Representation Learning

Electrocardiograms (ECGs) are widely used non-invasive measurements of cardiac activity and play a central role in clinical diagnosis. Recent multimodal approaches align ECG signals with clinical reports to incorporate diagnostic semantics, but clinical reports often fail to preserve the rich physiological structure of ECG waveforms, particularly across multiple levels of abstraction ranging from coarse diagnostic categories to fine-grained morphology. To address this limitation, we formulate ECG representation learning from an information-theoretic perspective and derive a tractable objective that jointly preserves signal structure and integrates clinical semantics. Based on this principle, we propose \textbf{MERIT} (Multimodal ECG Representation via Information Theory), a dual-branch pretraining framework combining masked ECG modeling with ECG--text contrastive alignment. Extensive experiments on PTB-XL and additional benchmarks demonstrate consistent improvements over prior methods, including gains exceeding $3$ F1 on PTB-XL All and $5$ F1 on SubClass classification. In zero-shot evaluation, MERIT further improves performance by up to $+2.66\%$ AUC and $+2.11\%$ F1 on PTB-XL SubClass, while also demonstrating robustness under multiple distribution-shift settings. Moreover, leveraging the learned ECG representations for ECG-conditioned clinical text generation with large language models improves text quality across several metrics, including ROUGE and METEOR. Together, these results demonstrate that MERIT learns more informative and clinically meaningful ECG representations, particularly for fine-grained clinical applications.

Machine unlearning aims to remove the influence of specific training records from a deployed model without retraining from scratch. Current protocols verify this at the output level through membership inference, retain accuracy, and forget-set accuracy, but a model can satisfy all three whilst still encoding forgotten records in its intermediate representations. We introduce RULER, a set of representation-level verification metrics. The oracle-comparative metric M2 measures whether forget-set records occupy the same representational position as in a model retrained without them. The oracle-free metric M4 detects residuals from the unlearned model's internal similarity structure alone, without retraining. Four approximate unlearning methods all pass output-level evaluation, yet under a linear mixed-effects model M2 detects significant residuals in 10 of 12 conditions (p<0.05), with effect sizes growing as the forget fraction increases. A fifth method, Bad Teacher, shows the same residuals despite a different forgetting mechanism. M4 acts as a pre-unlearning diagnostic across tabular, image, clinical text, and face-identity settings: it detects identity-level memorisation in face recognition models where no tested method fully erases the signal.

Predictive models trained on observational data often fail to generalise to the distributions they encounter when deployed, especially when the training data is a product of the system being optimised. Recommender systems are a canonical example: they are trained on interaction logs confounded by the deployed policy, past user behaviour, and platform filtering. As a result, the training distribution differs substantially from the candidate distribution scored at serving time, a gap that makes offline metrics unreliable predictors of online performance. We address the distribution shift problem with a method motivated by causal representation learning (CRL). We propose an information-theoretic disentanglement criterion and prove that its optimum depends only on the causal components of the input. We then derive a tractable variational lower bound that makes the criterion optimisable from finite observational data alone. The scope of our method is narrower than that of much of the CRL literature, in that we target better generalisation under distribution shift, not full identification of all latent causal factors. This narrower target is what makes the method practical, requiring only the existing confounded logs, applying to any standard supervised model, and adding no inference-time cost. Our headline evaluation is an A/B test with millions of users on Spotify, applied to a production ranker for personalised playlist generation. A capacity-matched CRL variant performed on par offline but delivered substantial online gains in listener engagement. Complementary evidence on the public KuaiRand recommendation dataset and a synthetic benchmark with known causal structure shows the same pattern: offline parity with baseline, gains under distribution shift. Across all three settings, adding our causal disentanglement objective yields meaningfully better out-of-distribution generalisation.

Vision-Language Models (VLMs) provide a promising foundation for autonomous driving planning, yet bridging semantic reasoning and precise 3D spatial forecasting remains a critical challenge. Existing representation strategies generally follow two paths: text-aligned methods flatten continuous spatial states into symbols, which compromises geometric structure and induces "spatial hallucinations"; dense visual methods preserve spatial topology but overwhelm standard tokenizers with redundant background textures, leading to "representation interference". To address these limitations, we introduce TPS-Drive, a novel framework centered on Task-Guided Representation Purification that empowers VLMs to Think in Purified Space. At its core, an Agent-Centric Tokenizer utilizes a task-guided vector quantization mechanism supervised by a frozen 3D detection head, which explicitly reallocates limited codebook capacity from pervasive static backgrounds to critical dynamic agents and effectively isolates spatial redundancy. Leveraging this purified spatial vocabulary, TPS-Drive employs a decoupled reasoning pipeline that sequentially performs scene understanding, future forecasting, and action generation. The framework is optimized via a progressive three-stage training paradigm, culminating in reward-driven refinement that surpasses pure imitation learning. Extensive experiments validate our approach: TPS-Drive achieves accurate agent spatial state forecasting and reduces collision rates in open-loop nuScenes evaluations, while establishing new safety records on the rigorous closed-loop NAVSIMv1 and NAVSIMv2 benchmarks.

Urban representation learning encodes complex urban environments into general-purpose embeddings for diverse downstream tasks and emerging urban foundation models. However, current evaluations are limited, typically focusing on one or two cities and tasks and relying on random splits that introduce spatial leakage, leading to inflated performance and weak support for cross-location generalization and fair comparison. To address this, we propose CityRep, a unified benchmark that evaluates urban representations across data modalities, cities, and tasks using spatially structured splits. CityRep consists of three key components: (1) a spatial unit-agnostic evaluation framework that supports heterogeneous urban representations through a standardized alignment module; (2) a unified evaluation protocol using block-based spatial splits to mitigate spatial leakage and enable rigorous model comparison; and (3) an extensible multi-city, multi-task benchmark suite spanning 8 cities and 8 tasks across regression, classification, and distribution prediction. We evaluate 11 representative urban representation models. Results show that performance is highly sensitive to the split protocol, with random splits inflating scores and altering model rankings. We also observe substantial variability across cities and tasks, underscoring the need for generalization-aware evaluation. CityRep is released as a reproducible benchmark with datasets, evaluation pipelines, and diagnostic tools to facilitate fair comparison and support future research in urban representation learning towards urban foundation models.

Clinical time-series learning is routinely constrained by small, heterogeneous cohorts and protocol drift, while its downstream use spans both classification (e.g., pathology diagnosis) and regression (e.g., temporal forecasting). These constraints make foundation-model pretraining appealing, but raises an important question of which inductive biases should the pretraining objective impose so that representations transfer across task types and subjects. We study this question in pathological gait analysis for spinal cord injury (SCI) via PathoFM, an encoder-centric transformer pretrained on multivariate gait windows with three complementary objectives: Local Completion (reconstruct contiguous masked spans to enforce local structure), Temporal Continuity (predict a masked mid-horizon continuation from an observed prefix to enforce smoothness and causal consistency), and Unsupervised In-Context Dynamics (support-query reconstruction conditioned on subject exemplar windows via attention). Empirically comparing objective families (grouping/contrastive, dynamics-based, and generative reconstruction), we find that dynamics-centric mixtures produce the most balanced transfer: grouping objectives favor discriminative margins but can degrade magnitude fidelity needed for continuous targets, whereas reconstruction-only objectives preserve waveform structure but may underperform on classification. Overall, combining local reconstruction with temporal continuity, and adding in-context conditioning when exemplar access is realistic, yields robust subject-generalizing representations.

Many learning problems require uncovering a hidden ordering that reveals structure in unordered data, such as monotonicity in sorting or spatial continuity in jigsaw reconstruction. In these settings, permutations can be learned as latent operators by optimizing objectives defined directly on the reordered output, often without access to ground-truth orderings. Differentiable relaxations such as Gumbel-Sinkhorn make this approach practical by approximating permutation matrices with doubly stochastic matrices. However, learning from structure without supervision induces a non-uniform uncertainty: some assignments become confident early, while others remain ambiguous. Existing methods control this process using a single global temperature, forcing all assignments to sharpen or diffuse simultaneously and leading to instability at scale. We introduce an entropy-adaptive formulation of Gumbel-Sinkhorn that locally modulates temperature based on assignment uncertainty. This allows confident assignments to discretize early while preserving exploration where uncertainty remains. Across sorting and jigsaw reconstruction tasks and in routing-style settings, adaptive entropy control improves training stability and final permutation quality relative to fixed-temperature baselines, particularly as problem size and assignment ambiguity increase.

