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Saturday 16 May

Machine Learning

Extending Pretrained 10-Second ECG Foundation Models to Longer Horizons

Electrocardiogram (ECG) foundation models pretrained on typical diagnostic 10-second ECG segments, have demonstrated strong transferability across a range of clinical applications. However, many real-world applications produce recordings that are typically longer, and are varied in duration during inference time. These 10-second models have no built-in way to combine information across time. Extending them to longer horizons introduces two challenges: structural incompatibilities arising from input-length disparities, and semantic challenges that limit meaningful temporal aggregation. We propose a parameter-efficient framework that extends pretrained ECG foundation models to longer and variable-length ECGs without retraining the backbone. Guided by a frozen pretrained 10-second model, we introduce a lightweight plug-in module that extends the model in two complementary ways: (i) structurally compatible long-sequence processing and (ii) semantically informed temporal modeling. Experiments on multiple long-horizon ECG tasks, datasets, and foundation model backbones demonstrate that our method enables robust long-horizon extension from pretrained snapshot models, consistently outperforming sliding-window and pooling-based baselines with strong parameter efficiency.
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All authors Wei Tang, Jinpei Han, Kangning Cui, Mattia Carletti, Fredrik K. Gustafsson, Shreyank N Gowda, Patitapaban Palo, Anshul Thakur, Lei Clifton, Jean-michel Morel, Raymond H. Chan, David A. Clifton, Xiao Gu

Machine Learning · Cross-listed from cs.CV

SHED: Style-Homogenized Embedding Alignment for Domain Generalization

Domain generalization aims to enhance model robustness against unseen domains with embedding distribution shifts. While large-scale vision-language models like CLIP exhibit strong generalization, their direct image-text embedding alignment suffers from inherent information asymmetry: images encode both class semantics and domain-specific styles, whereas text prompts primarily convey basic class cues. This asymmetry hinders generalization to novel domains in realistic scenarios. To address this, we propose Style-Homogenized Embedding alignment for Domain-generalization (SHED), a novel CLIP-based method that aligns style-homogenized embeddings instead of raw representations from encoders in CLIP. During training, SHED removes domain-specific style centroids from both image embeddings computed per source domains and text embeddings which are averaged across diverse prompt templates and stripped of a global centroid. For inference, considering the lack of target domain information, SHED projects diverse textual domain centroids into the visual space and aggregates predictions via membership weighting. Extensive experiments on five benchmarks show SHED achieves state-of-the-art performance, outperforming prior methods significantly (e.g., +4.0% on DomainNet vs. standard fine-tuning).
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Machine Learning

Emulating the Forced Response of Climate Models with Generative Machine Learning

Global climate models are essential tools to simulate past and potential future pathways of climate change, as well as associated climate impacts. Shared Socioeconomic Pathways (SSPs) describe a range of future scenarios of global economic and demographic development. These SSPs are intrinsically linked to changes in climate forcings – the external drivers, such as greenhouse gas and aerosol emissions, which change Earth's energy balance over time. These forcings act as boundary conditions in Earth System Models (ESM), providing insight into the potential climatic impacts of each SSP. Running an ESM, however, is extremely computationally expensive, conflicting with the need for large ensemble runs to provide robust estimates in the presence of internal variability and scenario uncertainty. Machine Learning emulators provide a promising avenue towards fast and cheap scenario generation, but until recently lacked uncertainty quantification and the ability to condition on external forcings. Here, we build upon recent work and extend it by training on multiple SSPs. We successfully generate scenarios of IPSL – CM6A – LR unseen during training and remain physically consistent with the underlying climate model, even under strong extrapolation scenarios. Our emulator is validated against MESMER – M, a statistical emulator of land surface temperature. Our research demonstrates that our model, ArchesClimate – SSP, does not simply imitate scenarios seen during training, but is actually capable of modeling the response of a climate state to diverse forcings. This is an important step towards reliable and rapid climate model scenario generation.
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All authors Graham Clyne, Julia Kaltenborn, Peer Nowack, Claire Monteleoni, Anastase Charantonis

