Ligand-based virtual screening (LBVS) is a practical first-pass tool in early-stage drug discovery, but existing benchmarks can overestimate performance through random negatives, easy decoys, limited target coverage, and non-standardized evaluation protocols. We introduce TopU-LBVS, a multi-target benchmark for LBVS under hard-negative screening conditions. Starting from curated ChEMBL~35 bioactivity data, TopU-LBVS covers 93 protein targets across 7 protein classes and constructs target-specific screening libraries with property-matched, structurally similar decoys at a fixed 1:40 active-to-decoy ratio. Libraries contain roughly 400 to 10,000 compounds and are designed to reduce simple physicochemical and nearest-neighbor fingerprint shortcuts. TopU-LBVS provides three fixed protocols. TopU-LBVS-full evaluates ChEMBL$^\ast \rightarrow$ TopU generalization across all 93 targets. TopU-LBVS-low evaluates low-data TopU $\rightarrow$ TopU learning within the hard-negative distribution. TopU-LBVS-mini provides a compact seven-target protocol with a paired random-decoy control that changes only the test decoys, enabling low-cost development and direct measurement of the gap between random ChEMBL$^\ast$ and TopU decoys. Across ten reference baselines spanning fingerprint methods, molecular GNNs, fingerprint hybrids, and modern molecular models, performance under random-decoy evaluation degrades sharply under hard-negative screening. We release data, fixed splits, evaluation code, and baseline implementations for reproducible comparison of future LBVS and molecular representation learning methods. Code and data are available at this https URL and this https URL.
https://arxiv.org/abs/2609.29740
A generalist vision encoder must capture semantic, spatial, language-aligned, and action-relevant cues within a unified representation, yet softmax attention underlying today's most capable visual backbones becomes prohibitively expensive at high resolution. A natural attempt to address both challenges is to distill multiple specialist teachers directly into an efficient architecture. We find that directly coupling these objectives degrades representation quality, as the student must simultaneously reconcile heterogeneous capabilities and adapt them to a different token-mixing architecture. We introduce IronViT, built on a simple principle: consolidate capabilities before constraining computation. IronViT first distills complementary specialists into a softmax attention capability bridge, then progressively transfers the consolidated representation to a hybrid softmax-linear attention encoder. A purpose-built data pipeline further curates the distillation corpus for higher information density and broader domain coverage. Across recognition, retrieval, dense prediction, multimodal understanding, and robotic learning, IronViT is competitive with leading specialist and generalist vision encoders. The softmax bridge achieves the strongest aggregate performance in multimodal understanding and robotic learning among the evaluated backbones, while the hybrid encoder retains broad transfer performance with an efficiency advantage that grows with input resolution. Together, these results show that consolidating capabilities before architectural conversion can yield a generalist visual encoder without inheriting the prohibitive high-resolution cost of conventional softmax attention.
https://arxiv.org/abs/2609.29252
Pathology foundation models (PFMs) have transformed computational pathology through powerful representation learning from histopathological images. PFMs provide rich, discriminative representations for whole slide image (WSI) analysis, enabling tasks such as slide-level classification under multiple instance learning (MIL). However, these representations may also encode non-biological signals associated with acquisition centers, potentially introducing spurious shortcuts into downstream predictions. In this work, we evaluate center-associated robustness in WSI classification using a controlled training setting with increasing class-center correlations quantified by Cramér's V. We benchmark six PFMs across four datasets and two MIL aggregators, while evaluating ComBat as a robustification strategy. We further introduce the Area Under the Cramér's V Curve (AUCC) to jointly capture absolute classification performance and its degradation as spurious correlation increases. Results show that center-related information encoded by PFMs propagates to WSI-level predictions, with robustness depending on both the PFM representation and MIL aggregation strategy. Additionally, ComBat harmonization does not provide consistent robustness gains across datasets.