Self-supervised pre-training paradigm has gained increasing prominence for learning transferable representations in medical imaging, yet existing methods for ultrasound (US) images operate at the image or frame level, overlooking the anatomical context for clinical-aligned representation learning. In this work, we propose an anatomy-anchored ultrasound self-supervision framework ANAUS that shifts representation learning from generic visual regions to clinically meaningful anatomical structures. Utilizing a learnable latent prompt engine alongside a one-time domain adaptation on existing public image-mask pairs, we empower the LP-SAM module to achieve annotation-free anatomy delineation at scale. Building upon this anatomical grounding, we propose a dual-policy self-supervised learning paradigm consisting of inter-view semantics-aware anatomy-separating alignment and contextual core-region prediction to enhance representation learning. Specifically, the former enforces feature invariance within identical anatomical regions while promoting discriminability across distinct structures; the latter compels the model to reconstruct corrupted regions, thereby capturing fine-grained structural details. Extensive evaluations on six public datasets demonstrate that ANAUS consistently outstrips current state-of-the-art methods while maintaining the computational efficiency essential for clinical deployment. Code is available at https://github.com/zhcz328/ANAUS.

While Vision Foundation Models (VFMs) excel at predictive tasks on satellite imagery, their performance can arise from visual correlations rather than underlying structural invariants, making even perception-based out-of-distribution accuracy a poor proxy for scientific utility. As a result, models may look correct without reasoning correctly, a discrepancy we term the Perception-Physics Paradox. To address this gap, we introduce scientific alignment as an implicit objective for representation learning in scientific domains. We study a principled, testable aspect of scientific alignment through structural isomorphism, which requires latent representations to uniquely identify physical systems up to a linear reparameterization. This perspective induces a hierarchy of necessary conditions and yields a systematic probing protocol for physical and causal interpretability. To operationalize this framework, we release TC-Bench, a global, reproducible benchmark dataset with an automated construction pipeline for tropical cyclone research, and show that current VFMs rely on visual shortcuts that collapse in intense regimes, indicating that scientific alignment does not arise as a natural byproduct of scaling alone.

In curriculum reinforcement learning (CRL), an agent incrementally accumulates knowledge over a sequence of tasks (i.e., a curriculum), and the learning process is aimed at using the accumulated knowledge to finally solve a challenging target task. While early CRL works focus on sequencing candidate tasks, recent research explores automatic curriculum generation. Among the rich CRL literature, the interpolation-based CRL paradigm is a main body, which automatically generates intermediate tasks by interpolating between the initial task distribution and the target task distribution in task space with meaningful distance metrics (i.e., can measure the task similarity). However, in challenging navigation tasks, the non-Euclidean context (task) space invalidates this assumption. To achieve automatic curriculum generation in complex task, we propose a novel automatic curriculum generation approach based on measurable task representation learning. To better measure the similarity, we propose to transform the task space to a latent space. Through a variational autoencoder structure that encodes the reward and the state transitions, we achieve a latent task representation with a task similarity measurement property, and two close task embeddings correspond to two similar tasks in terms of rewards and state transitions. Based on the learned task representation, we further develop an automatic curriculum generation scheme, which can effectively generate new tasks more and more similar to the target task. We evaluate our method in a variety of challenging navigation tasks, and the experiment results indicate that the proposed approach surpasses state-of-the-art CRL approaches based on interpolation and generative adversarial networks.

When Masked Diffusion Models (MDMs) generate sequences through iterative refinement, the rich internal computation over masked positions is discarded, forcing every subsequent refinement step to recompute the valuable internal information stored as model representations. To avoid a hard reset between denoising rounds, we propose Learned Relay Representations (Relay), a method that allows MDMs to be forward-thinking when denoising by explicitly learning how to propagate latent information for the benefit of future denoising steps. Relay introduces a differentiable per-token channel that passes information between forward passes and is trained via truncated backpropagation through time (BPTT). We show that this framework can be scaled to state-of-the-art Diffusion Language Models (DLMs), and is seamlessly compatible with techniques like block diffusion and KV caching. We first provide a thorough justification of the design choices in Relay on a challenging Sudoku-based planning task. We then scale Relay to Fast-dLLM v2, a state-of-the-art DLM, outperforming standard supervised finetuning on coding tasks while reducing inference latency by up to 32%. Our empirical results demonstrate that state-of-the-art DLMs can be explicitly trained to relay latent information forward across decoding steps, advancing the performance-latency Pareto frontier. We provide code for all our experiments.

Deep learning is increasingly viewed as a dynamical process in parameter space, yet many existing theories still treat training as a closed optimization system. This view is limited for real-world AI, where models operate under uncertainty, resource constraints, distribution shift, downstream decision risks, and human feedback. We propose Human-Centered Learning Mechanics (HCLM), a dynamical and information-theoretic framework for open and controlled learning systems. The central idea is that entropy regularization is useful only when the chosen entropy surrogate generates a non-degenerate information force along the optimization trajectory. Otherwise, entropy terms may produce weak, unstable, or misaligned gradients, causing the dynamics to collapse toward ordinary loss minimization. We introduce the notion of effective entropy and study tractable geometric entropy surrogates, including variance-based and log-determinant covariance proxies. The paper makes three contributions. First, it formalizes entropy regularization through effective information force and characterizes degenerate entropy regimes. Second, it derives convergence, entropy-flow, Wasserstein-gradient-flow, and noisy-representation generalization results under explicit assumptions. Third, it offers a conditional dynamical interpretation of scaling-law-like behavior as a balance between information injection, entropy dissipation, and residual risk, without claiming an unconditional derivation of empirical neural scaling laws. Controlled representation-learning experiments support the hypothesis that geometric entropy surrogates, especially log-determinant covariance entropy, induce stronger and more stable information forces than softmax-normalized entropy.

Robustness, domain adaptation, photometric/occlusion invariance, sensor drift, and alignment style are treated as separate literatures with separate method families. Under label-preserving deployment shift they share one geometric object: the covariance Sigma_task = Cov_{Q_n}(n) of ways inputs can change without changing the label. CORAL, adversarial training, augmentation, metric learning, Jacobian penalties, and alignment constraints are not independent tricks--they are estimators of Sigma_task. Fix that object and the Jacobian penalty is pinned by a matrix Sigma' whose range must cover range(Sigma_task)--the matching principle. We prove optimality in a linear-Gaussian model (Thm. A), necessity of range coverage for any quadratic penalty that zeros deployment drift (Thm. G), and the same dichotomy at global minima (Thm. A_global). Wrong-direction/signal-aligned controls (Lemma C; Cor. E/E) and seven estimators (Lemmas D1--D7), plus label-free TDI, yield a falsifiable recipe when Sigma_task must be learned. Thirteen blocks (ML through Qwen2.5-7B) test matched vs isotropic vs wrong-direction penalties on geometry and deployment drift. Twelve match theory where identifiability holds; Office-31 is a named eigengap failure. Partial passes: geometry can improve without every headline task metric moving. A pilot 7B DPO run (one epoch, 240 pairs): matched style-PMH preserves Style TDI where standard DPO degrades it. We do not claim standard training reaches global minima (assumption (O) is open), that estimated Sigma_task is always identifiable, or dominance on every leaderboard. We claim a falsifiable design recipe: estimate Sigma_task, match Sigma', run the controls, report task and geometry separately.

Recent advances in generative modeling show that pretrained representations can improve generation as conditioning features or alignment targets. Motivated by this, we study protein representations for predicting structures beyond conventional function annotation. We propose TriProRep, a structure-aware pretraining method that jointly models three aligned residue-level views: amino-acid identity, backbone geometry, and local full-atom geometry, discretely encoded via VQ-VAE tokenizers. By pretraining to recover original tokens from generator-corrupted views, TriProRep learns to distinguish plausible but incorrect cross-view augmentations from the original protein. We further introduce RepSP, a benchmark for evaluating protein representations in structure-predictive settings. RepSP tests three uses of representations: homodimer co-folding from apo-chain representations, residue-level prediction of homodimer-derived interaction properties, and representation-aligned monomer structure prediction. Across these tasks, TriProRep improves over sequence-only and prior structure-aware representation models, while maintaining competitive performance on conventional benchmarks.

