Machine Learning
Papers
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Friday 3 July
Deep reinforcement learning (DRL) in industrial control often suffers from lag and overshoot due to purely reactive control based on the current tracking error. To achieve anticipatory control without high computational overhead, we introduce a predictive formulation that augments the DRL state space with target velocities and future reference horizons. Evaluating eight configurations using proximal policy optimization (PPO) on a 1-degree-of-freedom (1-DoF) helicopter testbed, simulation results showed a 9-fold error reduction, lowering the mean absolute deviation from 2.73{\deg} to 0.31{\deg}. However, zero-shot transfer to physical hardware revealed a sim-to-real gap. Interestingly, a simpler configuration using a single, further look-ahead horizon matched the real-world top performance of the most complex model (1.11{\deg}). Overall, evaluating various combinations of prediction horizons and target velocities demonstrated that highly granular predictive data is not necessarily required for physical transfer.
Machine Learning
ACPO: Asymmetric Credit Policy Optimization via Mode-Local Entropy Surrogate
Outcome-supervised reinforcement learning scales to verifiable reasoning tasks, but trajectory-level rewards assign the same outcome signal to all sampled tokens, overlooking their unequal contributions to the reasoning process. Entropy provides a natural indicator of the model's decision state, yet using it for token-level credit assignment presents two key challenges: long-tail probabilities in large vocabularies corrupt both entropy values and gradients, and uncertainty carries distinct semantics across positive- and non-positive-advantage trajectories. We propose Asymmetric Credit Policy Optimization (ACPO), which replaces global entropy with the complement of the top-token probability as a mode-local proxy. Guided by gradient analysis, ACPO incorporates mismatch routing and saturation correction to shape policy updates into the desired asymmetric form, emphasizing uncertain decisions on positive trajectories while penalizing confident regions on failed ones. Theoretically, ACPO locally preserves the advantage direction while bounding surrogate error. Experiments on mathematical and coding reasoning benchmarks, including AIME 2025 and HumanEval Pro, show that ACPO consistently outperforms both entropy-aware methods (e.g., 80/20, GTPO) and strong outcome-supervised RL baselines (e.g., DAPO, SAPO).
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Machine Learning
Integrating Physics-Informed Neural Networks for Safe Reinforcement Learning in a 1-DoF Helicopter System
Deep reinforcement learning (DRL) offers powerful control for industrial cyber-physical systems (ICPSs), but its "black-box" exploration risks violating strict hardware safety limits. Typically, these constraints are managed through complex reward shaping. In this work-in-progress paper, we embed a differentiable physics model directly into the proximal policy optimization (PPO) actor loss function. By simulating short-horizon future trajectories during training, the policy is penalized for anticipated safety violations independent of the task-reward signal. Evaluated on a simulated 1-degree-of-freedom helicopter testbed with strict pitch constraints, our physics-informed soft regularizations substantially reduce constraint violations while maintaining reliable target tracking.
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Machine Learning · Cross-listed from cs.CV
Vidu S1: A Real-Time Interactive Video Generation Model
We introduce Vidu S1, a real-time interactive video generation model supporting voice control of digital characters. Users can control video generation content at any moment through voice instructions. Vidu S1 supports infinite-length real-time video generation without blurring, drift, or visual distortion. Built with TurboDiffusion and TurboServe, Vidu S1 outputs 540p real-time videos at up to 42 FPS on regular consumer GPUs. Users can upload custom images of real people, anime, and pets, and choose different voice tones for personalized experiences. Experiments show that Vidu S1 achieves the best performance across all test metrics while fully meeting real-time inference requirements. A playable online demo is available at https://vidu.com/vidu-stream.
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Machine Learning · Cross-listed from cs.DS
Dimension Reduction for Curves: Simplified and Generalized
We revisit random projections for reducing the dimension of high-dimensional polygonal curves. Drawing from the toolbox of randomized linear algebra, we give a considerably simplified proof of the known $O(\varepsilon^{-2}\log(nm))$ bound on the target dimension of a random projection that preserves the continuous Fréchet distance of polygonal curves up to a factor $(1\pm\varepsilon)$. Our proof is based on the concept of sparse oblivious subspace embeddings. While previous techniques were limited to the case of the Fréchet distance, our techniques are fairly general and extend to all possible distance measures that involve the maximum, a sum or an integral over Euclidean distances between pairs of points on both input curves. We define a generalized dissimilarity measure for curves that includes several popular measures such as Fréchet, $q$-DTW, Hausdorff, etc. as special cases and show that the same dimension reduction technique works for this generalized dissimilarity measure. Finally, we apply the same framework for dimension reduction to piecewise linear surfaces, after extending the distance measure suitably to such surfaces.
