Methods that recover individual latent variables of the world, from nonlinear ICA to dictionary learning and causal representation learning, anchor the latents to observations through reconstruction, auxiliary supervision, or distributional asymmetries such as non-Gaussianity. Methods without these anchors, including joint-embedding predictive architectures (JEPAs), identify the latent state only up to a linear transformation, so individual latents remain mixed. We close this gap: individual world latents can be provably recovered with no reconstruction, no decoder, and no labels. The key condition is Structural Diversity: different latents leave distinct dependency footprints on observations, just as no two snowflakes are alike. Building on the linear identifiability that LeJEPA provides, we prove that under Structural Diversity, DSReg (Dependency-Sparsity Regularization) recovers individual world latents up to signed permutation, without reconstruction or a decoder. It applies post hoc to any linearly identified representation, reusing trained checkpoints at no loss over joint training, and establishes the first fully identifiable JEPA that recovers every world latent. Moreover, as a condition on dependency footprints, Structural Diversity is strictly weaker than all structural conditions of prior identifiable latent variable models. Across synthetic regimes, world model probes, learned visual encoders, and external renderers, DSReg preserves dense prediction while improving individual-latent recovery and downstream use with scales.
https://arxiv.org/abs/2610.09457
In diffusion-based generation, a neural network can be trained to predict the clean data, the noise, or the velocity from a noisy input. These prediction targets are interconvertible and describe the same generative process, yet plain Diffusion Transformers operating on large pixel patches succeed with clean prediction and fail with noise or velocity prediction. We argue that this asymmetry arises because noisy targets require the residual stream to preserve noise-dependent input variation through depth for the final readout, forcing subsequent layers to compute on noisy representations. A spectrally concentrated clean target imposes a lighter demand, leaving greater freedom to organize hidden representations for subsequent computation. We call this preservation requirement *residual-stream burden* and show how it shapes representation learning in Diffusion Transformers. Controlled experiments indicate that the exploitable structure is spectral concentration in patch space and that the bandwidth of the persistent residual state is a key resource for noisy prediction. We further show that this account is consistent with recent decoupled pixel-space architectures, whose diverse designs all reduce the residual-stream burden on the main pathway. To examine this understanding from a complementary direction, we expand and reorganize the residual-stream bandwidth directly, introducing Spatially Indexed Hyper-Connections (SiHC) that reach FID 1.71 on ImageNet $256^2$. Together, these results identify residual-stream burden as a mechanism through which prediction targets and architecture jointly shape representation learning in Diffusion Transformers.
https://arxiv.org/abs/2609.33895
Conditional neural fields represent signals continuously, but their effectiveness depends on how the conditional latent representations are inferred from observed data. In meta-learning, this encoding occurs through gradient updates induced by the decoder, tying representation learning directly to decoder design. We formalize this connection by interpreting latent optimization as an optimization encoder, unifying the roles of second-order differentiation, latent parameterization, and task supervision. This concept enables second-order meta-learning for end-to-end training of the encoding procedure alongside the decoder, and clarifies which learning pathway first-order approximations discard. Guided by this view, we introduce Attentive Latent Fields (MetaLF), an equivariant transformer-based neural field that contextualizes a latent pointcloud through self-attention. These interactions shape both field predictions and the updates that construct their representation, allowing local observations to inform coherent non-local structure. Disentangling the inner encoding objective from outer task supervision unifies reconstruction, classification, and segmentation within an end-to-end meta-learning framework, using reconstruction-only latent adaptation at test time. Controlled experiments on polynomial fields link latent coordination to lower effective rank and stronger alignment with the underlying function space. Across image and 3D shape reconstruction, MetaLF improves fidelity within three to five gradient updates, while supporting semantic prediction across images, shapes, and volumes. Together, these findings position the optimization encoder perspective as a unified basis for designing neural fields around how representations are constructed, coordinated, and used.
