplete view. The encoder must maximize agreement between these partitions, implicitly inferring global anatomical layout and local pathological cues from partial evidence. This semantic partitioning forms an internal bottleneck that enforces long-range dependency modeling and structural coherence. S-PCL eliminates the need for hand-crafted augmentations, auxiliary decoders, and momentum encoders. The resulting architecture is streamlined, computationally efficient, and easy to scale. Extensive experiments on large-scale CXR benchmarks, including ChestX-ray14, CheXpert, RSNA Pneumonia and SIIM-ACR Pneumothorax, show that S-PCL achieves competitive performance while attaining the lowest GFLOPs and superior accuracy among existing SSL approaches.

Arterial spin labeling (ASL) perfusion MRI allows direct quantification of regional cerebral blood flow (CBF) without exogenous contrast, enabling noninvasive measurements that can be repeated without constraints imposed by contrast injection. ASL is increasingly acquired in research studies and clinical MRI protocols. Building on successes in structural imaging, recent efforts have implemented deep learning based methods to improve image quality, enable automated quality control, and derive robust quantitative and predictive biomarkers with ASL derived CBF. However, progress has been limited by variable image quality, substantial inter-site, vendor and protocol differences, and limited availability of labeled datasets needed to train models that generalize across cohorts. To address these challenges, we introduce ICHOR, a self supervised pre-training approach for ASL CBF maps that learns transferable representations using 3D masked autoencoders. ICHOR is pretrained via masked image modeling using a Vision Transformer backbone and can be used as a general-purpose encoder for downstream ASL tasks. For pre-training, we curated one of the largest ASL datasets to date, comprising 11,405 ASL CBF scans from 14 studies spanning multiple sites and acquisition protocols. We evaluated the pre-trained ICHOR encoder on three downstream diagnostic classification tasks and one ASL CBF map quality prediction regression task. Across all evaluations, ICHOR outperformed existing neuroimaging self-supervised pre-training methods adapted to ASL. Pre-trained weights and code will be made publicly available.

Learning versatile, fine-grained representations from irregular event streams is pivotal yet nontrivial, primarily due to the heavy annotation that hinders scalability in dataset size, semantic richness, and application scope. To mitigate this dilemma, we launch a novel self-supervised pretraining method that distills visual foundation models (VFMs) to push the boundaries of event representation at scale. Specifically, we curate an extensive synchronized image-event collection to amplify cross-modal alignment. Nevertheless, due to inherent mismatches in sparsity and granularity between image-event domains, existing distillation paradigms are prone to semantic collapse in event representations, particularly at high resolutions. To bridge this gap, we propose to extend the alignment objective to semantic structures provided off-the-shelf by VFMs, indicating a broader receptive field and stronger supervision. The key ingredient of our method is a structure-aware distillation loss that grounds higher-quality image-event correspondences for alignment, optimizing dense event representations. Extensive experiments demonstrate that our approach takes a great leap in downstream benchmarks, significantly surpassing traditional methods and existing pretraining techniques. This breakthrough manifests in enhanced generalization, superior data efficiency and elevated transferability.

We dream of a future where point clouds from all domains can come together to shape a single model that benefits them all. Toward this goal, we present Utonia, a first step toward training a single self-supervised point transformer encoder across diverse domains, spanning remote sensing, outdoor LiDAR, indoor RGB-D sequences, object-centric CAD models, and point clouds lifted from RGB-only videos. Despite their distinct sensing geometries, densities, and priors, Utonia learns a consistent representation space that transfers across domains. This unification improves perception capability while revealing intriguing emergent behaviors that arise only when domains are trained jointly. Beyond perception, we observe that Utonia representations can also benefit embodied and multimodal reasoning: conditioning vision-language-action policies on Utonia features improves robotic manipulation, and integrating them into vision-language models yields gains on spatial reasoning. We hope Utonia can serve as a step toward foundation models for sparse 3D data, and support downstream applications in AR/VR, robotics, and autonomous driving.

Digital ink -- the coordinate stream captured from stylus or touch input -- lacks a unified representation. Continuous vector representations produce long sequences and suffer from training instability, while existing token representations require large vocabularies, face out-of-vocabulary issues, and underperform vectors on recognition. We propose ScribeTokens, a tokenization that decomposes pen movement into unit pixel steps. Together with two pen-state tokens, this fixed 10-token base vocabulary suffices to represent any digital ink and enables aggressive BPE compression. On handwritten text generation, ScribeTokens dramatically outperforms vectors (17.33% vs. 70.29% CER), showing tokens are far more effective for generation. On recognition, ScribeTokens is the only token representation to outperform vectors without pretraining. We further introduce next-ink-token prediction as a self-supervised pretraining strategy, which consistently improves recognition across all token-based models and accelerates convergence by up to 83x. With pretraining, ScribeTokens achieves the best recognition results across all representations on both datasets (8.27% CER on IAM, 9.83% on DeepWriting).