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Machine Learning · Cross-listed from hep-th
Graph Neural Networks for the Graphical Bootstrap
We study a graph classification problem involving over 20 million graphs, arising from high-order perturbative computations of correlators in planar $\mathcal{N}=4$ super-Yang–Mills, a model closely related to the theory of the strong nuclear force. We benchmark graph neural networks, including graph transformers, achieving robust generalization to larger graphs with up to $99.996\%$ ROC AUC. Then, we analyze how the models can be used to gain a computational speedup compared to the traditional graphical bootstrap algorithm, through shrinking the redundant data by up to $85.5\%$ at the level of denominator graphs. Finally, we study the embeddings of the models to investigate their interpretability.
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Machine Learning
Observable- and Positional-Encoding-Dependent Symmetry Readout from Neural Network Weights
Post-hoc analysis of trained neural network weights often seeks to recover geometric structure directly from the parameters. We show that, for positional-encoding-equipped neural fields, the symmetry visible from weights is not the true symmetry group itself, but an observable symmetry set determined by the trained parameters, the positional encoding (PE), and readout observable. We formulate this dependence through an exact observability hierarchy, $G_{\mathrm{obs}}^{\mathrm{exact}} \subseteq G_{\mathrm{lift}}^{\mathrm{exact}}(\phi) \cap G_{\mathrm{true}}$, where $G_{\mathrm{lift}}^{\mathrm{exact}}(\phi)$ is the set of input transformations that the PE can exactly lift to the feature space. The hierarchy implies that even when a target function has a geometric symmetry, that symmetry may be structurally invisible to weight-level observables if the PE does not represent the corresponding transformation. We test this prediction using MLPs trained on two-dimensional signed distance functions with multiple shape symmetry groups, positional encodings, and Gram-based observables. The results show a consistent PE-dependent pattern: DyadicAxisPE supports $D_4$-sensitive readout but structurally suppresses $D_3$ rotations, TriAxisPE yields lower $D_3$ / $D_6$ readout scores under the tested Gram observables by replacing coordinate axes with three 120-degree-separated axes, and random Fourier features mainly exhibit a $\pi$-rotation response under these readouts. These findings show that PE design affects not only approximation behavior but also which structures are accessible to post-hoc weight-level readouts. This provides a basis for a principled observable-dependent symmetry readout.
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Machine Learning
Heterogeneous Graph Condensation via Role-Aware Clustering
Heterogeneous Graph Neural Networks (HGNNs) have exhibited remarkable efficacy in modeling complex systems with multiple types of nodes and relations, yet their training on large-scale heterogeneous graphs remains computationally prohibitive. Although graph condensation methods can effectively improve learning efficiency on large-scale graphs, existing condensation processes are mainly designed for homogeneous graphs and typically rely on computationally expensive gradient matching or bilevel optimization paradigms, rendering them impractical for heterogeneous settings. To address these limitations, we propose HGC-RC, a simple yet effective role-aware heterogeneous graph condensation framework. Specifically, HGC-RC first extracts semantically enhanced node embeddings via lightweight propagation. It then introduces a role-aware hybrid clustering strategy consisting of class-partitioned clustering for labeled target nodes to preserve class distributions and unsupervised type-wise clustering for non-target nodes to retain critical cross-type connectivity. Finally, a compact heterogeneous graph is efficiently reconstructed based on the resulting cluster assignments. Extensive experiments demonstrate that HGC-RC outperforms state-of-the-art baselines, offering a practical pathway to accelerate HGNN training on large-scale heterogeneous graphs without sacrificing task performance
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Machine Learning
Stacked LoRA for Subject-Adaptive EEG Foundation Models in Motor Imagery Decoding
Electroencephalography (EEG) decoding for brain-computer interfaces (BCIs) faces a major challenge: substantial inter-subject variability limits effective cross-subject generalization. Consequently, practical systems still rely largely on subject-specific models trained from scratch and requiring individual recalibration. EEG foundation models have recently emerged as a promising alternative; however, even large pretrained models cannot simply be used as fixed feature extractors and still require additional adaptation before they can be reliably applied to downstream tasks. In this work, we address this challenge through targeted adaptation strategies. Building on recent EEG foundation models such as REVE, LaBraM, and LUNA, we examine the impact of different low-rank adaptation strategies on motor imagery classification. We propose a framework that structurally decouples subject-invariant knowledge from subject-specific neural signatures: the low-rank update at each adapted layer is split into a Global adapter, trained jointly across all subjects, and Subject-Specific adapters, each absorbing individual variability. To assess the contribution of each path, we compare three adaptation strategies: (i) subject-specific LoRA (ii) global LoRA and (iii) stacked LoRA, combining both Global and Subject Specific adapters. Experiments on BCI Competition IV-2a, PhysioNet Motor Imagery, and the clinical Zuo2025 benchmark show that Stacked LoRA effectively mitigates inter-subject variability, achieving the best accuracy in the large majority of backbone and dataset combinations. Our analysis further reveals that the optimal balance between the global and subject-specific paths depends on the target population: a shared adapter is sufficient for large, diverse cohorts, whereas subject-specific adaptation is decisive under the high inter-session variability of clinical recordings.