The rapid evolution of generative AI, from GANs to modern diffusion models, has resulted in increasingly subtle discriminative clues. These fine-grained signals are often overshadowed by dominant, high-fidelity image content (e.g., the main subject), limiting the reliability of existing detectors that predominantly rely on global representations. To address this challenge, we propose the Peak-Guided Calibration (PGC) framework. PGC introduces a novel strategy that aggregates salient features via a peak-focusing mechanism. Specifically, by employing a peak-sensitive aggregation that accentuates the most discriminative local clues, PGC leverages these critical signals to calibrate the global decision. This approach recovers subtle patterns that would otherwise be submerged in the global context. Furthermore, to better simulate real-world threats, we introduce the CommGen15 dataset, a challenging benchmark comprising samples from 15 commercial models. Extensive experiments demonstrate that PGC achieves state-of-the-art performance. Specifically, it improves mean accuracy by +12.3% on our CommGen15 dataset, and sets new records on standard benchmarks, including GenImage (+2.1%), AIGI (+3.5%), and UniversalFakeDetect (+1.7%). Code is available at https://github.com/xiaoyu6868/PGC.

Causal representation learning (CRL) and traditional representation learning have largely developed along different trajectories. Traditional representation learning has been driven mainly by applications and empirical objectives, whereas CRL has focused more on theoretical questions, particularly identifiability. This difference in emphasis has created a gap between the two fields in terminology, problem formulation, and evaluation, limiting communication and sometimes leading to disconnected or redundant efforts. In this paper, we argue that these two fields should be brought into dialogue rather than treated as separate paradigms. To this end, we introduce a unified formulation in which the representation learning is characterized by two components: a task component, which specifies what information the learned representation is required to preserve, and a constraint component, which specifies what structure is imposed on the latent space. Under this formulation, the benefits run in both directions. CRL provides theoretical tools for understanding when structured latent constraints are useful or necessary, while traditional representation learning offers practical insights on task design and objective choice that can improve the development of CRL methods. To illustrate this interaction, we experimentally study how different task components affect the behavior of CRL methods under different structured constraints. Results on CausalVerse show that the effectiveness of causal constraints depends strongly on the tasks with which they are paired.

We introduce CoMET, \textit{\textbf{C}omposing \textbf{M}odality \textbf{E}ncoders with \textbf{T}abular foundation models}, a simple yet highly competitive method for multimodal classification: pass each modality through a frozen pre-trained backbone, compress the resulting embeddings with PCA, and concatenate as input into a Tabular Foundation Model (TFM) for prediction. We show that PCA alone suffices to act as an adaptor yielding strong, robust performance across modalities. When the \texttt{CLS} tokens of the foundation model align poorly with downstream tasks, we propose \textbf{PALPooling}, a lightweight adaptive token pooler that consistently improves representation quality. By composing strong frozen representation learning backbones with TFMs, our approach achieves state-of-the-art results across diverse multimodal benchmarks without any training. On hierarchical tasks with large fine-grained class spaces, our approach enables fast and scalable classification, handling datasets with over 500,000 samples and 2,000 classes without any fine-tuning. Overall, our results show that the composition of foundation models is a simple, yet powerful, out-of-the-box solution for multimodal learning, challenging the necessity of complex, end-to-end training pipelines for new problems.

EASA's learning-assurance guidance requires data-driven aviation systems to build and monitor their own situation representation, yet for neural networks the technical means to provide such evidence remain an open problem. We address this gap for a vision-based aircraft landing system: we propose that a minimally assurable model must at least be shown to separate content from style in its own situation representation. Showing that the model's predictions then rely largely on the contentful representation components leads to a concrete assurance path. To demonstrate this assurance path on a concrete model we train a vision transformer model for runway keypoint regression on the LARDv2 dataset. The model, which acts as the subject for our assurance demonstration, produces per-patch embeddings that we decompose into interpretable atoms via K-SVD sparse dictionary learning. A qualitative visualization confirms that contentful atoms track task-relevant runway structure and stylistic atoms track domain-specific appearance, and the regression head is shown to place almost all of its linear weight on contentful atoms. We further build on the content/style separation and define out-of-model-scope (OOMS) detection, a novel runtime assurance approach directly monitoring the model's situation representation. OOMS monitoring is complementary to operational design domain and output-space out-of-distribution monitoring and addresses concrete requirements of the recent EASA guidance. By directly analyzing a model's situation representation both at test time and runtime, this work delivers the first concrete piece of the representation-level evidence that EASA learning-assurance guidance demands, and points to mechanistic interpretability as a practical building block of future aviation safety cases.

Learning universal representations from electroencephalogram (EEG) signals is a cutting-edge approach in the field of neuroinformatics and brain-computer interfaces (BCIs). Conventionally, EEG is treated as a multivariate temporal signal, where time- or frequency-domain features are extracted for representation learning. This paper investigates a simple yet effective EEG representation, i.e., microstates. Microstates represent the building blocks of brain activity patterns at a microscopic time scale. We build a universal microstate tokenizer from a large medical EEG dataset by clustering continuous EEG signals into sequences of discrete microstates. The microstate tokenizer is then adopted universally across a series of downstream tasks, including sleep staging, emotion recognition, and motor imagery classification. Experimental results show that EEG representation learning with microstates outperforms traditional time-domain and frequency-domain features under different models and across different tasks. Further analysis shows that microstates offer greater interpretability and scalability, thereby opening up applications in both cognitive neuroscience and clinical research.

Learning generalizable trajectory representations from raw GPS traces remains difficult because the data is continuous, noisy, and irregularly sampled. Spatial tokenization is also challenging: fine grids yield sparse cells with weak embeddings, while coarse grids merge heterogeneous movement patterns into the same token. We present TrajTok, a trajectory encoder with a simple pretraining recipe for transferable trajectory embeddings. TrajTok first learns a multi-resolution hexagonal cell partition from the spatial distribution of GPS points, converting noisy GPS sequences into discrete cell tokens. To capture both geometry and kinematics, it uses a factorized transformer encoder with early per-modality self-attention blocks, cross-attention fusion layers, and spatiotemporal rotary position embeddings, ST-RoPE, to encode where and when each token occurs. TrajTok is pretrained with masked-token modeling that recovers both geometric structure and kinematic patterns from partial trajectory observations. On the Porto dataset, a frozen TrajTok encoder with lightweight task adapters achieves strong performance across trajectory similarity search, classification, estimated time of arrival, and full travel-time regression, outperforming multiple task-specific methods. The same frozen encoder supports both geometry-dominated and kinematics-dominated tasks, suggesting that TrajTok learns transferable trajectory structure rather than task-specific shortcuts. These results indicate that learned multi-resolution spatial tokenization combined with masked-token pretraining is a promising direction for general-purpose trajectory foundation models.

We study the max-margin solutions reached by mirror flow in deep neural networks with homogeneous activation functions. Extending classical results on gradient flow, we derive a novel balance equation for mirror flow from convex duality, enabling a characterization of the horizon function governing the induced margin. We further establish max-margin characterizations together with convergence rates and norm growth estimates. Finally, we support our theory through experiments on synthetic datasets and standard vision tasks. Concretely, we show that: (1) distinct non-homogeneous mirror maps can induce the same max-margin solution; (2) convergence can be extremely slow, including exponentially slow regimes; and (3) although all considered mirror maps exhibit feature learning, they can produce markedly different representations, ranging from sparse to dense neuron activations. Together, these results provide a unified perspective on sparse and dense feature learning in homogeneous neural networks, highlighting how mirror maps shape both optimization dynamics and the geometry of the learned classifiers.

Channel foundation models assume access to fully observed channels, an assumption that fails in deployment. We introduce PilotWiMAE, a self-supervised framework whose encoder ingests noisy pilot observations directly and whose attention factorizes along the axis separating temporal from joint space-frequency processing, an inductive bias inspired by the physics of the problem. Pilot input shrinks the observation space by up to two orders of magnitude and also removes the unrealistic assumption of full-CSI availability while incurring lower latency. The factorized design generates robust representations by exploiting the separable channel structure and allows a pretraining mask ratio of $99\%$. We pair patch-normalized reconstruction, which captures small-scale fading structure, with an auxiliary scale loss that recovers the large-scale fading features, and use an AWGN curriculum to match pilot noise at pretraining and deployment. Pretrained solely on $3.5$,GHz and evaluated at $28$,GHz across in-distribution and out-of-distribution settings, PilotWiMAE's cross-frequency beam selection and channel characterization beat supervised baselines despite operating on a smaller observation space. To weaken the coupling between decoder capacity and representation quality, we further propose a decoder-centric pretraining stage following the encoder-decoder joint pretraining, which allows PilotWiMAE to demonstrate competitive channel estimation without sacrificing representation quality. To foster further work in this direction, we release the PilotWiMAE pretrained weights and training pipeline, together with CSIGen, our Sionna-based ray-tracing channel-generation tool, and the channel datasets used in this work.