Masked Image Modeling has been one of the most popular self-supervised learning paradigms to learn representations from large-scale, unlabeled Earth Observation images. While incorporating multi-modal and multi-temporal Earth Observation data into Masked Image Modeling has been widely explored, the spatial dependencies between images captured from neighboring areas remains largely overlooked. Since the Earth's surface is continuous, neighboring images are highly related and offer rich contextual information for self-supervised learning. To close this gap, we propose NeighborMAE, which learns spatial dependencies by joint reconstruction of neighboring Earth Observation images. To ensure that the reconstruction remains challenging, we leverage a heuristic strategy to dynamically adjust the mask ratio and the pixel-level loss weight. Experimental results across various pretraining datasets and downstream tasks show that NeighborMAE significantly outperforms existing baselines, underscoring the value of neighboring images in Masked Image Modeling for Earth Observation and the efficacy of our designs.

Generative models have recently advanced $\textit{de novo}$ protein design by learning the statistical regularities of natural structures. However, current approaches face three key limitations: (1) Existing methods cannot jointly learn protein geometry and design tasks, where pretraining can be a solution; (2) Current pretraining methods mostly rely on local, non-rigid atomic representations for property prediction downstream tasks, limiting global geometric understanding for protein generation tasks; and (3) Existing approaches have yet to effectively model the rich dynamic and conformational information of protein structures. To overcome these issues, we introduce $\textbf{RigidSSL}$ ($\textit{Rigidity-Aware Self-Supervised Learning}$), a geometric pretraining framework that front-loads geometry learning prior to generative finetuning. Phase I (RigidSSL-Perturb) learns geometric priors from 432K structures from the AlphaFold Protein Structure Database with simulated perturbations. Phase II (RigidSSL-MD) refines these representations on 1.3K molecular dynamics trajectories to capture physically realistic transitions. Underpinning both phases is a bi-directional, rigidity-aware flow matching objective that jointly optimizes translational and rotational dynamics to maximize mutual information between conformations. Empirically, RigidSSL variants improve designability by up to 43% while enhancing novelty and diversity in unconditional generation. Furthermore, RigidSSL-Perturb improves the success rate by 5.8% in zero-shot motif scaffolding and RigidSSL-MD captures more biophysically realistic conformational ensembles in G protein-coupled receptor modeling.

Polysomnography (PSG) provides the gold standard for sleep assessment but suffers from substantial heterogeneity across recording devices and cohorts. There have been growing efforts to build general-purpose foundation models (FMs) for sleep physiology, but lack an in-depth understanding of the pre-training process and scaling patterns that lead to more generalizable sleep FMs. To fill this gap, we curate a massive corpus of 166,500 hours of sleep recordings from nine public sources and establish SleepBench, a comprehensive, fully open-source benchmark. Leveraging SleepBench, we systematically evaluate four families of self-supervised pre-training objectives and uncover three critical findings: (1) existing FMs fail to generalize to missing channels at inference; (2) channel-invariant feature learning is essential for pre-training; and (3) scaling sample size, model capacity, and multi-source data mixture consistently improves downstream performance.With an enhanced pre-training and scaling recipe, we introduce OSF, a family of sleep FMs that achieves state-of-the-art performance across nine datasets on diverse sleep and disease prediction tasks. Further analysis of OSF also reveals intriguing properties in sample efficiency, hierarchical aggregation, and cross-dataset scaling.

Edge classification on directed dynamic graphs is critical for understanding evolving user-item interactions and behavioral patterns in recommender systems and social platforms. Existing dynamic graph architectures typically process these interactions using shared parameters for nodes with semantically distinct roles, including source, destination, query, and neighbor. While abundant supervision in tasks such as link prediction provides sufficient gradient signal for models to implicitly deduce role semantics and overcome this conflation, there are often far fewer labels available for edge classification. We hypothesize that in such regimes, the ability of models to implicitly separate roles is restricted, degrading downstream performance. To empirically investigate this relationship, we introduce an experimental framework for sequence-based models that explicitly disentangles functional roles using targeted embeddings and an asymmetric pretraining objective. By providing architectural priors for these roles, the framework serves as an evaluative vehicle to isolate and measure the resulting performance delta across a range of label budgets. Our empirical evaluation demonstrates that this explicit role disentanglement yields substantial and consistent relative performance gains over baselines. Furthermore, representational analyses reveal that the mechanism by which the framework provides these benefits is a bifurcation of source and destination latent spaces that improves linear separability.

Electrocardiogram (ECG) analysis is crucial for diagnosing heart disease, but most self-supervised learning methods treat ECG as a generic time series, overlooking physiologic semantics and rhythm-level structure. Existing contrastive methods utilize augmentations that distort morphology, whereas generative approaches employ fixed-window segmentation, which misaligns cardiac cycles. To address these limitations, we propose RhythmBERT, a generative ECG language model that considers ECG as a language paradigm by encoding P, QRS, and T segments into symbolic tokens via autoencoder-based latent representations. These discrete tokens capture rhythm semantics, while complementary continuous embeddings retain fine-grained morphology, enabling a unified view of waveform structure and rhythm. RhythmBERT is pretrained on approximately 800,000 unlabeled ECG recordings with a masked prediction objective, allowing it to learn contextual representations in a label-efficient manner. Evaluations show that despite using only a single lead, RhythmBERT achieves comparable or superior performance to strong 12-lead baselines. This generalization extends from prevalent conditions such as atrial fibrillation to clinically challenging cases such as subtle ST-T abnormalities and myocardial infarction. Our results suggest that considering ECG as structured language offers a scalable and physiologically aligned pathway for advancing cardiac analysis.