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Machine Learning
STELLA: Efficient Sensor-to-LLM Translation for On-Device Human Activity Recognition
HAR is increasingly expected to run continuously on edge devices, yet recent LLM-based methods remain hard to deploy: raw sensor prompts are long, cloud inference adds latency and privacy risk, and fine-tuned LLM pipelines turn general-purpose models into task-specific classifiers. We present STELLA, an efficient sensor-to-LLM translation framework for on-device HAR that shifts the burden from LLM adaptation to sensor tokenization. A lightweight hierarchical tokenizer compresses an entire multi-channel inertial window into a fixed set of compact latent sensor tokens, which are projected into the embedding space of a frozen pretrained LLM and combined with a natural-language prompt for label scoring. This preserves activity-relevant temporal and cross-channel structure while keeping LLM-side computation predictable across sensor configurations. STELLA also supports on-device personalization, adapting only the lightweight tokenizer on small amounts of user-specific labelled data and augmenting inference with a local retrieval context, keeping the LLM, user data, and retrieval on device. Across seven public HAR datasets and eight benchmark settings, STELLA achieves new state-of-the-art performance, improving over prior methods by up to 11.83% F1; on-device personalization yields up to a further 21.91% F1 as user data accumulates after deployment. STELLA also outperforms representative time-series tokenizers under the same LLM pipeline and achieves real-time inference under practical mobile and edge budgets, showing that efficient sensor tokenization is a practical path toward accurate, private, and personalized LLM-based HAR on edge devices.
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Machine Learning
Robustness Meets Uncertainty: Evidential Adversarial Training for Robust Selective Classification
Safety-critical applications require classifiers that are both robust and reliable. Adversarial training is a widely adopted defense for improving robustness in deep neural networks; however, its effect on the reliability of predictive uncertainty remains underexplored. We investigate this gap through the lens of selective classification, which has rarely been systematically analyzed alongside adversarial robustness. We introduce a unified benchmark for the robustness-uncertainty trade-off. It standardizes architectures, augmentations, threat models, and evaluation metrics across clean, adversarial, and common-corruption settings. Across a wide range of state-of-the-art adversarial training methods, we uncover a recurring failure mode: several approaches improve robust accuracy while degrading uncertainty ranking, leading to poorer selective behavior. To address this, we propose Evidential Adversarial Training (EV-AT), which models uncertainty through a Dirichlet distribution and combines (i) an evidence-based loss promoting clean accuracy and reliable uncertainty with (ii) a robust evidence-alignment loss matching clean and adversarial predictions in log Dirichlet-parameter space. Extensive experiments show that EV-AT shifts the Pareto frontier of robustness-uncertainty trade-offs beyond prior state-of-the-art adversarial training methods. Our source code is publicly available at https://github.com/NicolasSournac/Robustness_Meets_Uncertainty.EV-AT.
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Machine Learning · Cross-listed from cs.CV
PixCon: Clean-Positive Contrastive Learning for Foundation-Model Semi-Supervised Segmentation
Can a simple labeled-pixel contrastive branch improve semi-supervised segmentation with a strong pretrained encoder? We study this question with PixCon, which adds a class-wise memory bank to a DINOv2-Base implementation of UniMatch V2. The bank stores ground-truth-labeled features only where the student prediction agrees with the label. A multi-positive contrastive loss uses these features to train the shared encoder-decoder; the head and bank are discarded at inference. This simplifies earlier labeled-pixel banks by removing confidence thresholds and learned ranking. On Pascal VOC with 183 labels, PixCon improves all three paired seeds by 0.20, 0.64 and 1.83 mIoU points, raising the mean from 87.01 to 87.90. With 92 labels the mean gain is 0.40 points; single-seed differences on Cityscapes and ADE20K range from -0.08 to +0.14 points. A predicted-label contrastive control reaches nearly the same Pascal accuracy, so these results support the added branch rather than an accuracy benefit from its correctness filter. An exact gradient decomposition distinguishes mislabeled-positive counts from their similarity-weighted influence. Separate teacher diagnostics find retained-pixel error rates of 1.8% on Pascal and 10.6% on ADE20K. These diagnostics do not measure the training bank or predict final accuracy. PixCon adds 15.3-19.7% iteration time in the measured runs and no inference computation. We report paired seeds, training cost and the limits of the evidence.