https://arxiv.org/abs/2609.28231
Standard contrastive learning frameworks are mainly designed from a semantic perspective, yet learning 2D visual representations that preserve 3D spatial structure is also important for scene understanding. In this work, we propose Depth-Guided Contrastive Learning (DGCL), a simple auxiliary objective that injects 3D spatial awareness into 2D contrastive representation learning. Our key idea is to use depth to convert local 3D proximity into contrastive similarity: pixels that are closer in 3D space are encouraged to have more similar representations than pixels that are farther apart. Instead of relying on absolute depth values, DGCL formulates supervision through relative 3D distance comparisons among randomly sampled pixels, making the objective invariant to depth scale, efficient to compute, and easy to integrate into existing contrastive frameworks. Experiments across different datasets and models show that DGCL consistently improves 2D representation learning and benefits semantic downstream tasks by stronger spatial and geometric understanding. The code is available on this https URL.
https://arxiv.org/abs/2609.28159
Brain-to-language decoding translates neural activity associated with language production, internal speech and perception into linguistic or expressive outputs. It offers a route to restoring communication after speech loss and a means of studying how the brain represents language. Advances in neural recording and representation learning have expanded the field from constrained recognition and acoustic reconstruction to text generation, streaming personalised speech and facial animation. This survey synthesises these developments across invasive and non-invasive measurements, drawing on a search without a lower year limit and source-led updates through September 2026. We connect Articulated, Inner and Perceived tasks to the neural populations they engage, the representations available to decoders and the outputs those representations can support. We examine model development, public resources and the evolution of evaluation, and compare published performance and communication costs within their reported protocols. The synthesis identifies complementary routes to progress: phonetic, acoustic and semantic targets preserve different aspects of a message; shared representations support reuse across recording conditions and tasks; and online communication increasingly depends on calibration, feedback and user control alongside decoding accuracy. Shared benchmarks enable algorithmic comparisons, while longitudinal studies reveal the demands of sustained use. We discuss these developments and their remaining limitations, then outline a prospective five-level trajectory from commands and language to meaning, scenarios and bidirectional cognitive exchange
https://arxiv.org/abs/2609.27650
Multimodal learning is emerging as a powerful paradigm for AI for Physics (AI4Physics), where predicting physical systems requires the joint interpretation of heterogeneous observations, measurements, and domain knowledge. However, existing approaches typically represent physical quantities and governing equations as generic numerical or textual tokens, overlooking the physical constraints that determine their spatiotemporal interactions. To address this limitation, we introduce the \textbf{physical-field modality} and propose \textbf{PhyMo}, a physics-grounded multimodal framework that organizes heterogeneous measurements through PDE-associated operators. PhyMo follows a three-stage learning procedure: the physical-field encoder is first pretrained through field reconstruction under PDE residual supervision, its representations are subsequently aligned with visual embeddings in a shared latent space, and the fused multimodal representations are finally processed by corresponding downstream prediction heads. Experiments on five datasets spanning diverse physical environments show that PhyMo achieves state-of-the-art performance, compared to the strongest baseline on each dataset, demonstrating the superiority of PhyMo on multimodal representation learning in AI4Physics.
https://arxiv.org/abs/2609.27554
Photographic composition aims to provide visual guidance for improving the framing, viewpoint, and spatial arrangement of an image. Early methods primarily rely on image cropping to enhance composition, which is restricted to the viewpoint and spatial arrangement of the input image. Recent methods have explored image understanding and editing to improve composition, but they mainly focus on instruction following and aesthetic quality, overlooking the importance of 3D scene geometry consistency for photographic composition. In this work, we propose GeoComposer, a novel geometry-grounded photographic composition framework that analyzes the composition of a given image to generate textual guidance and synthesizes a visual exemplar that enhances the composition of the given image. To promote geometry-grounded composition, we propose a geometry-aware representation learning mechanism that leverages geometric priors from a visual geometry foundation model to shape the intermediate representations of the composition editing model. This mechanism preserves both global structural relationships and local fine-grained correspondences for geometry-grounded composition. Furthermore, we propose a reinforcement learning strategy guided by a hybrid reward that jointly optimizes instruction following, aesthetic quality, and geometric consistency. This enables the model to generate visual exemplars that faithfully follow the composition instructions while remaining visually appealing and geometrically consistent. Extensive experiments show the superiority of our approach over state-of-the-art methods, highlighting its effectiveness in generating visually appealing and geometrically consistent composition.