https://arxiv.org/abs/2610.08075
Dynamic multimodal learning aims to learn robust representations by adaptively modeling information discrepancies across modalities. However, existing methods still suffer from two limitations: (i) static cross-modal alignment strategies usually impose uniform constraints on all samples while overlooking sample-wise variations, potentially leading to unreasonable over-alignment; and (ii) confidence- or uncertainty-aware fusion methods often fail to adequately account for feature magnitude and confidence differences across modalities. For modality pairs with significant feature magnitude differences or small confidence gaps, it might be unreliable to strictly align fusion weights according to confidence. To address these issues, we propose an Alignment- and Calibration-driven Multimodal Learning framework (ACML). Specifically, ACML incorporates a dynamic cross-modal triplet alignment module, which enforces strong semantic consistency for high-confidence positive pairs while encouraging diverse representation learning between high- and low-confidence positive pairs according to their confidence gaps. Additionally, ACML introduces a difference-aware attention calibration strategy that adaptively adjusts attention regularization based on feature magnitude and confidence differences across modalities, thereby mitigating biases caused by unreasonable fusion constraints. Extensive experiments on multiple multimodal benchmark datasets demonstrate that ACML consistently achieves superior performance and robustness over recent state-of-the-art methods.
https://arxiv.org/abs/2610.07928
Videofluoroscopic Swallowing Study (VFSS) is one of the gold standard for diagnosing swallowing disorders, providing dynamic X-ray imaging of the swallowing process. Automated kinematic analysis in VFSS relies fundamentally on precise anatomical keypoint localization. However, existing studies focus on limited keypoints (e.g., cervical vertebrae or the hyoid) and overlook critical regions such as the soft palate, while annotating only active swallowing segments and ignoring abundant non-swallowing data, resulting in poor data efficiency. Moreover, leveraging this unlabeled data via standard semi-supervised learning is suboptimal, as generic methods are prone to spatial bias. In medical X-rays with fixed layouts, models tend to memorize absolute coordinates rather than understanding anatomical structures. To tackle these challenges, we introduce VFSSKep, a novel dataset that extends annotations to the soft palate and incorporates large-scale unlabeled data. We further propose S$^3$KL, a Structure-aware Semi-Supervised Keypoint Localization framework designed to overcome spatial bias. It integrates a Structure-Aware Learning strategy to extract high-resolution structural cues for structure-aware representation learning, and a Structural Representation Consistency Learning strategy with block shuffling to enforce invariant structural recognition. Experiments show our method achieves state-of-the-art semi-supervised performance, even with unlabeled and 25% labeled data surpassing fully supervised learning with 100% labeled data. Code and data will be made publicly available at: this https URL.
https://arxiv.org/abs/2610.07726
Most existing MEG and EEG (M/EEG) visual decoding methods align brain signals with a single global embedding extracted from a pretrained visual encoder, leaving open whether intermediate patch representations, which preserve richer and more granular rich visual information, can improve representation learning. To address this question, we introduce the Residual Patch Adapter (RPA), a lightweight, modular adapter that leverages all patch tokens from an intermediate layer of a ViT visual encoder for alignment. Through extensive ablation analyses, we first show that pooling or masking patch tokens degrades the learned representation, demonstrating that retaining the full set of patch tokens is important for EEG alignment, while the CLS token provides little unique information. We then use a series of six quantitative feature analyses to show that both higher-level semantics and lower-level visual features, including color and texture, are essential for this EEG-to-image alignment. Under current protocols, our system achieves Top-1 accuracies of 95.4\% within-subject and 35.5\% cross-subject on THINGS-EEG2, and 65.2\% and 6.7\%, respectively, on THINGS-MEG, achieving state-of-the-art (SOTA) performance across both datasets. Evaluations with alternative brain encoders, including pretrained EEG foundation models, demonstrate that the approach extends beyond the projection-based EEG encoder. Furthermore, we provide a plug-and-play interface that allows RPA to be replaced by convolution, attention, or ConvNeXt alternatives. Together, these findings provide significant insight into M/EEG-to-image representation learning by establishing design principles for leveraging the latent space of visual encoders, and open new directions for brain--image alignment and non-invasive brain--computer interface (BCI).