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Machine Learning
Spectral Rewiring for Exploration, Purification, and Model Merging
Reinforcement learning has become a standard post-training recipe for large language models, but dense full-parameter updates create two deployment-relevant bottlenecks: suppressed reasoning performance, often reflected by premature saturation of test-time scaling, and interference when consolidating multiple capabilities through multi-domain training or model merging. We show that the reasoning-effective component of these updates is largely concentrated in the base model's spectral space, motivating Subspace-Aligned Rewiring (SAR), a post-hoc editing method that retains this spectral core while removing orthogonal components. SAR therefore preserves reasoning gains and filters residual update directions that suppress performance or amplify cross-domain interference. Across several model families and scales, SAR extracts compact reasoning cores using as little as approximately 0.58% of total parameters: it preserves over 99% of post-training performance and improves high-k exploration in mathematical reasoning, and generalizes to agentic coding by improving six of seven open benchmarks on an in-house model. SAR also purifies mixed-domain training updates by releasing suppressed coding capability while maintaining math reasoning and instruction following. It further enables model merging across experts, yielding cross-domain generalization that surpasses previous merging baselines and even the best single-domain experts. Overall, SAR shows that extracting reasoning-effective updates from parameter geometry can serve as a training-free mechanism to improve reasoning and multi-domain performance.
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Machine Learning
LACE-SVD: Loss-Aware SVD with Cumulative Error Correction for LLM Compression
The rapid growth in the parameter scale of large language models (LLMs) has created a strong demand for efficient compression techniques. As a hardware-agnostic and highly compatible approach, low-rank compression has been widely adopted to reduce both memory footprint and computational cost. However, existing SVD-based methods are still largely driven by local reconstruction objectives, overlooking two critical limitations: rank budgets are often allocated without explicitly considering layer-wise loss sensitivity, and local approximation errors can propagate and accumulate through the residual stream, leading to amplified global deviations from the original model. To address these issues, we propose LACE-SVD, a Loss-Aware SVD framework with Cumulative Error correction for LLM compression. LACE-SVD first estimates the calibration negative-log-likelihood increase induced by candidate layer-wise compression ratios and solves a budget-constrained allocation problem to assign rank budgets. It then refines the compressed model with closed-form local updates and introduces a propagation-aware correction for residual-stream output modules, reducing layer-output discrepancy as a proxy for cumulative error propagation. Experimental results demonstrate that at a high compression ratio (0.6), the WikiText-2 PPL of our method on LLaMA-7B (32.57) is significantly better than that of Dobi-SVD (46.18).
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Machine Learning
SHiPPO: Recurrent Memory with Transported Polynomial Projections
HiPPO gives recurrent states memory semantics as coefficients of online polynomial projections, but in fixed channel coordinates. Modern selective SSMs, by contrast, rely on token-dependent control and channel interaction. We introduce SHiPPO (Sylvester HiPPO), a transported projection-memory prior that lifts HiPPO coefficient memories into a moving channel frame. For any fixed or realized right-transport path, SHiPPO transports the approximation family and channel metric together; conditional on that path, the state is ordinary HiPPO in a tied moving frame and follows Sylvester coefficient dynamics, preserving the left online-memory operator while adding right-action transport. For selective-SSM execution, we derive a restricted group-local realization with controller-compatible right actions, exponential-adjusted updates, exact block-affine scan, and recurrent decoding. We also give a simultaneous-reducibility criterion identifying when right transports collapse to static mixing plus independent scalar or blockwise banks. Controlled diagnostics show that larger current-token write rank improves ordinary prediction error but cannot recover order-sensitive changes to already-written memory; transported-memory variants recover this signal, which disappears when the transport pathway is removed. A finite-field associative-recall diagnostic with interleaved bindings, operations, and queries provides complementary autoregressive evidence while leaving the preferred right-action realization open. Taken together, these results support SHiPPO as a mechanistically grounded transported-memory prior, with evidence focused on memory mechanisms rather than broad sequence-modeling dominance.