https://arxiv.org/abs/2609.26620
Recent advances in generative video models have enabled the synthesis of visually realistic content, posing significant challenges to synthetic video detection. Existing detectors often rely on appearance artifacts, semantic inconsistencies, and temporal patterns that may be generator-specific, limitating generalization to unseen synthesis models. We investigate whether responses to a pretrained generative model provide more transferable forensic cues. Our key observation is that real and AI-generated videos exhibit distinct \emph{velocity responses} under a pretrained Flow Matching video model. This distinction persists when different pretrained video-generation backbones are used as probes, suggesting that velocity responses offer transferable forensic signals beyond visual artificts. Motivated by this observation, we propose \textbf{TRACE} (\emph{\underline{T}rajectory \underline{R}epresentation \underline{a}nd \underline{C}onsistency \underline{E}stimation}), a generation-process-aware framework for AI-generated video detection. TRACE leverages a pretrained video DiT as a velocity-field probe to extract representations at multiple flow time points, and models cross-frame consistency through velocity differences between adjacent frames. We further introduce a \emph{Real-Centered Trajectory Optimization} objective that encourages generator-invariant representation learning. Extensive experiments on AIGVDBench demonstrate that TRACE generalizes effectively across diverse generators, substantially outperforming prior state-of-the-art methods on unseen open- and closed-source video generation models.
https://arxiv.org/abs/2609.25775
Cable routing requires coordinated control of global cable topology and changing local contacts. We present CableVLA, an end-to-end multimodal vision-language-action framework that converts simulation-privileged supervision into deployable cable-topology and tactile representations. TopoHead distills node-level physics and current and future cable-topology information into causal visual context for the action expert. TacSense uses complementary frame and taxel branches to learn contact dynamics from resistive arrays, with simulator-derived kinematics and contact events providing supervision beyond the measured force map. A contact gate activates force-tactile residuals that refine the next 8 arm-and-gripper actions of a frozen topology-conditioned policy. Across 345 MuJoCo evaluations, CableVLA improves success from 62.6% for the $\pi_{0.5}$-V visual baseline to 84.9%. TacSense achieves pronounced gains in slip-transition recognition over a CNN-LSTM baseline with a similar parameter count, and this advantage persists under frozen-encoder probes. Topology prediction and 57-task tactile evaluations assess representation quality, while policy adaptation studies evaluate downstream control performance. Cross-simulator and real-robot comparisons further examine zero-shot policy transfer under changes in dynamics and sensing.
https://arxiv.org/abs/2609.25606
Recent advances in pixel-space diffusion models have narrowed the image quality gap with latent-space diffusion, but still converge more slowly and lag behind in final image quality. We argue that a key reason is the lack of an explicit representation prior: unlike latent diffusion, which usually denoises in a compact and structured latent space, pixel diffusion needs to learn denoising-friendly representations and pixel generation simultaneously from raw RGB space. To address this problem, we propose PixelDiT2, an end-to-end pixel-space diffusion model designed to decouple representation learning from pixel generation without introducing an autoencoder or latent reconstruction bottleneck. We propose representation grounding that uses a frozen pretrained vision foundation model to provide explicit per-patch representation guidance throughout denoising, allowing the pixel diffusion transformer to focus more on pixel generation. On ImageNet-256x256, PixelDiT2 achieves an FID of 1.46 after 600 epochs; at 512x512 resolution, PixelDiT2 achieves an FID of 1.48 after 680 epochs.