Machine Learning · Cross-listed from stat.ML

CAST: Causal Anchored Simplex Transport for Distribution-Valued Time Series

Many decision-facing stochastic systems are observed through aggregate distributions rather than scalar trajectories: queue occupancies, mobility shares, public-health mixtures, generation-source shares, ecological compositions, and air-quality severity profiles all live on the probability simplex and evolve over time. We study causal (online) forecasting for these distribution-valued time series and argue that the transition operator itself should be structured around the simplex. We introduce CAST (Causal Anchored Simplex Transport), a successor-local operator that (i) retrieves empirical successors from causal context, (ii) stabilizes them with a persistence anchor, and (iii) applies a bounded local stochastic transport on ordered supports; every stage preserves the simplex by construction. We identify a structural failure mode, latent transition-kernel aliasing, where similar observed distributions evolve differently under different contextual regimes, and prove that any forecaster depending only on an aliased summary incurs an irreducible weighted Jensen-Shannon excess-risk lower bound, while the CAST hypothesis class contains the regime-aware Bayes successor; for ordered supports an additional Pinsker separation holds whenever the transported successor lies outside the no-transport anchor hull. On eleven public and simulated benchmarks spanning ecology, energy, diet, mortality, employment, air quality, severe weather, mobility, and G/G/1, G_t/G/1 queue occupancy, CAST attains the best average rank on both one-step KL (1.27) and autoregressive rollout JSD (1.91), winning 8/11 sections on each metric against a broad statistical, compositional, recurrent, convolutional, and Transformer baseline set, and top-2 on all 11 sections for offline KL. Component ablations and a controlled synthetic aliasing experiment corroborate the theory.
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All authors Jiecheng Lu, Jieqi Di, Runhua Wu, Yuwei Zhou

Machine Learning · Cross-listed from stat.ML

A Fourier perspective on the learning dynamics of neural networks: from sample complexities to mechanistic insights

Neural networks trained with gradient-based methods exhibit a strong simplicity bias: they learn simpler statistical features of their data before moving to more complex features. Previous analyses of this phenomenon have largely focused on settings with (quasi-)isotropic inputs. In this work, we study the simplicity bias from a Fourier perspective, which allows us to include two key features of natural images in the analysis: approximate translation-invariance and power-law spectra. We first show experimentally that simple neural networks trained on image classification tasks first rely on amplitude information – related to pair-wise correlations between pixels – before exploiting phase information, which encodes edges and higher-order correlations. In view of this, we introduce a synthetic data model for translation-invariant inputs that allows precise control over amplitudes and phases while remaining tractable. We rigorously establish that for isotropic and high-dimensional inputs, classification based on phase information alone is a genuinely hard task: online stochastic gradient descent (SGD) cannot distinguish the structured inputs from noise within $n \ll N^3$ steps, but needs at least $n \gg N^3 \log^2{N}$ steps. In contrast, we show both experimentally and theoretically that power-law spectra can dramatically accelerate the speed of learning phase information, even if the spectra do not help with classification. Simulations with two-layer networks trained on textures and with deep convolutional networks on ImageNet and CIFAR100 confirm this non-trivial interaction between amplitudes and phases, providing mechanistic insights into how deep neural networks can learn natural image distributions efficiently.
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Machine Learning

AIM: Adversarial Information Masking for Faithfulness Evaluation of Saliency Maps

Post-hoc saliency methods are widely used to interpret deep neural networks, but their faithfulness is difficult to evaluate reliably. Existing evaluations mask features according to saliency-induced feature ordering and measure performance degradation, but this degradation can be confounded by the masking operator: zero masking may create out-of-distribution artifacts, while interpolation-based masking may preserve residual predictive information. We propose Adversarial Information Masking (AIM), a saliency-guided adversarial feature replacement framework for evaluating both saliency-map faithfulness and masking-operator reliability. AIM replaces selected features with values from an adversarial counterpart of the input and compares degradation under complementary masking orders. We assess reliability using random-attribution bias and stability of explanation-method faithfulness rankings. Experiments on image, audio, and EEG tasks suggest that AIM reduces masking-induced bias compared with zero and interpolation-based masking, while revealing modality-dependent differences between signed and unsigned attributions.
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Machine Learning

ArtifactLinker: Linking Scientific Artifacts for Automatic State-of-the-Art Discovery