Blood-based biomarkers underpin clinical diagnosis and management, yet their interpretation relies largely on fixed population reference intervals that ignore stable, intra-patient variability. As such, population-based interpretation can mask meaningful deviation from an individual's baseline, risking delayed disease detection. To remedy this, there have been increasing efforts to personalize blood biomarker interpretation using individual testing histories. However, these methods may overfit to sparse data, inflating false-positive rates and unnecessary follow-up, and can also unwittingly include unrecognized or subclinical disease. Here, we leverage nearly 2 billion longitudinal laboratory measurements from over 1.6 million individuals across North America, the Middle East, and East Asia, to show that while laboratory values are highly individual, purely personalized intervals routinely overfit, classifying up to 68% of measurements as abnormal, without corresponding associations with adverse clinical outcomes. We then introduce NORMA, a conditional transformer-based framework that generates reference intervals by conditioning on both a patient's history and population-level data about "normal" variation. NORMA-derived intervals achieve higher precision for predicting outcomes, including mortality, acute kidney injury, and chronic disease. These findings caution against over-personalization in laboratory medicine and demonstrate that anchoring individual trajectories to population-level priors outperforms either approach alone. To promote transparency, we publicly release the model, code, and an interactive user interface for accessible, individualized laboratory interpretation.

Classifying protein topology is essential for deciphering biological function, but progress is held back by the lack of large-scale benchmarks that avoid duplicates and by models that do not scale well. We introduce TEDBench, a large-scale, non-redundant benchmark for protein fold classification constructed from the Encyclopedia of Domains (TED) and Foldseek-clustered AlphaFold structures. We show that on TEDBench, current protein representation learning methods either require very large models or fail to deliver strong performance. To address this challenge, we propose Masked Invariant Autoencoders (MiAE), a self-supervised framework for protein structure representation learning. MiAE uses an extremely high masking ratio of up to 90% with an $\mathrm{SE(3)}$-invariant encoder and a lightweight decoder that reconstructs backbone coordinates from the latent representation and mask tokens. MiAE scales well and outperforms supervised counterparts and state-of-the-art baselines on TEDBench, establishing a strong recipe for protein fold classification. To test transfer beyond AlphaFold structures, we further benchmark on a curated dataset from experimental structures of CATH v4.4. TEDBench is available at https://github.com/BorgwardtLab/TEDBench.

Modeling hyperspectral imagery (HSI) across different sensors presents a fundamental challenge due to variations in wavelength coverage, band sampling, and channel dimensionality. As a result, models trained under a fixed spectral configuration often fail to generalize to other sensors. Existing Vision Transformer (ViT) approaches either rely on implicit spectral modeling with fixed channel assumptions or adopt explicit spatial-spectral attention with prohibitive computational cost, leading to a fundamental trade-off between efficiency and expressiveness. In this work, we introduce Low-rank Efficient Spatial-Spectral ViT (LESSViT), a sensor-flexible architecture for cross-spectral generalization. LESSViT is built on LESS Attention, a structured low-rank factorization that models joint spatial-spectral interactions through separable spatial and spectral components, reducing the complexity of full spatial-spectral attention from $O(N^2 C^2)$ to $O(rNC)$, where $N$ is the number of spatial tokens, $C$ is the number of spectral channels, and $r$ is the rank of the low-rank approximation. We further incorporate channel-agnostic patch embedding and wavelength-aware positional encoding to support flexible spectral inputs. To enable efficient and robust pretraining, we introduce a hyperspectral masked autoencoder (HyperMAE) with decoupled spatial-spectral masking and hierarchical channel sampling. We evaluate LESSViT under a cross-spectral generalization setting that simulates cross-sensor variability. Experiments on the SpectralEarth benchmark demonstrate that LESSViT improves robustness under spectral shifts while remaining competitive in-distribution, and explicit and efficient spatial-spectral modeling is essential for scalable and generalizable hyperspectral representation learning.

Multimodal representation alignment is pivotal for large language models and robotics. Traditional methods are often hindered by cross-modal information discrepancies and data scarcity, leading to suboptimal alignment spaces that overlook modality-unique features. We propose CodeBind, a framework that optimizes multimodal representation spaces through a modality-shared-specific codebook design. By incrementally aligning target and bridging modalities, CodeBind bypasses the need for fully paired data. Unlike traditional hard alignment, CodeBind decomposes features into shared components for semantic consistency and specific components for modality-unique details. This design utilizes a compositional vector quantization scheme, where a shared codebook bridges modality gaps and modality-specific codebooks mitigate representation bias by preventing dominant modalities from overshadowing others. Validated across nine modalities (text, image, video, audio, depth, thermal, tactile, 3D point cloud, EEG), CodeBind achieves state-of-the-art performance in multimodal classification and retrieval tasks.

Recent healthcare foundation models have achieved strong predictive performance through large scale self supervised learning, yet their latent representations frequently entangle physiologic severity, intervention intensity, observational structure, and institutional workflow into shared embedding directions. While effective for downstream prediction, such representations remain semantically opaque and unstable under contextual shift. We introduce AURORA, Adaptive Uncertainty aware Representations through Orthogonalized Relational Alignment, a new framework for healthcare representation learning based on contextual latent geometry. Rather than optimizing a single unified embedding manifold, AURORA decomposes representations into orthogonal semantic subspaces corresponding to distinct contextual factors and learns relational consistency objectives within each subspace. This induces latent spaces that are both semantically disentangled and geometrically interpretable. Across multiple clinical prediction and retrieval tasks, AURORA consistently outperforms reconstruction, contrastive, and self distillation baselines while substantially improving contextual disentanglement, neighborhood purity, and robustness under institutional distribution shift. Our results suggest that latent geometry itself constitutes an important axis of healthcare foundation model design and that explicitly structuring representation space according to contextual semantics provides a complementary direction beyond conventional predictive compression objectives.

Rainfall-induced landslides pose a growing risk worldwide as climate change intensifies extreme rainfall events. To provide sufficient evacuation time, landslide early warning systems (LEWS) for real-time disaster monitoring must estimate near-future landslide risk by integrating observed rainfall with short-term rainfall forecasts from spatio-temporal environmental data streams. Although recent landslide prediction methods have improved predictive performance using statistical and deep learning approaches, most assume accurate rainfall inputs. In operational settings, however, landslide prediction relies on rainfall forecasts, which often contain spatial displacement of rainfall fields due to forecasting uncertainties. Such displacement can alter local accumulated rainfall and degrade prediction accuracy. To address this challenge, we propose a novel LEWS robust to rainfall field displacement. The key idea is to learn latent representations from rainfall and terrain data that remain stable under displacement in rainfall field motion, enabling reliable geospatial data integration for landslide risk estimation. The landslide prediction model is trained using Rainfall-Motion-Aware Contrastive Learning (RMCL), which introduces temporally correlated rainfall field perturbations to emulate forecast-induced displacement in rainfall-driven spatio-temporal environmental data streams. Experiments were conducted using two years of rainfall and terrain data across Japan, covering 19 regions with landslide events. The proposed system achieved up to 37% higher precision than state-of-the-art baselines. These results demonstrate that modeling rainfall as a moving spatial field and addressing rainfall field displacement during learning significantly improve the reliability of short-term landslide prediction in operational early warning systems.