https://arxiv.org/abs/2609.31698
Robotic systems often exhibit unstable modes, along which small perturbations and disturbances can cause unbounded growth unless corrected through feedback. Controlling such systems from high-dimensional visual observations requires representations that preserve these modes. Joint-embedding predictive architectures (JEPAs) provide a natural framework for learning such representations and their dynamics from visual data. However, we demonstrate that next step prediction combined with anti-collapse regularization does not guarantee that controllable unstable modes are preserved: the training loss can be minimized while these modes are collapsed, making stabilization from the learned representation impossible. To address this, we augment world-model training with an action reconstruction objective (i.e., an inverse dynamics loss) that encourages control-aware representations, namely, visual representations that preserve crucial features for control. We prove that exact action reconstruction makes the encoder injective on the finite-horizon reachable subspace. Thus, the encoder cannot discard any state direction reachable by an action sequence within $H$ steps. Moreover, we show that, as $H$ grows, the dominant eigenspace of the finite-horizon controllability Gramian converges to the controllable unstable subspace. We establish our theoretical results for linear systems and demonstrate empirically that our findings extend to nonlinear visual control tasks (CartPole, Walker2D, and PointMaze), highlighting the benefits of control-aware representation learning.
https://arxiv.org/abs/2610.07540
Protein-molecule virtual screening is increasingly cast as a problem of representation learning in a shared embedding space. Existing methods rely on dense holistic alignment, entangling invariant binding determinants with nuisance correlations and limiting transfer to new targets. It has been noted that binding in protein-molecule systems involves sparse cross-modality interactions: binding is governed by a small contact interface and a few decisive local interactions (e.g., hydrogen bonds, hydrophobic contacts, and salt bridges) rather than the global structures of the protein and molecule. We hypothesize that uncovering and leveraging sparse interaction patterns is critical for generalization beyond the training data, as these patterns are reusable and expected to improve performance across different scenarios. In this paper, we aim to identify and leverage sparse interaction patterns, and verify our hypothesis. Since the training data contain only observed binding pairs, we formalize this prior via a V-structure causal model under Heckman-style selection, and establish three theoretical results: (i) the latent concepts of interacting proteins and molecules are not identifiable without appropriate sparsity constraints; (ii) these concepts and their sparse interactions are component-wise identifiable under structural sparsity conditions; and (iii) a low-rank relaxation of these conditions yields subspace identifiability of the concepts and interactions. Inspired by these principles, we propose CausalBind with three implementation variants. Extensive experiments on DUD-E and LIT-PCBA benchmarks show that all variants consistently outperform strong retrieval baselines, with the largest gains on LIT-PCBA early enrichment, and further generalize to target- and scaffold-level out-of-distribution splits. Code is available at this https URL.
https://arxiv.org/abs/2610.07340
Strong image generation models are conditioned on class labels, aligned to frozen pretrained encoders, or built on separately trained autoencoders. While effective, generation then depends on supervision or pretraining: labels must be annotated, and encoders or autoencoders pretrained for the target domain. We study joint generative and self-supervised representation learning in a single model, enabling self-conditioned generation without labels or pretrained models. This is challenging because the objectives are mismatched: contrastive learning consumes clean augmented views and favors coarse, invariant semantics, while flow matching consumes noisy images and must preserve the fine detail and spatial layout that contrastive learning discards. We propose SCION (Self-conditioned Generation on Self-supervised representation), whose core is a single pixel-space encoder conditioned on the flow timestep and an embedding. For representation learning, this conditioning embedding is a learned global vector shared across images, with the encoder's [CLS] token yielding the semantic representation trained by the contrastive loss. For generative training, the conditioning embedding is the image's own [CLS] representation, while patch tokens pass through a decoder to predict the image. To sample without a reference image at inference, we jointly learn a prior over the embedding. Gradient-norm balancing and stop-gradient mechanisms enable joint optimization in one run. SCION is self-supervised and self-contained, with no labels or pretrained models. On ImageNet 256x256, with the JiT-B recipe and no representation guidance, SCION reaches 8.92 FID, surpassing class-unconditional iREPA, which aligns to pretrained DINOv2 (46.44), and RCG, which conditions on it (14.27). With JiT-L, SCION achieves 5.89 FID without guidance and 3.47 with representation guidance, outperforming RCG with the ADM recipe (6.24).