Scientific artifacts such as models and datasets are foundations for research. With the rapid growth of platforms like HuggingFace, researchers now have access to a large number of artifacts. Yet, a key challenge remains: how can we automatically discover the state-of-the-art (SOTA) model for a given dataset by fully leveraging existing artifacts? We formalize this task as automatic SOTA discovery by modeling HuggingFace as an artifact graph, where nodes are models/datasets and edges represent evaluations. We propose ArtifactLinker, a two-stage framework: (1) ranking promising unobserved model–dataset links using Graph Neural Networks (GNNs) or graph-augmented Large Language Models (LLMs), and (2) verifying top-ranked links via coding experiments with LLM-based agents. We further introduce a benchmark named ArtifactBench with 14,053 artifacts and 51,337 relations to evaluate the performance of both stages. Results show that (1) graph structures between existing artifacts are effective for missing link prediction; (2) end-to-end ranking and verification with ArtifactLinker help discover potential SOTA results and research insights.
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All authors Haofei Yu, Jiaxuan You, Peter Clark, Bodhisattwa Prasad Majumder, Kyle Richardson

Machine Learning

Tensor Channel Equivariant Graph Neural Networks for Molecular Polarizability Prediction

We introduce a tensor-channel equivariant graph neural network for direct prediction of molecular polarizability tensors. Building on the efficient PaiNN architecture, we augment the hidden representation with explicit symmetric rank-2 tensor channels aligned with the decomposition of polarizability into isotropic and anisotropic components. In contrast to approaches that construct tensor outputs only at readout, our model propagates tensor structure throughout message passing using geometrically motivated tensor bases. This yields a target-aligned architecture for tensor-valued molecular prediction. On optimized QM7-X geometries, the proposed model achieves lower full-tensor and anisotropic error than both a PaiNN-style readout baseline and a dielectric MACE baseline under matched training conditions and at nearly identical parameter count. In this controlled setting, it also outperforms MACE while remaining substantially faster at inference. Ablation studies show that the gain does not arise from increased capacity alone, but from the combination of explicit tensor propagation and a traceless target parameterization matched to the anisotropic part of the polarizability tensor. Among the tensor bases considered, the strongest results are obtained from interactions between learned directional features, indicating that these are particularly effective for modeling molecular polarizability. Rotational equivariance tests further confirm that all compared models are numerically equivariant, so the observed improvements are attributable to better learning of the target tensor itself. Overall, our results show that for structured tensor-valued targets, propagating target-aligned tensor features can outperform both readout-only tensor construction and a more general higher-order equivariant model in the present training setting.
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Machine Learning · Cross-listed from cs.CV

Mind the Gap: Learning Modality-Agnostic Representations with a Cross-Modality UNet

Cross-modality recognition has many important applications in science, law enforcement and entertainment. Popular methods to bridge the modality gap include reducing the distributional differences of representations of different modalities, learning indistinguishable representations or explicit modality transfer. The first two approaches suffer from the loss of discriminant information while removing the modality-specific variations. The third one heavily relies on the successful modality transfer, could face catastrophic performance drop when explicit modality transfers are not possible or difficult. To tackle this problem, we proposed a compact encoder-decoder neural module (cmUNet) to learn modality-agnostic representations while retaining identity-related information. This is achieved through cross-modality transformation and in-modality reconstruction, enhanced by an adversarial/perceptual loss which encourages indistinguishability of representations in the original sample space. For cross-modality matching, we propose MarrNet where cmUNet is connected to a standard feature extraction network which takes as inputs the modality-agnostic representations and outputs similarity scores for matching. We validated our method on five challenging tasks, namely Raman-infrared spectrum matching, cross-modality person re-identification and heterogeneous (photo-sketch, visible-near infrared and visible-thermal) face recognition, where MarrNet showed superior performance compared to state-of-the-art methods. Furthermore, it is observed that a cross-modality matching method could be biased to extract discriminant information from partial or even wrong regions, due to incompetence of dealing with modality gaps, which subsequently leads to poor generalization. We show that robustness to occlusions can be an indicator of whether a method can well bridge the modality gap.
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All authors Xin Niu, Enyi Li, Jinchao Liu, Yan Wang, Margarita Osadchy, Yongchun Fang