Decoding visual information from electroencephalography (EEG) signals remains a fundamental challenge in brain-computer interfaces and medical rehabilitation. Existing EEG visual decoding methods mainly focus on learning a single global EEG embedding for cross-modal alignment, but they largely overlook the staged and hierarchical characteristics of human visual processing. To address this limitation, we propose a neuroscience-inspired staged representation learning framework that reformulates EEG visual decoding as a stage-specific representation decomposition problem. The proposed framework organizes EEG representation learning into three complementary phases: low-level visual representation learning, high-level semantic representation learning, and integrative information fusion. To strengthen semantic modeling, we further introduce a multimodal dual-level semantic learning mechanism that separates coarse label-level semantics from fine image-level visual-semantic information. In addition, semantic latent channels are introduced as computational representation channels generated from observed visual EEG signals, expanding the channel-level semantic representation space for structured semantic abstraction and cross-modal alignment. Extensive experiments on the THINGS-EEG benchmark demonstrate that the proposed method achieves superior performance under subject-dependent zero-shot evaluation and improved exact retrieval under subject-independent zero-shot evaluation. Additional analyses, including layer-wise retrieval, temporal accumulation, expanded multi-image retrieval, and ablation studies, further support the effectiveness of staged decomposition and structured semantic modeling. These results suggest that explicitly modeling staged perceptual, semantic, and integrative representations provides an effective neuroscience-inspired framework for EEG-based visual decoding.

Multimodal pre-training demonstrates strong generalization performance, but this paradigm is often impractical in domains where paired data are scarce. A promising alternative is post-hoc multimodal alignment, which aligns separately pre-trained unimodal encoders using a limited number of paired examples. However, existing methods focus primarily on aligning global representations, missing patch-token relations. This may hinder transfer to tasks that require fine-grained cross-modal matching beyond coarse sample-level semantics. To address this issue, we propose a post-hoc alignment method that learns token-level cross-modal structure using relative representations. Specifically, we represent images and texts through their token-level similarities to a set of learnable anchors in each modality space, which are trained to induce consistent cross-modal similarity patterns for matched pairs. Despite learning only the anchors without heavy projection layers, our approach consistently outperforms existing methods in zero-shot classification, cross-modal retrieval, and zero-shot segmentation by a substantial margin. This highlights the importance of modeling fine-grained cross-modal structure for effective post-hoc multimodal alignment with limited paired data.

Masked language modeling (MLM) is the standard objective for training protein language models, typically implemented by randomly masking individual residues at a fixed rate (e.g., 15%). This practice implicitly assumes that all sequence positions contribute equally to representation learning. In downstream fitness prediction tasks, however, protein sequences are governed by three-dimensional structural dependencies and long-range residue contacts that induce strong nonlocal couplings between residues. We introduce Bucket Masking, a structure-aware masking strategy that selects groups of residues based on their proximity in three-dimensional space, preferentially masking structurally coupled regions during training. By conditioning the masking distribution on residue contacts, Bucket Masking shifts the learning objective toward modeling long-range interactions that are critical for protein function. Across four downstream protein fitness prediction tasks, Bucket Masking enables up to a 14% improvement over standard random masking, excelling at predicting higher-order mutational interactions. Through controlled ablations, we show that these improvements arise from mask placement rather than span size, establishing masking as a positional inductive bias.

Learning latent representations from complex data is central to modern machine learning, spanning temporal, multimodal, and partially observed systems. In such settings, representations are better understood as latent states capturing underlying system dynamics, rather than as mere compressed summaries of observations. Yet current approaches remain fragmented, relying on distinct -- and often implicit -- assumptions about what these states should represent. We argue that this fragmentation reflects a more fundamental limitation: latent representations are typically learned from underconstrained objectives that fail to specify the properties that meaningful latent states should satisfy. As a result, multiple representations can satisfy the same objective, leading to ambiguity in their structure and interpretation. While many of the underlying principles have been explored in isolation, their interactions have not been explicitly formalized. In this work, we propose constrained latent state modeling (CLSM) as a unifying perspective. We identify a set of core properties -- predictive sufficiency, minimality, temporal coherence, observation compatibility, invariance to nuisance factors, and structural constraints -- and show that they are intrinsically coupled through fundamental trade-offs. Revisiting major modeling families through this lens, we show that existing approaches can be interpreted as enforcing different subsets of constraints, thereby occupying distinct regions of a common design space. This perspective reframes persistent challenges such as lack of identifiability as consequences of underconstrained formulations, rather than isolated technical limitations. More broadly, CLSM provides a principled framework to make design choices explicit, to analyze trade-offs, and to guide the development of more interpretable, robust, and task-aligned latent state models.

Estimating the number of distinct elements in a data stream is well understood when repeated elements are identical. In modern settings, however, observations are high-dimensional and noisy, so repeated instances of the same object are only approximately similar -- for example, different images of the same individual may vary significantly at the pixel level. Classical sketches such as HyperLogLog rely on consistent hash values for identical elements and break down in this regime. Recent work on robust distinct counting in general metric spaces achieves $\widetildeΘ(\sqrt{n})$ memory, which is tight in the worst case. We show that substantially improved memory guarantees are possible under geometric structure common in learned representations. We introduce MaxSketch, a simple max-linear sketch built from random Gaussian projections, and prove that it succeeds in estimating the number of distinct latent objects. Concretely, we show that under this assumption $m = \widetilde{O} (\log n / \varepsilon^2)$ random projections (and hence $\widetilde{O} (\log n/\varepsilon^2)$ memory) suffice to recover the true distinct count within a $(1+\varepsilon)$ factor. Experiments on image streams confirm that MaxSketch accurately estimates distinct counts and generalizes beyond the training regime. Our results bridge classical streaming algorithms and modern representation learning, showing how geometric structure can fundamentally reduce the complexity of distinct counting.

Continual learning requires models to adapt to new data while preserving previously acquired knowledge. At its core, this challenge can be viewed as principled one-step adaptation: incorporating new information with minimal interference to existing representations. Most existing approaches address this challenge by modifying model parameters or architectures in a supervised, task-specific manner. However, the underlying issue is representational: tasks require distinct yet structured representations that can be selectively updated without disrupting representations, while structure should reflect intrinsic organization in the data rather than task boundaries. In sequential data, time-delayed dependencies provide a natural signal for uncovering this organization, revealing how fundamental representations give rise to more specific ones. Inspired by the modular organization of the human brain, we propose MoRe, a framework that identifies modularity in the representation itself rather than allocating it at the architectural level. MoRe decomposes knowledge into a hierarchy of fundamental and specific modules with identifiability guarantees, enabling principled module reuse, alignment, and expansion during adaptation while preserving old modules by construction. Experiments on synthetic benchmarks and real-world LLM activations demonstrate interpretable hierarchical structure, improved plasticity-stability trade-offs, suggesting MoRe as a principled foundation for continual adaptation

For reinforcement learning in data-scarce domains like real-world robotics, intensive data reuse enhances efficiency but induces overfitting. While prior works focus on critic bias, representation-level instability in Self-Predictive Learning (SPL) under high Update-to-Data (UTD) regimes remains underexplored. To bridge this gap, we propose Robust Representation via Redundancy Reduction (R2R2), a regularization method within SPL. We theoretically identify that standard zero-centering conflicts with SPL's spectral properties and design a non-centered objective accordingly. We verify R2R2 on SPL-native algorithms like TD7. Furthermore, to demonstrate its orthogonality to prior advancements, we extend the state-of-the-art SimbaV2, which originally lacks SPL, by integrating a tailored SPL module, termed SimbaV2-SPL. Experiments across 11 continuous control tasks confirm that R2R2 effectively mitigates overfitting; specifically, at a UTD ratio of 20, it improves TD7 by ~22% and provides additional gains on top of SimbaV2-SPL, which itself establishes a new state-of-the-art. The code can be found at: https://github.com/songsang7/R2R2

Recent advances in AI have been primarily driven by large-scale neural architectures that excel at function approximation, rather than by tailored inductive biases and inference or learning strategies that could be important for resource-efficient real-world perception and planning through the solution of inverse problems. In this work, we consider the possibility of enabling robust inversion of continuous forward processes $p \mapsto y$ by learning representations of $y$ that are bijectively aligned with $p$ while remaining insensitive to perturbations in $y$ caused by noise or model mismatch. We propose Twincher, a class of architectures based on stacks of structured diffeomorphic transformations and tailored adversarial training strategies that enable learning such bijective representations. We provide a public API for training and inference and empirically demonstrate the ability of the proposed architecture to efficiently learn bijective representations of synthetic systems, thereby enabling robust and efficient iterative inverse inference. Compared to a baseline inverse-modeling approach, the method exhibits improved data efficiency and robustness, providing initial evidence for the potential of bijective representation learning in robotics, vision, and physical AI.