https://arxiv.org/abs/2609.24919
Forest inventories increasingly rely on artificial intelligence (AI) models to derive forest attributes from large-scale 3D point clouds. Current models are typically specialized to a single task, sensor, and forest type, making adaptation expensive in terms of annotations, computation, and expertise. We ask whether a single pretrained model can instead learn transferable representations across diverse forest inventory settings. Inspired by recent developments in language modelling and computer vision, we take a step toward a foundation model (FM) for 3D forestry. Using LitePT as backbone, we first establish a strong supervised baseline that sets a new state of the art on forest semantic and instance segmentation, tree species classification, and age regression benchmarks. We then curate a large-scale unlabelled corpus spanning airborne, UAV, and mobile laser scanning across diverse forest ecosystems, and pretrain the same backbone using self-supervised learning. We systematically evaluate representation learning strategies by comparing training from scratch, supervised pretraining, and self-supervised pretraining across four representative forestry tasks, under varying annotation budgets. Compared with training from scratch, self-supervised pretraining accelerates model convergence and consistently improves performance when annotations are scarce. Compared with task-specific supervised pretraining, self-supervised pretraining yields more transferable representations across downstream forestry tasks. These findings identify the practical regime in which pretrained representations are most valuable and suggest that instance discrimination, rather than forest semantics, is the main remaining obstacle to a general-purpose 3D forest foundation model. Code and models are available at: this https URL.
https://arxiv.org/abs/2609.24787
Latent world models learn predictive representations for autonomous driving, but the relational semantics these states preserve often remain implicit. We investigate whether traffic scene graphs can serve as privileged semantic supervision for latent world representations. Building on LAW, we construct actor-centric scene graphs from nuScenes 3D annotations, encode their serialized relational structure using a frozen text embedding model, and align the visual latent representations with this semantic target during training. We remove the supervision branch at inference, so it requires neither scene graphs nor 3D annotations and adds no test-time computation. On nuScenes, our method reduces average trajectory L2 error from 0.661 to 0.622 (5.9%) and collision rate from 0.456 to 0.217 (52.4%) relative to our retrained LAW baseline. It also outperforms an unstructured caption-style semantic target, supporting the benefit of explicit relational structure for latent world-model representation learning.
https://arxiv.org/abs/2609.24626
Tactile sensing is an essential modality for robots performing contact-rich, dexterous manipulation, particularly under visual occlusion. While pre-trained image encoders are standard in robot learning pipelines, tactile encoders are still commonly trained from scratch from raw, noisy signals, which might limit their expressivity. Existing self-supervised learning (SSL) approaches focus predominantly on vision-based tactile sensors, leaving distributed electronic skins largely unaddressed. These sensors, however, have a distinctive property: their sensing elements are sparse and irregularly arranged over the surface they cover, which makes direct reuse of visual SSL methods suboptimal. We present Tactile-JEPA, an efficient self-supervised pre-training method that uses the spatial arrangement of tactile sensors to learn topology-aware representations. Specifically, it is trained to predict the embeddings of masked sensing elements from the unmasked remainder, using the sensor connectivity graph to guide spatial masking. Our analysis shows that effective tactile representations require capturing both local contact details and the global state of the tactile surface, which we achieve through dual-scale masking. Across three diverse datasets spanning magnetic and piezoresistive sensors, different robot embodiments, and single- and paired-sensor configurations, Tactile-JEPA reduces force estimation error by 6.3% and in-hand orientation error by 20.8% over the prior state-of-the-art, with consistent gains in other downstream applications, including policy learning. Overall, our results demonstrate that the benefit of tactile sensing depends critically on the quality of encoder pre-training, a problem which Tactile-JEPA addresses directly. Code is available at this https URL.