Machine Learning

SE-GA: Memory-Augmented Self-Evolution for GUI Agents

Autonomous Graphical User Interface (GUI) agents often struggle with multi-step tasks due to constrained context windows and static policies that fail to adapt to dynamic environments. To address these limitations, this work proposes the Self-Evolving GUI Agent (SE-GA), a novel framework that integrates hierarchical memory structures with an iterative self-improvement mechanism. At the core of our approach is Test-Time Memory Extension (TTME), which facilitates long-term planning by dynamically retrieving episodic, semantic, and experiential memories to provide salient contexts during inference. To ensure continuous learning, we introduce Memory-Augmented Self-Evolution (MASE), which is a training pipeline that adopts the data collected by TTME to stabilize and enhance the agent's foundational policy. Extensive evaluations across both offline and online benchmarks demonstrate SE-GA achieves state-of-the-art performance, reaching success rates of 89.0% on ScreenSpot and 75.8% on the challenging AndroidControl-High dataset. Furthermore, significant improvements on the AndroidWorld benchmark highlight the superior generalization to dynamic environments. Open source code: https://github.com/jinshilong-dev/SE-GA
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Machine Learning · Cross-listed from cs.RO

Plan First, Diffuse Later: Extrinsic Graph Guidance for Long-Horizon Diffusion Planning

Compositional diffusion models offer a promising route to long-horizon planning by denoising multiple overlapping sub-trajectories while ensuring that together they constitute a global solution. However, enforcing local behavior over long chains is often insufficient for a coherent global structure to emerge. Recent works tackle this limitation through intrinsic search, which explores multiple paths during the denoising process. While intrinsic search improves global coherence, it comes at the cost of repeated evaluations of an already compute-heavy model. In this work, we argue that extrinsic search, performed outside the denoising process, offers a more effective mode of exploration for long-horizon planning while naturally enabling the use of classical algorithms to solve unseen combinatorial tasks at test time. Our eXtrinsic search-guided Diffuser (XDiffuser) first computes a plan over a state-space graph – serving as a lightweight local connectivity oracle for the diffusion model. The plan is then used to guide denoising for a single trajectory, effectively offloading the burden of exploration. XDiffuser outperforms diffusion-based baselines on long-horizon tasks, with particularly large gains in the low-quality data regime and on unseen tasks beyond goal-reaching, including multi-agent coordination and TSP-style reasoning. Project website: https://yanivhass.github.io/XDiffuser-site/
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All authors Yaniv Hassidof, Adir Morgan, Yilun Du, Kiril Solovey

Machine Learning

PhysioSeq2Seq: A Hybrid Physiological Digital Twin and Sequence-to-Sequence LSTM for Long-Horizon Glucose Forecasting in Type 1 Diabetes

Accurate long-horizon glucose forecasting is critical for automated insulin delivery systems, which help people with type 1 diabetes (T1D) manage their glucose and avoid dangerous hypoglycemia. However, standard recursive long short-term memory (LSTM) networks suffer from systematic negative bias at longer horizons due to error compounding, while purely mechanistic ordinary differential equation (ODE) models fail to generalize across individuals when parameterized at the population level. We propose PhysioSeq2Seq, a hybrid architecture that combines patient-specific physiological modeling with a sequence-to-sequence (Seq2Seq) LSTM. For each glucose segment, twin matching searches a population of 300 parameterized digital twins to identify the best-fitting physiological match from a 3-hour continuous glucose monitoring (CGM) history. The 10 internal ODE state variables of the matched twin are injected as exogenous covariates into both the encoder and decoder of the Seq2Seq LSTM. This simultaneous 48-step prediction strategy eliminates recursive error compounding, while the ODE features provide a physics-grounded constraint that bounds long-horizon drift within physiologically plausible ranges. PhysioSeq2Seq was trained on CGM and insulin data from 348 participants in the Type 1 Diabetes Exercise Initiative (T1DEXI) dataset and evaluated on 74 held-out participants. At the 240-minute horizon, PhysioSeq2Seq achieves a mean absolute error of 39.28 mg/dL and a mean error of -10.62 mg/dL, reducing bias by 13.89 mg/dL over the recursive LSTM and reducing mean absolute error by 28.62 mg/dL over the ODE-based digital twin. These results show that eliminating architectural feedback and injecting patient-matched physiological states is an effective and clinically meaningful strategy for long-horizon glucose forecasting in T1D.
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All authors Phat Tran, Neville Mehta, Clara Mosquera-Lopez, Robert H. Dodier, Lizhong Chen, Peter G. Jacobs