Few-shot action recognition (FSAR) requires models to generalize to novel action categories from only a handful of annotated samples. Despite progress with vision-language models, existing approaches still suffer from semantic-temporal misalignment, where static textual prompts fail to capture decisive visual cues that appear sparsely across sequences, and from inadequate modeling of multi-scale temporal dynamics, as short-term discriminative cues and long-range dependencies are often either oversmoothed or fragmented. To address these challenges, we propose Semantic Temporal Adaptive Representation Learning (STAR), a unified framework, consisting of a semantic-alignment component and a temporal-aware component, effectively bridging the semantic and temporal gaps and transferring the sequence modeling capability of Mamba into the FSAR. The semantic alignment module introduces a Temporal Semantic Attention (TSA) mechanism, which performs frame-level cross-modal alignment with textual cues, ensuring fine-grained semantic-temporal consistency. The temporal-aware module incorporates a Semantic Temporal Prototype Refiner (STPR) that integrates semantic-guided Mamba blocks with multi-frequency temporal sampling and bidirectional state-space refinement, yielding semantically aligned prototypes with enhanced discriminative fidelity and temporal consistency. Furthermore, temporally dependent class descriptors derived from large language models (LLMs) provide long-range semantic guidance. Extensive experiments on five FSAR benchmarks demonstrate the consistent superiority of STAR over state-of-the-art methods. For instance, STAR achieves up to 8.1% and 6.7% gains on the SSv2-Full and SSv2-Small datasets under the 1-shot setting, and 7.3% on HMDB51, validating its effectiveness under limited supervision. The code is available at https://github.com/HongliLiu1/STAR-main.

Segmenting small and sparse structures in large-scale images is fundamentally constrained by voxel-level, lattice-bound computation and extreme class imbalance -- dense, full-resolution inference scales poorly and forces most pipelines to rely on fixed regionization or downsampling, coupling computational cost to image resolution and attenuating boundary evidence precisely where minority structures are most informative. We introduce SEMIR (Semantic Minor-Induced Representation Learning), a representation framework that decouples inference from the native grid by learning a task-adapted, topology-preserving latent graph representation with exact decoding. SEMIR transforms the underlying grid graph into a compact, boundary-aligned graph minor through parameterized edge contraction, node deletion, and edge deletion, while preserving an exact lifting map from minor predictions to lattice labels. Minor construction is formalized as a few-shot structure learning problem that replaces hand-tuned preprocessing with a boundary-alignment objective: minor parameters are learned by maximizing agreement between predicted boundary elements and target-specific semantic edges under a boundary Dice criterion, and the induced minor is annotated with scale- and rotation-robust geometric and intensity descriptors and supports efficient region-level inference via message passing on a graph neural network (GNN) with relational edge features. We benchmark SEMIR on three tumor segmentation datasets -- BraTS 2021, KiTS23, and LiTS -- where targets exhibit high structural variability and distributional uncertainty. SEMIR yields consistent improvements in minority-structure Dice at practical runtime. More broadly, SEMIR establishes a framework for learning task-adapted, topology-preserving latent representations with exact decoding for high-resolution structured visual data.

Geospatial foundation models have primarily focused on raster data such as satellite imagery, where self-supervised learning has been widely studied. Vector geospatial data instead represent the world as discrete geoentities with explicit geometry, semantics, and structured spatial relations, including metric proximity and topological relationships. These relations jointly determine how entities interact within space, yet existing representation learning methods remain fragmented, often restricted to specific geometry types or partial spatial relations, limiting their ability to capture unified spatial context across heterogeneous geoentities. We propose NARA (Neural Anchor-conditioned Relation-Aware representation learning), a self-supervised framework for vector geoentities. NARA learns context-dependent representations by jointly modeling semantics, geometry, and spatial relations within a unified framework and captures relational spatial structure beyond proximity alone, enabling rich contextualized representations across heterogeneous geoentities of points, polylines, and polygons. Evaluation on building function classification, traffic speed prediction, and next point-of-interest recommendation shows consistent improvements over prior methods, highlighting the benefit of unified relational modeling for vector geospatial data.

Proteins encode diverse functions within complex three-dimensional structures, yet most deep learning representations remain highly entangled, obscuring the biophysical signals that underlie function. Here we introduce ProtDiS, a knowledge-guided framework that decomposes pretrained protein micro-environment embeddings into biologically grounded and task-relevant dimensions. Inspired by the information bottleneck principle, ProtDiS learns representations that balance informativeness and compression, yielding structural features that are more specific, independent, and information-efficient, and achieving consistent improvements across twelve downstream tasks, with the largest gains under structure-based splits. Protein- and residue-level analyses further show that ProtDiS differentiates proteins with similar folds but divergent functions and captures fine-grained biophysical signals critical. These findings suggest that knowledge-guided decomposition provides a general and interpretable approach for structuring latent spaces in protein structural modeling. The source code and implementation details are publicly available at https://github.com/AI-HPC-Research-Team/ProtDiS.

Clinical EEG interpretation requires reasoning over full EEG sessions and integrating signal patterns with clinical context. Existing EEG foundation models are largely designed for short-window decoding and do not incorporate clinical context. We introduce CLEF, a clinically grounded long-context EEG foundation model. CLEF represents EEG sessions as 3D multitaper spectrogram tokens, enabling tractable Transformer modeling at session scale, and aligns embeddings with neurologist reports and structured EHR data through contrastive objectives. We evaluate CLEF on a new 234-task benchmark spanning disease phenotypes, medication exposures, and EEG findings, with more than 260k EEG sessions from over 108k patients. CLEF outperforms prior EEG foundation models on 229 of 234 tasks, improving mean AUROC from 0.65 to 0.74. Reconstruction-only pretraining surpasses prior EEG foundation models, while report and EHR alignment yields further gains. Held-out concept and external-cohort experiments suggest that these representations transfer beyond observed alignment targets. These results support session-scale, clinically grounded representation learning as a promising foundation-model paradigm for clinical EEG.

Pre-trained language models advance patent classification and retrieval by encoding claims as flat token sequences, but they overlook the dependency hierarchy among claims. Incorporating this hierarchy into self-attention poses two challenges. First, claim dependencies include relation types with different levels of reliability, so treating them uniformly may allow noisy technical relations to interfere with more reliable legal citations. Second, claim dependencies are defined at the claim level, whereas Transformer attention operates over tokens, making direct structural injection nontrivial. We propose the Patent Heterogeneous Attention-Guided Graph Encoder (PHAGE), which constructs a typed claim graph that distinguishes legal citations from technical relations. PHAGE projects this claim-level topology into token-level attention through a connectivity mask and learnable relation-aware biases, and fine-tunes the encoder using a dual-granularity contrastive objective that combines inter-patent taxonomy with intra-patent topology. At inference, the graph-specific attention components are removed, allowing representations to be generated through a standard encoder forward pass without CDG construction. Experiments on patent classification, retrieval, and clustering show that PHAGE consistently outperforms domain-adapted and citation-aware baselines, demonstrating the value of claim-level structural guidance for graph-free patent representation learning.

Understanding how chemical language models (CLMs) learn chemical meaning from molecular string representations, rather than only surface-level string patterns, is an important question in chemical representation learning and machine learning for chemistry. Chirality provides a demanding test case: enantiomers can differ greatly in pharmacological activity and toxicity, yet CLMs often struggle to distinguish chiral configurations reliably. Here we present Pan-CORE (Pan-Chemical Omniscale Representation Engine), a family of autoregressive Transformer-based encoder-decoder models for SMILES translation, and use high-temporal-resolution checkpoint analysis to investigate how chiral information is learned during training. Across all tested Pan-CORE variants, we observe a reproducible jump-up in which chiral-token accuracy rises abruptly after a long plateau, suggesting that chiral learning stagnation is not explained by model capacity alone and instead reflects the complexity of chiral constraints. Analyses of attention dynamics, residual-stream trajectories, and latent-space geometry support an encoder-centered mechanism in which chiral-token representations undergo transient destabilization and reconstruction, seen as a V-shaped drop and recovery in vector norm and directional stability, together with a clear reorganization of chiral molecular representations in the latent space. Encoder-decoder cross-evaluation further supports the encoder-centered nature of the transition, and targeted attention-head ablation identifies a small set of chiral-sensitive heads whose removal selectively reduces chiral-token accuracy even in the fully trained model. These findings show that SMILES translation can serve as a useful experimental system for mechanistic analysis of semantic emergence in CLMs, with implications for interpretable chemical representation learning.