https://arxiv.org/abs/2610.05711
RGB-D semantic segmentation has made notable progress by fusing RGB and Depth, yet mainstream models still learn features almost exclusively from pixel-level supervision, lacking direct high-level semantic constraints. This raises a central question-can external knowledge such as language priors inject stronger semantic discriminability into mainstream RGB-D segmentation models. We present DTFormer, a novel tri-modal (RGB-D-Text) semantic segmentation framework. At its core is Text-guided Semantic Alignment Module (TSAM) that first encodes textual cues into a set of semantic prototypes and then explicitly aligns multi-modal RGB-D features with these prototypes at multiple encoder and decoder layers. This design imposes strong semantic regularization on representation learning, guiding the network toward more discriminative features. Extensive experiments on multiple benchmarks show that DTFormer delivers consistent gains while remaining simple and efficient. Our results demonstrate that explicit semantic alignment offers an effective and practical route to improving RGB-D semantic segmentation. The code will be released upon acceptance.
https://arxiv.org/abs/2610.07014
This paper examines the role of Novel View Synthesis (NVS) in geometric representation learning. In principle, NVS should reason about 3D scene structure, thereby enabling transferable multi-view geometric representations. Yet, existing encoder-based NVS methods yield poor representations. This is not because of a lack of supervisory signal, but rather due to inconspicuous architectural choices: \textit{spatially expressive decoders} that dilute representational capabilities of the scene encoder, and \textit{low-level pixel-space targets} that hinder feature learning. We present SNAP, a self-supervised encoder-decoder transformer that addresses both through a pose-conditioned local decoder and a latent-space reconstruction objective. SNAP is task agnostic, and we show that it is competitive with special-purpose geometry-supervised methods. SNAP also performs competitively against self-supervised representations across five tasks: visual localization, pose estimation, point correspondence, depth estimation, and robot manipulation. Remarkably, SNAP's patch features exhibit emergent viewpoint invariance that approaches heavily supervised models despite lower compute and data budgets. Under camera shifts where standard 2D representations collapse, SNAP degrades more gracefully, revealing that restricting decoder expressivity actively prevents the suppression of transferable geometric structure. this https URL
https://arxiv.org/abs/2610.03717
Tactile sensing is particularly valuable for contact-rich robotic manipulation. Recent work has made substantial progress in tactile representation learning for robotic manipulation. However, similar tactile observations can arise from interaction conditions with very different task-risk implications, such as sensor noise, task-necessary variations, and emerging undesirable contact. Without context-grounded risk information, these cases can be ambiguous to downstream policies, leading to unnecessary corrections to benign variations or delayed responses to genuinely risky contact. To address this limitation, we propose Risk-Aware Tactile Encoding (RATE), which learns tactile representations that encode task-conditioned interaction risk. Specifically, history-conditioned prediction captures interaction context, while alert supervision associates this context with task-conditioned risk. The learned risk-aware representation complements conventional tactile features through a lightweight residual adapter. Experiments in both simulation and the real world demonstrate substantial improvements in task success, with controlled ablations confirming the complementary benefits of alert-guided learning and predictive temporal modeling.
https://arxiv.org/abs/2610.03538
Authorship Attribution (AA) requires capturing fine-grained stylistic characteristics, making it particularly challenging in zero-shot (ZS) settings where no task-specific supervision is available. In this work, we investigate the effect of author representations on ZS AA by evaluating a label-only prompting baseline together with three author representation strategies: representative writing samples, LLM-generated descriptions, and style embeddings (LISA). The first three approaches perform attribution using LLM prompting, while the embedding-based approach uses style embeddings with cosine similarity. We investigate the influence of prompt design and propose a two-stage embedding-based attribution framework that combines candidate space reduction with embedding-dimension selection. The results show that label-only ZS AA is ineffective, while incorporating author-specific representations consistently improves attribution performance. Among the evaluated approaches, the proposed two-stage LISA framework achieves the strongest overall performance, whereas LLM-generated style descriptions provide a substantially more compact representation of author style at the cost of some attribution performance. These findings demonstrate the importance of author representation in ZS AA, while indicating that current open-source LLMs remain insufficient for robust attribution without more effective representation learning.