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Machine Learning
OmniFocus: Query-Guided Modality-Balanced Token Compression for Omni-Modal Large Language Models
Omni modal large language models (OmniLLMs) have attracted wide attention for their ability to jointly process audio and video, but they generate large token sequences under audio-visual inputs, leading to substantial inference cost. Existing audio-visual token compression methods often rely on unimodal guidance, overlooking the temporal locality of query-relevant evidence in audio-visual inputs and implicitly assuming that the two modalities share a temporally aligned information density distribution. We propose OmniFocus, a training-free query-guided token compression method for OmniLLMs that performs independent importance estimation for video and audio, enabling a modality-symmetric compression design that preserves modality-specific salient evidence while maintaining audio-visual alignment, thereby mitigating the modality bias issue that can arise from unimodal-guided compression. Experiments on the Qwen2.5-Omni model family across four audio-visual benchmarks show that OmniFocus maintains strong compressed performance at low token retention ratios and outperforms existing baselines on several major benchmark scores at 25% token retention. On DailyOmni with Qwen2.5-Omni-7B at 25% token retention, OmniFocus maintains 59.40 accuracy while delivering up to 1.38$\times$ prefill speedup relative to the full-token baseline, highlighting a favorable practical accuracy-efficiency trade-off.
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Machine Learning
Out-of-distribution Neural Inference in Dynamical Ising Models
Neural networks are increasingly used to infer hidden physical structure from dynamical observations, yet it remains unclear whether their out-of-distribution performance reflects transferable physical rule learning. We address this question in a controlled inverse problem: reconstructing interaction graphs of a kinetic Ising model from Glauber magnetization trajectories. Across convolutional, graph, Transformer, and hybrid architectures, we find that data-driven training produces distinct and reproducible statistical strategies under topology and temperature shifts. Edge-population diagnostics reveal that Transformer-based models tend to preserve the link density of the training ensemble, whereas convolutional models can collapse toward sparse- or no-link predictions that appear out-of-distribution stable by exploiting the majority no-link class. Thus, high in-distribution accuracy and apparent out-of-distribution robustness do not necessarily imply a learned dynamics-to-structure rule. Instead, neural reconstruction can be governed by architecture-dependent statistical priors. Our results identify a concrete failure mode of standard data-driven learning in physical inverse problems and motivate rule-guided principles for machine-learning-assisted scientific discovery.
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Machine Learning · Cross-listed from cs.CV
HyperVAttention: Efficient Sparse Attention with Spatio-Temporal Clustering for Video Diffusion
Video Diffusion Transformers (VDiTs) have demonstrated significant capabilities in high-fidelity video generation. However, their ability to produce long-duration videos is fundamentally constrained by the quadratic complexity of the self-attention mechanism. Recent clustering-based sparse attention methods improve the quality-speed trade-off by grouping semantically similar tokens, but their practical efficiency remains limited by two bottlenecks: substantial clustering overhead and low CTA utilization caused by irregular cluster-induced blocks. We propose HyperVAttention (HVA), a training-free sparse attention framework that addresses both bottlenecks jointly. To reduce clustering overhead, we introduce 3D local-window clustering, which exploits the spatio-temporal locality of video tokens to restrict centroid search to fixed local neighborhoods, and implement it with a custom Triton kernel for efficient execution. We further propose a hybrid clustering strategy that performs full clustering only at anchor steps and updates only subset tokens at intermediate steps, leveraging the temporal stability of cluster assignments across denoising steps. To improve CTA utilization, we present hardware-aware cluster merging that minimizes CTA-aligned execution cost through parallel agglomerative merging, improving block density and approximation fidelity by utilizing idle tile capacity. Together, these components reduce clustering overhead, avoid redundant updates, and better align sparse attention with the fixed tile structure of modern GPU kernels. Experiments on Text-to-Video generation show that HVA establishes a new Pareto frontier for training-free sparse attention in video diffusion, reducing end-to-end latency by up to $2.13\times$ while improving fidelity over existing training-free sparse attention baselines.
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Machine Learning
Can Model Merging Improve Aggregation in DiLoCo?
Model merging techniques, which aggregate independently finetuned models into one to combine their capabilities, have become a topic of significant interest in recent years, with a broad array of methods having been proposed to tackle this problem. Simultaneously, an emerging trend in distributed learning has been the use of methods such as local SGD and DiLoCo, which greatly reduce communication costs by periodically aggregating the independently trained local models. However, these communication-efficient methods have been shown to degrade in performance relative to the FLOP-matched data-parallel gold standard as the number of independent local models grows and as the number of local training steps before global communication is increased. In this work, we draw an explicit analogy between the pseudo-gradient aggregation step in local SGD/DiLoCo and task arithmetic-based model merging, establishing a straightforward way to utilize merging methods in the context of distributed optimization. We then evaluate multiple state-of-the-art model merging methods in this setting and identify one method in particular, Iso-C, as a promising approach for improving DiLoCo. We find that DiLoCo SGD with Iso-C aggregation outperforms not only simple pseudo-gradient averaging but even the momentum-based DiLoCo, despite lacking a momentum mechanism itself. Building on this finding, we propose IsoLoCo, which adapts Iso-C for distributed training by equipping it with Nesterov momentum. Our empirical evaluations on language model pre-training across varying numbers of local workers show that IsoLoCo significantly outperforms DiLoCo, with the gap between them widening as the number of workers increases. This advantage remains present across model sizes and inner step counts, confirming that merging-inspired aggregation is an effective strategy for low-communication distributed training.