Machine Learning · Cross-listed from cs.CV

Thinking with Patterns: Breaking the Perceptual Bottleneck in Visual Planning via Pattern Induction

Planning from raw visual input remains a significant challenge for current Vision-Language Models (VLMs), when the complexity of input is beyond their one-step perception capability. Motivated by recent advances in Thinking with Images (TWI), a reasonable solution is to decompose the perception process into simpler steps by iteratively acquiring and incorporating local visual evidence. However, even though current VLMs are well-trained in general TWI ability, their perceptual bottleneck in the planning domain remains. To tackle this challenge, we formulate TWI as a tool to gradually build and reflect an accurate internal world model. We find that the resulting training-free planning strategy enables VLMs to solve tasks that are far beyond their initial capabilities, at the cost that too many TWI operations would significantly increase the computational overhead. To further improve efficiency, we propose Pattern Inference, a novel TWI strategy enabling VLMs to actively recognize known visual patterns in the new tasks and directly infer local world model structures. To obtain these patterns, we propose Pattern Induction, an online inductive learning strategy treating visual patterns as composite and reusable experts, which are autonomously discovered and optimized from experience. Experimental evaluations in FrozenLake, Crafter and CubeBench domains show that our approaches achieve a desirable balance between accuracy and efficiency.
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All authors Yichang Jian, Boyuan Xiao, Zhenyuan Huang, Yifei Peng, Yao-Xiang Ding

Machine Learning · Cross-listed from stat.ML

HYVINT: Intensity-Driven Hypergraph Generation with Variational Embeddings

Hypergraphs provide a principled framework for modeling polyadic interactions, with applications in recommendation systems, social networks, and molecular modeling. Hypergraph generation remains challenging because incidence structures are discrete, sparse, and governed by heterogeneous higher-order interactions. Existing generators often rely on implicit latent spaces or continuous incidence decoders, which provide limited mechanistic interpretation of how node-hyperedge incidences arise. To address these limitations, we propose HYVINT, an intensity-driven hypergraph generative framework. Our key innovations are twofold: (i) we develop an intensity-driven incidence formation mechanism for hypergraphs that links latent interaction strength to binary incidence, and (ii) we derive a tractable lower-bound variational estimator for learning latent representations. We provide generation error bounds with asymptotic convergence rates and empirically show that HYVINT achieves strong fidelity while maintaining substantial novelty and diversity on synthetic and real-world hypergraphs.
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Machine Learning · Cross-listed from cs.CV

ReLATE: Learning Relative Representations for Post-Hoc Multimodal Alignment

Post-hoc multimodal alignment connects independently pretrained vision and language encoders while keeping them frozen, offering an alternative to joint pretraining when paired data are scarce. A central design challenge is to construct comparable representations across heterogeneous feature spaces while retaining local information relevant to distinct semantic concepts within each input. We propose Relative Alignment with Learnable Anchors and Token Evidence (ReLATE), which learns modality-specific anchors that jointly define relative representations and determine token contributions to each relative coordinate. Image patches and text tokens are represented by their similarities to anchors within their respective frozen feature spaces. Anchor-wise Similarity Pooling (ASP) then weights and aggregates these similarities separately for each anchor to construct the corresponding relative coordinate. A sample-level symmetric contrastive objective aligns the resulting image and text representations by optimizing only the anchors, without updating the encoders. Experiments on 13 general-domain benchmarks across four vision-language tasks demonstrate improvements over the compared post-hoc alignment methods under matched paired-data budgets, with further evaluations across data scales and encoder combinations. Beyond the general domain, we evaluate ReLATE in pathology as a specialized-domain application. By aligning frozen pathology image and biomedical language encoders, ReLATE matches or exceeds the evaluated pathology-specific vision-language models in balanced accuracy on three zero-shot classification benchmarks.
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Machine Learning · Cross-listed from stat.ML