https://arxiv.org/abs/2610.03531
Vector geospatial data represent the world as discrete geoentities, such as roads, buildings, and points of interest, each with semantic attributes, geometry, and spatial relations to other geoentities, including metric proximity and topology. Existing methods for learning geoentity representations typically support a single geometry type or model only a subset of these relations, limiting their ability to capture spatial context across heterogeneous geoentities and support diverse downstream tasks. We propose NARA (Neural Anchor-conditioned Relation-Aware representation learning), a novel self-supervised representation framework for heterogeneous vector geoentities. NARA contextualizes geoentities through spatial-context-aware attention that models spatial autocorrelation using geometry distance modulated by topological relations across surrounding points, polylines, and polygons. NARA introduces masked geoentity semantic modeling and geometry-aware spatial relation modeling, as well as relation-conditioned regularization that encourages similar representations for geoentities sharing the same spatial relation to a common reference entity, while accounting for spatial autocorrelation. NARA's frozen, task-agnostic encoder outperforms state-of-the-art methods, each with an architecture tailored to its respective task, across traffic-speed prediction for polylines, building-function classification for polygons, and next point-of-interest prediction for points.
https://arxiv.org/abs/2605.12276
Molecular learning models are strongly shaped by their underlying representations. Yet standard sequential and graph formalisms struggle to explicitly encode higher-order topology, such as ring systems and recurring motifs. Existing higher-order representations can capture these structures directly, but they are often computationally demanding and difficult to decode into valid molecules. Here, we introduce Higher-order Grammar Representation (HGR), a principled, topology-aware framework that lifts molecules to combinatorial complexes and parses each complex into a compact sequence of production rules under a context-free higher-order grammar. By serialising higher-order topology into rule sequences, HGR makes these structures directly compatible with standard sequence models, avoiding the computational overhead of explicit higher-order encodings while preserving topological expressiveness. To reduce benchmark bias towards simple ring systems, we construct RingDiv, a ring-enriched benchmark containing 1.18 million molecules, including the curated RingDiv300k subset, and introduce the ring diversity index (RDI) to quantify ring-system coverage. In molecular generation, HGR-based models uniquely combine 100% validity by construction with leading distributional alignment, ranking first in FCD on all five generation benchmarks. In representation learning, HGR-FM achieves the highest mean AUC across seven MoleculeNet benchmarks under both transfer protocols, improving on the strongest baseline by 8.3 and 3.3 AUC points under probing and full fine-tuning, respectively. Collectively, these results establish HGR as an efficient higher-order representation for molecular generation and transferable representation learning.
https://arxiv.org/abs/2610.02186
Existing genome-wide association studies (GWAS) of brain imaging provide predefined or deep-learning-derived imaging phenotypes, yet these phenotypes come from either volumetric scans or cortical surface meshes, so each captures only part of the heritable variation in brain anatomy. Here we introduce MEVA (Mesh-Enhanced Volumetric Autoencoder), a self-supervised framework that encodes voxel-level image intensity together with cortical mesh geometry, including curvature and cortical thickness at each surface vertex, into one shared set of imaging features. Combining the mesh and volumetric inputs in MEVA yields modest performance gains in age and sex prediction over models that use either input alone. When these features serve as phenotypes for GWAS in the UK Biobank, they reveal more genome-wide significant loci than features learned from volumes alone or from meshes alone. These results suggest that adding cortical surface geometry to volumetric self-supervised learning captures additional heritable variation and so increases the number of loci detected.