Ego-centric driving videos available online provide an abundant source of visual data for autonomous driving, yet their lack of annotations makes it difficult to learn representations that capture both semantic structure and 3D geometry. Recent advances in large feedforward spatial models demonstrate that point maps and ego-motion can be inferred in a single forward pass, suggesting a promising direction for scalable driving perception. We therefore propose a label-free, teacher-guided framework for learning autonomous driving representations directly from unposed videos. Unlike prior self-supervised approaches that focus primarily on frame-to-frame consistency, we posit that safe and reactive driving depends critically on temporal context. To this end, we leverage a feedforward architecture equipped with a lightweight autoregressive module, trained using multi-modal supervisory signals that guide the model to jointly predict current and future point maps, camera poses, semantic segmentation, and motion masks. Multi-modal teachers provide sequence-level pseudo-supervision, enabling LFG to learn a unified pseudo-4D representation from raw YouTube videos without poses, labels, or LiDAR. The resulting encoder not only transfers effectively to downstream autonomous driving planning on the NAVSIM benchmark, surpassing multi-camera and LiDAR baselines with only a single monocular camera, but also yields strong performance when evaluated on a range of semantic, geometric, and qualitative motion prediction tasks. These geometry and motion-aware features position LFG as a compelling video-centric foundation model for autonomous driving.

Neural simulators promise efficient surrogates for physics simulation, but scaling them is bottlenecked by the prohibitive cost of generating high-fidelity training data. Pre-training on abundant off-the-shelf geometries offers a natural alternative, yet faces a fundamental gap: supervision on static geometry alone ignores dynamics and can lead to negative transfer on physics tasks. We present GeoPT, a unified pre-trained model for general physics simulation based on lifted geometric pre-training. The core idea is to augment geometry with synthetic dynamics, enabling dynamics-aware self-supervision without physics labels. Pre-trained on over one million samples, GeoPT consistently improves industrial-fidelity benchmarks spanning fluid mechanics for cars, aircraft, and ships, and solid mechanics in crash simulation, reducing labeled data requirements by 20-60% and accelerating convergence by 2$\times$. These results show that lifting with synthetic dynamics bridges the geometry-physics gap, unlocking a scalable path for neural simulation and potentially beyond. Code is available at https://github.com/Physics-Scaling/GeoPT.

Dense Bird's Eye View (BEV) semantic maps are central to autonomous driving, yet current multi-camera methods depend on costly, inconsistently annotated BEV ground truth. We address this limitation with a two-phase training strategy for fine-grained road marking segmentation that removes full supervision during pretraining and halves the amount of training data during fine-tuning while still outperforming the comparable supervised baseline model. During the self-supervised pretraining, BEVFormer predictions are differentiably reprojected into the image plane and trained against multi-view semantic pseudo-labels generated by the widely used semantic segmentation model Mask2Former. A temporal loss encourages consistency across frames. The subsequent supervised fine-tuning phase requires only 50% of the dataset and significantly less training time. With our method, the fine-tuning benefits from rich priors learned during pretraining boosting the performance and BEV segmentation quality (up to +2.5pp mIoU over the fully supervised baseline) on nuScenes. It simultaneously halves the usage of annotation data and reduces total training time by up to two thirds. The results demonstrate that differentiable reprojection plus camera perspective pseudo labels yields transferable BEV features and a scalable path toward reduced-label autonomous perception.

Self-supervised learning (SSL) and diffusion models have respectively advanced representation learning and generative modeling for high-dimensional 3D visual data, yet they are often developed as separate paradigms. Their unification remains challenging under multi-source heterogeneity, as anatomical content must be preserved for analysis while acquisition-related style varies across centers and affects synthesis. In this paper, we propose MeDUET, a 3D Medical image Disentangled UnifiEd PreTraining framework in the variational autoencoder latent space. MeDUET formulates unified pretraining as an empirical factor identifiability problem, aiming to learn domain-invariant content factors for anatomy and domain-specific style factors for appearance. To improve factor separation, MeDUET first uses token demixing with a standard adversarial domain regularizer to establish basic content-style specialization, and further introduces Mixed Factor Token Distillation and Swap-invariance Quadruplet Contrast to reduce mixed-region factor leakage and organize factor spaces with factor-wise invariance and discriminability. With these learned factors, MeDUET transfers effectively to both synthesis and analysis, yielding higher fidelity, faster convergence, and better controllability for synthesis, while achieving competitive or superior domain generalization and label efficiency on diverse datasets, tasks, and modalities. Overall, MeDUET shows that multi-source heterogeneity can serve as useful supervision, with disentanglement providing an effective interface for unifying 3D medical image synthesis and analysis. Our code is available at https://github.com/JK-Liu7/MeDUET.