Representation learning in electronic health records (EHR) has largely followed paradigms inherited from natural language processing, relying on sequence modeling and reconstruction based objectives that treat clinical labels as ground truth. However, real world clinical supervision is inherently weak, arising from heterogeneous, noisy, and institution specific labeling processes such as billing codes, heuristic phenotypes, and incomplete annotations. In this work, we propose WISTERIA, a weakly supervised representation learning framework that models labels as stochastic observations of an underlying latent clinical state. Instead of optimizing against a single supervision signal, WISTERIA constructs multiple weak supervision operators and learns representations by enforcing consistency across their induced label distributions. This multi view formulation induces an implicit denoising mechanism, allowing the model to recover clinically meaningful structure by reconciling disagreement between noisy labelers. We further incorporate ontology aware regularization in the label space to impose semantic structure over supervision signals. Empirically, WISTERIA improves predictive performance across standard EHR benchmarks, demonstrates strong robustness to label noise, and exhibits superior cross institutional generalization compared to sequence based pretraining objectives. These results suggest that explicitly modeling the supervision process rather than treating labels as fixed targets provides a more appropriate inductive bias for learning robust and clinically meaningful representations from EHR data.

The core challenge in unsupervised anomaly detection is identifying abnormal patterns without prior knowledge of their characteristics. While existing methods have addressed aspects of this problem, they often struggle to learn a robust representation of the normal data distribution that is distinct from anomalous patterns. In this paper, we present a novel framework, Unified Unsupervised Anomaly Detection ($\text{U}^2\text{AD}$), that comprehensively addresses anomaly detection in multivariate time series. Our approach learns the underlying data distribution of normal samples by utilizing score-based generative modeling. We introduce a novel time-dependent score network and a unified training objective that together delineate the manifold of normal data while considering both local and global temporal contexts. Reconstruction is then performed via a deterministic sampling process using an ordinary differential equation solver. Our extensive experimental evaluations demonstrate that $\text{U}^2\text{AD}$ not only outperforms current state-of-the-art methods in detection accuracy but also identifies anomalies at significantly earlier stages of their occurrence.

Identifying operons is a fundamental step in understanding prokaryotic gene regulation, as classifying genes into operons supports the reconstruction of regulatory networks, functional annotation of unannotated genes, and drug candidate development. Experimental approaches such as RT-PCR and RNA-seq provide precise evidence of operon structure, but are laborious and largely limited to well-studied model organisms, making scalable computational methods essential for genome-wide operon identification. Prior computational approaches have employed traditional classifiers such as logistic regression and decision trees, motivating our use of these as physicochemical baselines. The DGEB benchmark evaluates operonic pair classification by embedding each sequence independently with a pre-trained protein language model and computing pairwise cosine similarity. In contrast, our Siamese MLP learns a classifier over the fused embedding space, which is theoretically better motivated for binary classification, as cosine similarity can yield meaningless scores depending on the regularization of the embedding model. While protein language model embeddings substantially outperform physicochemical features in ROC-AUC, a learned Siamese MLP head does not significantly improve over unsupervised cosine similarity in Average Precision, suggesting that the geometry of the embedding space already captures the functional relationships needed for this task. Nonetheless, our Siamese MLP achieves a ROC-AUC of 0.71, competitive with state-of-the-art models on the DGEB leaderboard. These findings indicate that protein language model embeddings are a viable, scalable foundation for operonic pair classification across diverse microbial genomes, with implications for automated genome annotation, regulatory network reconstruction, and characterization of organisms lacking experimental operon annotations.

This paper investigates robust representation learning in offline goal-conditioned reinforcement learning (GCRL). Particularly in sparse reward scenarios, learning representations that align state and goal latents is a challenge that frequently culminates in representation divergence where the encoder drifts toward a low-dimensional, goal-agnostic subspace that destabilizes policy learning. We address this issue by showing that an agent must acquire a fundamental understanding of its environment across multiple scales, from local physical dynamics to long-horizon goal-directed structure. Building on this insight, we propose Ms.PR, a framework that leverages multi-scale predictive supervision to enforce goal-directed alignment within the latent space. We demonstrate that Ms.PR leads to improved representation quality and strong performance on both vision and state-based tasks. Furthermore, we show that our approach is exceptionally resilient under realistic, challenging data regimes, maintaining state-of-the-art performance across a wide variety of tasks, trajectory stitching scenarios, and extreme noise conditions.

We propose Representational Effective Theory (RET), a framework for describing large language model computation in terms of learned macrostates rather than microscopic details. RET learns these macrostates from hidden-state trajectories using a BYOL/JEPA-style self-supervised objective, coarse-graining activations into macrovariables that preserve higher-level structure relevant for prediction and interpretation. We evaluate whether these macrovariables are practically relevant for interpretability: RET yields temporally consistent states that reveal "mental-state" trajectories of reasoning, capture high-level semantic structure, support early prediction of behavioral outcomes such as sycophancy, and provide causal handles for steering generations toward interpretable computational phases. Together, these results suggest that LLM computation admits useful effective descriptions via RET: high-level, dynamically meaningful variables that support interpretation, prediction, and intervention.

Sparse autoencoders (SAEs) have been used widely to decompose and interpret neural network activations, especially those of transformer language models. One key issue with SAEs is their inability to directly model multidimensional features. Instead, SAEs may tile such features by a set of independent directions that must be grouped together after the SAE training phase, impeding discoverability and interpretation of learned feature representations. We begin to address this issue by introducing the Sparse MIXture of Autoencoders (SMIXAE) architecture. Empirically, we provide evidence that SMIXAE models have success both in directly learning previously identified manifold structures, as well as finding novel structures, within the open source Gemma 2 2B and 9B models. Finally, we discuss several limitations and point towards areas for future work.

Learned representations are often invariant to rotational transformations, leaving individual dimensions non-identifiable and interchangeable. We study how Matryoshka Representation Learning (MRL) induces a task-aligned privileged basis distinct from variance-based or regularizer-induced orderings. In the linear setting, we prove that full-prefix MRL recovers the ordered principal directions, and can be computed efficiently using shared statistics. Empirically, we demonstrate that MRL yields consistent per-dimension structure aligned with task signal, where coordinate magnitude reflects informativeness.

Hallucination detection has become increasingly important for improving the reliability of large language models (LLMs). Recently, hybrid approaches such as HaMI, which combine semantic consistency with internal model states via Multiple Instance Learning (MIL), have achieved state-of-the-art performance. However, these methods incur substantial computational overhead due to repeated sampling and costly semantic similarity computations. In this work, we first provide a theoretical analysis of HaMI in terms of decision margins, revealing that scaling internal states with semantic consistency leads to an enlarged decision margin. Motivated by this insight, we revisit classical sentence classification models from a margin enlargement perspective, aggregating token-level features via max pooling and directly estimating sentence scores using a lightweight MLP. Without requiring semantic consistency computations, our approach achieves substantial efficiency improvements while maintaining competitive performance with state-of-the-art baselines through adaptive aggregation of internal feature representations. Code is available at https://github.com/FUJI1229/Hallucination_Detection.

Deep vision models degrade sharply in low-data regimes, particularly in medical imaging where labeled samples are scarce. We show this arises not merely from overfitting but from a geometric failure: finite-sample noise corrupts the embedding covariance, collapsing the eigengap and limiting the number of recoverable signal-bearing modes. We develop a spectral theory of finite-sample representation learning that quantifies the recoverable dimension K(N), the number of eigenmodes that can be stably estimated from N samples. Using perturbation theory and concentration bounds, we show that only modes with eigenvalues above the noise floor $\|\hatΣ - Σ\|_{\mathrm{op}} \sim \sqrt{D/N}$ are reliable, yielding a truncated Mahalanobis energy that governs classification performance. Under a power-law spectral model, this energy can be approximated by a truncated Riemann zeta function, linking eigenvalue decay to data efficiency and AUC. Within this framework, multimodal learning acts as spectral stabilization: vision-language models impose low-rank constraints that suppress noise-dominated directions and preserve the eigengap, increasing K(N) under data scarcity. Across MNIST and multi-disease neuroimaging, we show that multimodal training maintains more stable modes and improves class separation, even when unimodal models achieve comparable few-shot accuracy. These results identify spectral collapse as a fundamental bottleneck in low-data learning. We use truncated Mahalanobis energy and K(N) to diagnose encoder quality, and introduce zeta-based spectral filtering as a principled approach to improve data efficiency.