https://arxiv.org/abs/2609.24385
Atomic activity understanding aims to recognize and localize structured traffic behaviors that jointly encode motion patterns and their grounding in road topology. Unlike conventional action recognition, atomic activities are multi-agent, multi-label, and topology-aware: multiple activities co-occur while many agents remain inactive. We introduce Action-Slot, a structured action-centric representation learning framework. Slot attention is widely used for object-centric decomposition, but its permutation-invariant design and object-level inductive bias are misaligned with atomic activity semantics. We reformulate slot learning as structured activity decomposition through three designs: (1) category-aligned action slots that anchor slots to predefined activity categories, (2) parallel spatio-temporal slot updating for holistic video-level reasoning, and (3) background and negative-slot regularization that enforces competition between foreground activities and irrelevant regions. Together these establish an activity-centric inductive bias that disentangles concurrent and asynchronous activities directly from raw video. Beyond recognition, the learned representations encode transferable spatio-temporal grounding signals. We further propose an attention-difference-based pseudo mask selection framework that suppresses false positives by measuring attention changes before and after candidate region removal, enabling weakly supervised localization without dense annotations. To support systematic evaluation, we introduce TACO, a balanced synthetic dataset with full atomic activity coverage and pixel-level annotations. Experiments on OATS, TACO, and annotated nuScenes show superior recognition, strong sim-to-real transfer, and state-of-the-art weakly supervised localization.
https://arxiv.org/abs/2609.24127
Contrastive self-supervised learning has achieved strong performance by learning representations from multiple augmented views of the same image. However, most existing methods construct positive pairs using independently sampled stochastic augmentations, which may alter semantic content and ignore the intrinsic geometry of the data distribution. In this work, we propose OTCLR, an optimal transport-aware framework for contrastive learning representations that generates geometry-consistent positive samples. Instead of directly contrasting two randomly augmented views, we construct intermediate views between the original image and its augmented variants through entropic optimal-transport displacement interpolation. These transport-interpolated samples serve as positive views that better preserve image structure while explicitly modeling spatial distributional geometry. To further promote smooth representation learning, we evaluate auxiliary Sinkhorn regularization terms that encourage transport-interpolated views to remain consistent with their endpoint images. The proposed method can be incorporated into standard contrastive learning pipelines without modifying the encoder architecture. Experiments on multiple benchmark datasets show that our approach improves representation quality and transfer learning performance compared with conventional augmentation-based contrastive learning baselines.
https://arxiv.org/abs/2609.24125
Zero-shot brain-to-image retrieval requires robust alignment between noisy EEG responses and visual representations. Existing EEG-vision alignment methods often operate in sensor space and apply fixed visual supervision to all responses, ignoring both spatial mixing in scalp EEG and response-wise variability in alignment reliability. We propose an adaptive cortically constrained EEG-vision alignment method for zero-shot brain-to-image retrieval. The method reconstructs EEG responses into predefined ROI-level source-pattern representations and encodes them with a Neuro-ROI Attention Encoder. To handle response-wise variability, we introduce an evidence-based adaptive visual supervision strategy that weights detail-controlled visual targets using model-based alignment evidence. On THINGS-EEG, the proposed method achieves strong 200-way zero-shot retrieval performance, with ROI-level attribution providing post hoc interpretability of the learned source-pattern representations. These results show that cortically constrained representation learning and adaptive supervision can jointly support EEG-vision alignment for zero-shot brain-to-image retrieval.
https://arxiv.org/abs/2609.24109
Clinical multimodal models must often predict before all chest X-ray (CXR) and electronic health record (EHR) inputs are available. Existing approaches align observed representations, model missingness, or reconstruct across modalities, but do not jointly exploit within-patient and clinically similar inter-patient evidence. We propose GLR-MM, a Graph-Based Global-Local Reconstruction framework for early ICU mortality prediction. It maps five CXR-EHR modalities to a shared space, reconstructs missing embeddings through complementary local cross-modal and global graph-attention branches, adaptively fuses their estimates, and optimizes class-balanced prediction, reconstruction, and contrastive objectives. On 9,620 MIMIC-derived ICU stays, we evaluate 10%, 30%, and 50% random modality missingness with shared deterministic masks. MUSE performs better under mild and moderate missingness, whereas GLR-MM achieves higher AUROC and AUPRC at 50% by 0.0088 and 0.0249, respectively. These results indicate that graph-guided reconstruction is most useful when inputs are severely incomplete.