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Machine Learning
Do ECG Foundation Models Transfer to Rare Cardiac Diseases? Evidence from Brugada Syndrome Detection
Background: Foundation models (FMs) trained on large-scale unlabeled physiological data have emerged as a promising paradigm for medical artificial intelligence. Their ability to capture clinically meaningful, transferable representations for rare diseases remains largely unproven. This study investigates whether FM pre-training provides genuine clinical generalization benefits beyond improved optimization for rare electrocardiographic (ECG) phenotypes. Methods: We systematically evaluated nine publicly available ECG FMs for Brugada syndrome detection on the BrSwiss cohort (294 patients, 87 cases) and the independent external HUCA cohort (363 patients, 76 cases), under three strategies (from-scratch training, linear probing, full fine-tuning) across several configurations, including a 3% data ablation and zero-shot cross-site transfers. Results: Pre-training was necessary for high-capacity architectures unable to converge from scratch (AUC gain up to 0.411, p < 0.05), but gave no significant gain for compact architectures already converged on labeled data alone. On full BrSwiss, the best fine-tuned FM (ECG-CPC, AUC = 0.962) only marginally exceeded the strongest supervised baseline (ECG-CPC from scratch, AUC = 0.932; p = 0.091). At matched training-set size, the data-efficiency advantage on BrSwiss-3% (AUC gain = 0.055, p < 0.01) did not replicate on HUCA. Under zero-shot cross-site transfer, FM-based pipelines did not generalize better than supervised baselines, all approaching chance-level performance. Conclusion: For Brugada syndrome detection, FM pre-training is mechanical rather than semantic, providing optimization stability rather than transferable clinical knowledge. These findings challenge the assumption that large-scale pre-training inherently encodes clinically meaningful representations, highlighting the central role of model architecture and data-domain alignment.
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Machine Learning
Back to Basics: Improving Molecular Understanding in LLMs via SMILES-Graph Translation
Recent advances in molecular large language models have led to strong performance on molecular understanding and generation tasks, yet these gains often come without reliable structural grounding. In particular, existing approaches conflict with the chemistry principle that structure determines function: despite their downstream success, current molecular LLMs perform poorly on basic structure recognition, suggesting that they fail to capture molecular graphs from canonical SMILES. To remedy this, we propose MolBasic, a structure-first framework that strengthens structural comprehension via SMILES-Graph translation. MolBasic is built around a multi-level structure perception benchmark, where bidirectional SMILES-Graph conversion serves as the core task to align sequential and topological representations. On top of this foundation, we employ a progressive learning scheme with a standardized Chain-of-Thought (CoT) to steer models from structure acquisition toward higher-level molecular reasoning. Experiments show that MolBasic substantially improves structural understanding and yields robust gains on downstream tasks, including property prediction and objective optimization, supporting our structure-first paradigm.
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Machine Learning
Transfer Learning in High-dimensional Ising Models
In high-dimensional Ising model estimation, target sample sizes are often limited, and effectively using auxiliary binary datasets of unknown relevance remains challenging. To address this, we propose Trans-Ising, a transfer learning method that combines a loss-based source screening rule with a two-stage estimation procedure. The method first identifies informative auxiliary sources using held-out target pseudolikelihood to prevent negative transfer. It then computes an initial estimator via pooled nodewise $\ell_1$-regularized logistic regression, followed by a target-only correction step using a folded-concave penalty. Theoretically, we establish fixed-node $\ell_2$ and $\ell_1$ error bounds, exact graph selection consistency, and the conditional consistency of the screening rule. Through extensive simulations and real-data analyses, we demonstrate that Trans-Ising achieves lower estimation errors than both target-only estimation and naive data pooling.