Prediction-Intervention Games and Invariant Sets

We consider the following two-player game: using observational data, the leader chooses a prediction function for a response variable $Y$ from given covariates. The follower then reacts with an intervention on some covariates in the underlying structural causal model to maximize their own objective. The leader knows the intervention targets, but may have limited knowledge of the follower's objective. We call this setup a prediction-intervention game, a special case of a Stackelberg game. Finding an optimal strategy for the leader is generally difficult. To avoid severe performance loss, the leader may base their prediction on the causal parents of $Y$, or more generally on an invariant subset of covariates. We prove, for two common classes of follower objectives, that predictors based on the stable blanket, an invariant subset, are at least as good as those based on the causal parents. We further upper bound the leader's post-intervention risk by a worst-case risk over allowed interventions and strengthen existing distribution generalization results to analyze this bound: we give sufficient conditions under which stable-blanket predictors are worst-case optimal, and show by examples that these conditions cannot in general be dropped. Finally, we discuss practical strategies for settings with known and unknown graph, and test them on simulated and real-world data.
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Machine Learning

Decoupling KL and Trajectories: A Unified Perspective for SFT, DAgger, Offline RL, and OPD in LLM Distillation

Knowledge distillation is central to LLM post-training, yet its design space remains poorly understood, especially alongside reinforcement learning (RL). We show that the prevailing paradigms, off-policy distillation and on-policy distillation (OPD), implicitly couple two orthogonal choices: prefix source and token-level KL direction. This follows from decomposing sequence-level KL over autoregressive response distributions: forward KL pairs teacher prefixes with token-level forward KL, and reverse KL pairs student prefixes with token-level reverse KL. We argue this coupling is not intrinsic: decoupling the two axes yields four valid objectives. We establish gradient-level identities showing forward KL gives SFT-style cross-entropy matching with teacher soft targets, whereas reverse KL gives an RL-style policy-gradient objective with a dense teacher-student log-ratio reward, connecting them to off-policy SFT, DAgger-style on-policy SFT, offline-RL-style distillation, and OPD. We conduct an extensive controlled study on math reasoning, evaluating the four objectives both as standalone methods and as initializations for subsequent RL. The results reveal three tradeoffs: KL direction induces an accuracy-entropy tradeoff, prefix source a quality-compute tradeoff, and training length an accuracy-stability tradeoff. Motivated by these findings, we propose KL mixing and an entropy-gated length curriculum. KL mixing shows long-sequence distillation requires substantial forward-KL weight to prevent entropy collapse and length inflation without sacrificing accuracy. The entropy-gated length curriculum improves Avg@k and Pass@k by 3.6 and up to 5.8 points, and cuts average response length by roughly 3x versus fixed long-horizon training. Our results provide a framework and practical methods for designing reasoning distillation objectives that balance accuracy, diversity, compute, and RL behavior.
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All authors Anhao Zhao, Haoran Xin, Yingqi Fan, Junlong Tong, Wenjie Li, Xiaoyu Shen

Machine Learning

Confidence Geometry Reveals Trace-Level Correctness in Large Language Model Reasoning

Large language models (LLMs) generate not only reasoning text, but also token-level confidence trajectories that record how uncertainty evolves during inference. Whether these trajectories are relevant to reasoning correctness remains unclear. Here we show that confidence trajectories encode a content-agnostic confidence geometry associated with trace-level final-answer correctness. Using only token-level confidence values, without access to the input question, reasoning text, hidden states, or external verifiers, we find that low-dimensional representations of confidence trajectories separate correct from incorrect reasoning traces. Across GSM8K, MATH, and MMLU, this geometric separation is quantitatively linked to downstream predictability: stronger clustering of correct and incorrect traces, measured by the Davies–Bouldin index, consistently corresponds to higher correctness-discrimination AUC. We further show that correctness-related information is enriched in the tail of reasoning, suggesting that late-stage confidence dynamics carry key correctness signals. We propose NeuralConf, a lightweight estimator that learns from confidence trajectories for correctness evaluation. Under a fixed trace budget, NeuralConf-derived scores improve confidence-weighted answer aggregation over majority voting, tail confidence, and other static baselines. These results reveal that LLMs expose trace-intrinsic statistical signals of correctness through their own confidence dynamics, offering a route to improve inference using information already present within generation.
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Machine Learning