https://arxiv.org/abs/2609.23876
Modern conditional generative models face significant challenges when learning complex covariate dependencies. While sufficient dimension reduction (SDR) provides a principled approach to compress these dependencies, traditional SDR frameworks were not formulated for conditional generation. To bridge this gap, we propose Belted Engression, a unified and architecturally parameter-efficient framework for generative distributional regression. Our approach establishes an end-to-end compress-then-generate paradigm driven by sufficient representation learning, embedding a structural bottleneck into the generative architecture. Theoretically, we prove that the standard SDR condition is equivalent to a law-preserving generative factorization, which is achieved at the global optimum of the population Belted Engression objective. Furthermore, by uncovering a localized Bernstein-type control for the energy-score loss, we establish finite-sample convergence rates that are sharper than those of existing results. We also prove that this belted architecture is strictly smaller, operating with an asymptotically vanishing parameter count relative to the unstructured baseline. Extensive simulations and real-world applications demonstrate that Belted Engression achieves superior distributional prediction and SDR recovery with fewer trainable parameters.
https://arxiv.org/abs/2609.23789
Bimanual interaction produces complementary tactile views of the same physical process, yet existing tactile representation learning largely models the two hands independently or combines them only for downstream prediction, leaving their cross-hand relationship unexplored. To exploit this overlooked structure, we introduce BiView-Touch, a tactile-only framework that completes masked target-hand latents from the remaining visible target-hand regions and the synchronized full contralateral hand. A student encoder with a geometry-conditioned directional decoder predicts full-view EMA latent targets, while temporal and layout counterfactuals encourage sensitivity to synchronized and anatomically organized source information. Controlled ablations and source-context interventions show that BiView-Touch learns structured cross-hand dependence on temporally aligned and anatomically organized contralateral tactile context, rather than benefiting from bilateral input alone. On the public HumanTouch dataset, its frozen representations consistently outperform representative self-supervised baselines across low-label settings. With only 5\% downstream labels, BiView-Touch achieves relative balanced-accuracy gains of 7.1\% on bilateral wrist-motion recognition and 14.1\% on force-derived interaction-phase recognition. We further introduce BVT-20, a 20-task bilateral tactile dataset, and demonstrate transfer across recording sessions and pretraining corpora, including transfer to a held-out bimanual task. Our code and dataset details are available on the anonymous project page: this https URL.
https://arxiv.org/abs/2609.23352
Acoustic representation learning is crucial for speech processing, yet low-resource languages (LRLs) face severe data scarcity, limiting the effectiveness of traditional and self-supervised methods. As a promising alternative, in this work, we propose to enhance acoustic representation trough a cross-modal transfer knowledge approach, based on heterogeneous graph neural networks (HGNNs), where acoustic and linguistic entities are modeled as distinct node types within a unified graph. Through message-passing mechanisms, linguistic nodes explicitly transfer knowledge to acoustic nodes, enabling structured and interpretable cross-modal information flow. To highlight this knowledge transfer and its benefits, we measured standard clustering metrics as an intrinsic evaluation of acoustic representation, and to emphasize applicability, we performed isolated-word recognition tasks using an English benchmark and a Cameroonian language dataset in low resources settings . Results demonstrate that acoustic representations consistently benefit from linguistic knowledge propagated through the graph. To our knowledge, this is the first demonstration of explicit cross-modal knowledge transfer for acoustic representation learning using HGNNs, highlighting a promising direction for speech representation in low-resource settings.
https://arxiv.org/abs/2609.23194