https://arxiv.org/abs/2610.02114
Predicting the future evolution of a scene is a fundamental capability for world modeling. Recent work has shown that operating in the feature space of Vision Foundation Models (VFMs) yields semantically rich representations that support diverse future scene understanding tasks. However, existing approaches rely on two-stage pipelines, where VFM features are first compressed using fixed dimensionality reduction (e.g., PCA) or independently trained autoencoders, and a separate predictor is trained on top of the resulting frozen latent space. This decoupling between representation learning and temporal prediction, as well as approaches that apply predictors directly on raw VFM features, provides no guarantee that the latent space is structured for predictable dynamics. In this work, we propose Latent-Foresight, an end-to-end framework that jointly learns a latent tokenizer and a flow-based generative dynamics model, explicitly shaping the representation to support temporal predictability. To enable stable joint optimization, we introduce several key design choices that prevent latent collapse and align reconstruction with generative objectives. Extensive experiments show that our approach learns more temporally coherent latent representations and consistently outperforms two-stage baselines across multiple future scene understanding tasks and prediction horizons, while eliminating separate training stages, including during high-resolution adaptation. We provide the implementation code and model weights at this https URL
https://arxiv.org/abs/2610.01942
Action chunking improves the performance of policies learned by behavioural cloning, and several mechanisms have been proposed to explain why, including temporal consistency, horizon reduction, representation learning, and reduced error compounding. We instead study what happens to an action error once it enters the system. At each state, we inject a small action error and measure how fast it grows or shrinks under two execution regimes: open-loop, where the rest of the chunk is replayed without replanning, and closed-loop, where the policy replans after the perturbation. The fitted rate labels each state as contracting, expanding, or unresolved. Across twelve manipulation tasks from three benchmark suites, we find that confidently stable states are rare, while error amplification is common among states whose propagation rate can be resolved. We further find that the measured propagation rate depends strongly on the fitting horizon: amplification is typically front-loaded, so short windows can overestimate longer-horizon propagation. Finally, we train predictors on these labels and find that a state's open-loop regime can be recovered from camera frames and proprioception alone, while its closed-loop propagation is only partially recoverable because it also depends on how the policy acts after the perturbation. These results suggest that error-compounding arguments alone do not provide a complete account of action chunking: neither passive open-loop dynamics nor policy replanning consistently contracts an injected error, and replanning rarely turns open-loop amplification into confident contraction. This suggests that closed-loop reactivity should be trained explicitly, using perturbation- and tree-coverage-oriented training to expose policies to deviations they must recover from, rather than expected to emerge reliably from standard imitation learning.
https://arxiv.org/abs/2610.01626
Existing work on Semantic IDs (SIDs) for generative recommendation treats SID construction as a representation learning problem: encode items into a quantised latent space and read off codes. We argue this view is incidental. SID construction is, at heart, a recursive clustering problem, and once stated this way the natural object to cluster is a graph whose nodes carry semantic content and whose edges carry collaborative signal; SID assignment becomes a hierarchical graph partition. This reframing yields a unified framework, Graph-Informed Semantic IDs (GrIS), that subsumes prior approaches rather than displacing them. RQ-VAE and RQ-KMeans are recovered as the special case where the graph is empty, exposing content-only quantisation as one corner of a larger design space along two so-far-collapsed axes: graph construction and recursive partition algorithm. We explore two contrasting instantiations: RecDMoN, which performs hierarchical assignment via differentiable graph pooling, and RQ-GAE, which extends RQ-VAE with graph-aware item representations and a graph reconstruction objective. On multiple real-world datasets, GrIS consistently improves over CF-aware SOTA, with gains of up to +52\% Hit@10. Because graph construction and partition are explicit, separately configurable components, improvements on either axis can be combined and evaluated systematically.
https://arxiv.org/abs/2610.01533
Causal representation learning aims to discover robust features by exploiting the causal structure underlying data generation. Existing methods require specifying the causal structure a priori, yet different structures demand fundamentally incompatible invariance constraints, and misspecification leads to representations that discard predictive information. We introduce SaCRL, a framework that jointly identifies the causal structure and learns the corresponding invariant representation without prior structural knowledge. Our approach formulates structure selection as a soft optimization over candidate invariances using HSIC-based violation metrics, with adaptive weights that automatically concentrate on the achievable structure. We provide theoretical guarantees for structure identification, including under random-feature approximation, invariance satisfaction, and out-of-distribution generalization. Empirically, SaCRL recovers the true structure on synthetic and semi-synthetic Bayesian-network benchmarks, outperforms fixed-invariance baselines on Colored MNIST, achieves state-of-the-art accuracy on three DomainBed benchmarks (PACS, VLCS, OfficeHome), and degrades gracefully under structural misspecification and limited environment diversity. Code is available at: this https URL.
https://arxiv.org/abs/2610.00968