Refining visual representations by eliminating their internal feature-level redundancy is crucial for simultaneously optimizing the performance and computational cost of models in visual tracking. To enhance their performance, many contemporary Transformer-based trackers leverage a larger number of historical template frames to capture richer spatio-temporal cues. However, this strategy leads to a massive number of input visual tokens. This creates two critical issues: it imposes a quadratic computational burden and can also degrade the tracker's overall performance. To bridge this gap, we propose a compress-then-interact tracking framework, ETCTrack, that learns to efficiently compress template tokens from historical template frames into a robust target representation, moving beyond handcrafted rules. Our method first employs the Adaptive Token Compressor to dynamically construct compact yet highly discriminative template tokens by filtering out redundant visual tokens. These refined template tokens are then processed by our Hierarchical Interaction Encoder to achieve a deep, adaptive interaction with the search features. Refined search features ensure subsequent precise target localization. Experiments on seven benchmarks demonstrate that our method outperforms current state-of-the-art trackers. ETCTrack-B224 reduces the number of template tokens by 60%, leading to a 21.4% reduction in MACs with only a 0.4% drop in accuracy. The source code are available at https://github.com/PJD-WJ/ETCTrack.

Contrastive Representation Learning (CRL) has achieved strong empirical success in multiple machine learning disciplines, yet its theoretical sample complexity remains poorly understood. Existing analyses usually assume that input tuples are identically and independently distributed, an assumption violated in most practical settings where contrastive tuples are constructed from a finite pool of labeled data, inducing dependencies among tuples. While one recent work analyzed this learning setting using U-Statistics to estimate the population risk, the techniques used therein require the risk of each class to concentrate uniformly, making excess risk bounds scale in the order of $ρ_{\min}^{-{1}/{2}}$ where $ρ_{\min}$ denotes the probability of the rarest class. Such a dependency can be overly pessimistic in the extreme multiclass settings where there are many tail classes which contribute minimally to the overall population risk. Our contributions are two-fold. Firstly, we improve upon the previous work and prove a bound with a sample complexity of the same order as the number of classes $R$, regardless of the distribution over classes. Furthermore, we formulate a different estimator that captures the concentration of the risk \textit{across classes}, enabling sharper bounds in extreme multi-class learning scenarios, especially where class distributions are long-tailed. Under mild assumptions on the class distributions, the resulting sample complexity is $\mathcal{O}(k)$ where $k$ is the number of samples per tuple.

We present a new operator-theoretic representation learning framework for offline reinforcement learning that recovers the directed temporal geometry of a controlled Markov process from hitting time observations. While prior art often produces symmetric distances or fails to satisfy the triangle inequality, our framework learns a Hilbert-space displacement geometry where expected hitting times are realized as linear functionals of latent displacements. We prove that this representation exists under latent linear closure and is uniquely identifiable up to a bounded linear isomorphism. For finite-dimensional implementations, we show that global hitting-time error is bounded by one-step transition error amplified by the environment's transient spectral radius. Furthermore, we provide finite-sample guarantees accounting for approximation, statistical complexity, and trajectory-label mismatch. Derived from this theory, we curate Isomorphic Embedding Learning (IEL) as a new goal-agnostic foundation policy learning algorithm that anchors a HILP-style consistency objective with explicit hitting-time regression to ensure that the learned geometry reflects actual decision-time progress. This asymmetric and compositional structure enables robust graph-based multi-stage planning for long-horizon navigation. Our experiments demonstrate that IEL improves the state of the art of learning foundation policy policies from offline maze locomotion data. Our code can be found on https://github.com/MagnusBoock/IEL

Graph-level representations are crucial tools for characterising structural differences between graphs. However, comparing graphs with different cardinalities, even when sampled from the same underlying distribution, remains challenging. Unsupervised tasks in particular require interpretable, scalable, and reliable size-aware graph representations. Our work addresses these issues by tracking the structural diversity of a graph across coarsening levels. The resulting graph embeddings, which we denote diversity curves, are interpretable by construction, efficient, and directly comparable across coarsening hierarchies. Specifically, we track the spread of graphs, a novel isometry invariant that is inherently well-suited for encoding the metric diversity and geometry of graphs. We utilise edge contraction coarsening and prove that this improves expressivity, thus leading to more powerful graph-level representations than structural descriptors alone. Demonstrating their utility over a range of baseline methods in practice, we use diversity curves to (i) cluster and visualise simulated graphs across varying sizes, (ii) distinguish the geometry of single-cell graphs, (iii) compare the structure of molecular graph datasets, and (iv) characterise geometric shapes.

We study the grokking phenomenon through the lens of topology. Using persistent homology on point clouds derived from the embedding matrices of a range of models trained on modular arithmetic with varying primes, we identify a clear and consistent topological signature of grokking: a sharp increase in both the maximum and total persistence of first homology ($H_1$). Persistence diagrams reveal the emergence of a dominant long-lived topological feature together with increasingly structured secondary features, reflecting the underlying cyclic structure of the task. Compared to existing spectral and geometric diagnostics -- specifically, Fourier analysis and local intrinsic dimension -- persistent homology provides a unified geometric and topological characterization of representation learning, capturing both local and global multi-scale structure. Ablations across data regimes and control settings show that these topological transitions are tied to generalization rather than memorization. Our results suggest that persistent homology offers a principled and interpretable framework for analyzing how neural networks internalize latent structure during training.

Domain generalization requires identifying stable representations that support reliable classification across domains. Domains may differ in low-level attributes, such as color, texture, or visual style, while preserving the same structural relationships among their underlying components. Existing methods primarily address these differences by improving the training process or aligning features across domains. However, since they leave this shared compositional structure implicit, they may overlook a more reliable source of invariance and consequently generalize less effectively to unseen domains. We propose Compositional Relational Invariance from Spatial Primitives (CRISP), an image classification framework that factors visual recognition into visual primitives and their relational composition. We represent these compositions using soft unary, binary, and ternary predicates over primitive locations and appearance, yielding differentiable measures of spatial and visual alignment that can be learned end-to-end. To learn primitives and relational structure jointly, we design an end-to-end architecture with three components: (1) a visual backbone that extracts generalized features, (2) a concept bottleneck layer that maps these features to primitive heatmaps with differentiable spatial coordinates, and (3) a structural scoring layer that evaluates candidate spatial relations among the detected primitives. Finally, we compute class probability from the joint evidence of its class-specific relational compositions and localized primitive appearance. We evaluate \method{} on five real-world image-classification datasets from the widely used DomainBed suite, covering shifts in depiction style, dataset provenance, and camera-trap location and achieving the new state-of-the-art on both benchmarks.

Anomaly detection in medical images is a challenging task, since anomalies are not typically available during training. Recent methods leverage a single pretext task coupled with a large-scale pre-trained model to reach state-of-the-art performance. Instead, we propose to learn multiple self-supervised and pseudo-labeling tasks from scratch, using a joint model based on Mixture-of-Experts (MoE). By carefully integrating multiple proxy tasks, the joint model effectively learns a robust representation of normal anatomical structures, so that anomaly scores can be derived based on how well the multi-task learner (MTL) solves each task during inference. We perform comprehensive experiments on BMAD, a recent benchmark that comprises a broad range of medical image modalities. The empirical results indicate that our multi-task learner is an effective anomaly detector, outperforming all state-of-the-art competitors on BMAD. Moreover, our model produces interpretable anomaly maps, potentially helping physicians in providing more accurate diagnoses.

Estimating causal effects from observational data has become increasingly critical in diverse fields including healthcare, economics, and social policy. The fundamental challenge in causal inference arises from the missing counterfactuals and the selection bias. Existing methods are largely limited to point estimates and lack the capacity for distribution modeling. In this work, we propose RepFlow, a novel framework that formulates causal effect estimation as a joint optimization problem integrating representation learning with Conditional Flow Matching (CFM). RepFlow mitigates selection bias by minimizing the entropically regularized Wasserstein distance between treated and control representations. To enhance numerical stability, we further introduce an $L_2$ normalization constraint on latent representations. This balanced representation enables the flow model to accurately capture the distribution of potential outcomes. Extensive experiments across a wide range of benchmarks demonstrate that RepFlow consistently outperforms existing methods in both point and distributional causal effect estimation.