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Machine Learning · Cross-listed from cs.CV
CONFLUX: A Latent Diffusion Model for 3D Chest-CT Synthesis with RL Post-Training
Controllable generative models of 3D medical images can synthesize volumes with specified clinical attributes, but this demands samples that are simultaneously high-fidelity, natively 3D, and faithful to the requested conditioning. We present CONFLUX, a latent diffusion model for chest computed tomography (CT): a 3D variational autoencoder compresses each volume, and a rectified-flow transformer generates in the latent space. Generation is conditioned on structured radiological metadata (18 abnormality findings, sex, age, and reconstruction kernel) through adaptive layer normalization. The model leads strong volumetric baselines on tri-planar Frechet distance (FID 32.3 vs. 74.6 for MAISI) while exposing direct control over clinical attributes. To strengthen that control we add an online reinforcement-learning post-training stage (group-relative policy optimization) that rewards how reliably a classifier recovers the requested findings from each generated volume. Judged by a separate, independent classifier, post-training removes 47% of the shortfall relative to real-scan reliability. We release the model and a ~200k synthetic chest-CT dataset with conditioning metadata spanning a wide variety of clinical findings.
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Machine Learning
MABLE: Masked Autoencoding with Bi-Lipschitz Decoding for Embeddings and Graph Metric Learning
We propose MABLE (Masked Autoencoding with Bi-Lipschitz Decoding for Embeddings and Graph Metric Learning), a self-supervised framework for learning node and graph embeddings from large, heterogeneous graphs, demonstrated here on geospatial mineral-exploration data. MABLE combines masked reconstruction with fixed cosine-similarity losses that align matched augmented views while keeping unpaired embeddings well spread. A bi-Lipschitz feature decoder ties a low-dimensional reconstruction component of each node embedding to feature similarity, while matched-node consistency shapes the remaining context used by graph pooling. Lipschitz-controlled pooling helps stabilize graph-level representations under perturbations of retained node embeddings, while augmentation alignment trains robustness to masking, node dropping, and sampling variation. Across local copper and regional Arabian Shield studies, MABLE embeddings provide complementary downstream signal and produce coherent embedding-derived layers for hypothesis generation without learned discriminators or hard-negative selection.
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Machine Learning
Rank-Order N-of-M Codes for Sparse Distributed Memory: Disentangling Representation and Learning Effects in Noise Robustness Against Contemporary Neuromorphic Architectures
Large language models remain limited as continual learning systems, motivating renewed interest in Sparse Distributed Memory (SDM) as an explicit online episodic memory. CALM (Nechesov and Ruponen, 2025) identifies its threshold-binary encoder as an open design question. This paper evaluates rank-order N-of-M encoding (Furber et al., 2007) as an alternative. We make three contributions. First, a faithful reimplementation validates the published architecture by confirming exact equivalence between WheelSDM and RankOrderSDM (cosine similarity 1.0000 across 10 seeds) and reproducing the documented divergence of RDLIF neurons under interference. Second, multi-seed capacity experiments show RankOrderSDM outperforming StandardSDM by 13.4 percentage points at saturation in the scaled configuration and by 0.8 percentage points at the published architecture scale. Third, BER robustness experiments disentangle representation and learning effects, showing that the large robustness gain arises primarily from the interaction of rank-order encoding with MAX-Hebbian learning, while the encoder alone provides only a small advantage under matched learning conditions. Experiments on GloVe-100 embeddings confirm this small but consistent encoding benefit on real structured data, whereas sentence embeddings exhibit a ceiling effect at low memory load. A secondary analysis shows that idealized rank-order encoding requires half the component-level encoding energy of SpikingMamba's SI-LIF neurons at four-bit precision, although decoder costs dominate overall system energy. These results identify which components of the original rank-order SDM architecture provide measurable benefits for contemporary memory-augmented AI systems, offering practical guidance for architectures such as CALM.
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Machine Learning
Individual Parameters in Weight-Sparse Transformers Appear Interpretable
A central goal of mechanistic interpretability is to understand how neural networks work and what each individual component does. Dominant circuit-finding approaches focus on a specific behavior and reverse-engineer the role of components on the associated sub-distribution. However, past work has shown that components can have different functions that are active on different subsets of the input distribution. In this work we ask whether a single weight can be understood globally across the full training distribution by characterizing when it matters (the inputs on which ablating it changes the model's predictions). We introduce an automated LLM pipeline that writes a short, human-readable description of when a weight matters and verifies it on held-out text, crediting a weight only if its description generalizes. Across two sparse and two dense transformers, the fraction of weights that are interpretable (in this sense) is higher in sparse transformers than in dense ones, a gap that widens once unreliable descriptions are discarded. Our results show that a meaningful fraction of a sparse transformer model's weights can be interpreted: 12 to 31% of weights have a single short description that identifies what the weight is used for.
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Machine Learning · Cross-listed from cs.CV
Incentivizing Vision Language Models to Search for Long Video Question Answering
We introduce VSeek, an agentic framework that transforms long-video question answering (LVQA) from a passive, single-pass perception task into a multi-turn retrieval process. VSeek utilizes a natural language-driven search to identify relevant context within long videos and is post-trained with reinforcement learning (RL) to jointly formulate targeted search queries and reason over retrieved clips for LVQA. While RL post-training has revolutionized reasoning in symbolic domains such as mathematics and code, its application to long-video understanding remains hindered by a lack of verified rewards. To ensure that the retrieved context is relevant, we propose a novel neuro-symbolic approach that bridges open-ended natural language with discrete visual verification. Specifically, complex user queries are compiled into formal temporal logic specifications for systematically decomposing natural language questions into a definitive checklist of required atomic visual primitives, such as key objects and activities, along with their temporal ordering. These systematically derived grounding events provide the critical feedback signal for RL post-training, enabling dense, verifiable rewards based on the successful retrieval of these specific visual elements rather than relying entirely on outcome-only answer accuracy. By explicitly optimizing for this verifiable evidence-seeking behavior, VSeek improves Pass@1 scores by up to 8% and Pass@4 scores by 15% on long-video understanding benchmarks compared to base models. We open-source our code at https://utaustin-swarmlab.github.io/VSeek.
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Machine Learning
A Precedent-Guided Co-Scientist for Side-Effect-Aware Drug Redesign
We propose PRECEDE, a precedent-guided co-scientist for side-effect-aware drug redesign that revises a parent compound to mitigate a specified side effect while preserving therapeutic function. Rather than isolated molecular generation, PRECEDE frames redesign as evidence-grounded reasoning over drug–side-effect associations, biomedical knowledge graphs, and precedents of safety-driven optimization, coordinated by an LLM orchestrator with explicit policies and human-review checkpoints. We position PRECEDE as a human-supervised AI-for-science workflow in which hypotheses remain auditable, falsifiable, and bounded by prior pharmacology.
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Machine Learning
Missingness as Signal: Channel-Independent Spectrogram Learning for Clinical Time Series Prediction
Clinical time series prediction in intensive care units remains challenging due to heterogeneous physiological variables and informative missingness. The presence or absence of a measurement can reflect clinical decisions and patient severity, and thus missingness can serve as a predictive signal rather than a simple data artifact. This work presents CISM, a Channel-Independent Spectrogram framework with a Missingness stream for clinical multivariate time series prediction. CISM converts each clinical variable into a variable-wise time-frequency spectrogram, preserves variable identity through variable-aligned encoding, and aligns an explicit missingness stream with the spectrogram representation. Experiments on an in-hospital mortality task derived from MIMIC-IV show that CISM achieves the highest mean AUROC (0.7225), AUPRC (0.3308), and F1 (0.3808) among the compared time series, missingness-aware, vision, and time-frequency baselines. Ablation studies further show that observation patterns provide a meaningful informative signal. Pixel-level mask injection improves performance over plain spectrogram inputs and recovers much of this predictive value. The aligned missingness stream contributes a further, complementary gain in both AUROC and AUPRC. These results highlight the importance of modeling observation patterns as structured signals in clinical time series prediction.
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Machine Learning
In-context learning from self-generated trajectories for adaptive model reduction
High-fidelity simulations of complex physical systems are often too expensive for repeated prediction, design, and control. Reduced-order models address this computational cost by compressing high-dimensional dynamics into low-dimensional representations that can be evaluated rapidly, but they often lose accuracy when online dynamics drift beyond the offline training data. Adaptive methods address this limitation by updating the reduced subspace online using external, out-of-span information, such as full-order corrections or sensor snapshots. We discovered that a complementary and previously unexploited in-span adaptation channel exists within the current reduced subspace. To exploit this channel, we continually update the reduced representation using the model's own predictions through an incremental singular-value decomposition with a forgetting factor. This produces a trajectory-informed spectral preconditioner in which the reduced subspace remains unchanged, while the basis is reweighted and realigned according to the directions visited by the evolving dynamics. This internal reorganization prepares the basis to absorb future out-of-span corrections more effectively, improving adaptation without requiring additional external information. We expose the mechanism through a three-dimensional spiral example and demonstrate its benefits on nonlinear partial differential equations, including viscous Burgers and Fisher–KPP dynamics. We also discuss how in-span learning can be interpreted as a dynamical-systems analogue of in-context learning. More broadly, in-span learning suggests a new principle for computational science, revealing that model-generated trajectories contain more usable information than previously recognized.