VQ-Atom: Semantic Discretization of Local Atomic Environments for Molecular Representation Learning

Large language models succeed by combining large-scale pretraining with meaningful discrete tokens. In molecular machine learning, SMILES is widely used as a token representation, but it is primarily a linearization format for molecular graphs rather than a semantic decomposition of chemistry. We propose VQ-Atom, a semantic tokenization framework that assigns discrete atom-level tokens based on local chemical environments via vector quantization. Unlike SMILES tokens, VQ-Atom tokens encode graph-local chemical context and are aligned with molecular structure. On protein-cold drug–target interaction prediction using the KIBA dataset, VQ-Atom substantially improves global ranking performance, achieving AUROC of 0.79 while substantially outperforming both SMILES-based and continuous molecular representations under an identical downstream architecture. Furthermore, VQ-Atom enables approximately 3 times faster downstream training than continuous atom-level representations by replacing per-atom continuous features with reusable discrete tokens. These results suggest that molecular tokenization is not merely a preprocessing step, but a central design choice. In particular, well-structured tokens can encode substantial chemical semantics, reducing the burden on downstream learning. VQ-Atom can be interpreted as defining a molecular language, where tokens correspond to chemically meaningful atomic environments, suggesting that token design may constitute an additional axis of machine learning research alongside architecture, objectives, and optimization.
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Machine Learning · Cross-listed from cs.CL

AgentKernelArena: Generalization-Aware Benchmarking of GPU Kernel Optimization Agents

GPU kernel optimization is increasingly critical for efficient deep learning systems, but writing high-performance kernels still requires substantial low-level expertise. Recent AI coding agents can iteratively read code, invoke compilers and profilers, and refine implementations, yet existing kernel benchmarks evaluate single LLM calls rather than full agent workflows, and none include both kernel-to-kernel optimization and unseen-configuration generalization testing. We present AgentKernelArena, an open-source benchmark for measuring AI coding agents on GPU kernel optimization. The benchmark contains 196 tasks spanning HIP-to-HIP optimization, Triton-to-Triton optimization, and PyTorch-to-HIP translation, and evaluates complete agent workflows in isolated workspaces using gated compilation, correctness, and performance checks, centralized scoring and an unseen-configuration generalization protocol that tests whether optimizations transfer to input configurations the agent never observed. Across production agents including Cursor Agent, Claude Code, and Codex Agent, we find near-perfect compilation and high correctness rates on most task categories, with the strongest configurations achieving mean speedups of up to 6.89x on PyTorch-to-HIP, 6.69x on HIP-to-HIP, and 2.13x on Triton-to-Triton tasks. Our unseen-configuration evaluation shows that HIP-to-HIP and Triton-to-Triton optimizations largely transfer to unseen input shapes, while PyTorch-to-HIP exhibits substantial correctness drops, indicating that agents generating kernels from scratch frequently hardcode shape-specific assumptions. AgentKernelArena is designed as a modular, extensible framework for rigorous evaluation of agentic GPU kernel optimization across agents, tasks, and hardware targets.
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All authors Sharareh Younesian, Wenwen Ouyang, Sina Rafati, Mehdi Rezagholizadeh, Sharon Zhou, Ji Liu, Yue Liu, Yuchen Yang, Hao Li, Ziqiong Liu, Dong Li, Vikram Appia, Zhenyu Gu, Emad Barsoum

Machine Learning · Cross-listed from cs.CR

Universal Graph Backdoor Defense: A Feature-based Homophily Perspective

Graph neural networks (GNNs) have achieved remarkable success in relational learning. However, their vulnerability to graph backdoor attacks (GBAs) poses a significant barrier to broader adoption in high-stakes applications. Despite recent advances in graph backdoor defense (GBD), existing methods primarily focus on subgraph-based GBAs, relying on the assumption that poisoned target nodes are explicitly connected to subgraph triggers. Our empirical results reveal that such structure-centric approaches fail to defend against emerging feature-based GBAs that preserve graph topology. Therefore, in this paper, we study a novel problem of universal graph backdoor defense. First, we investigate the shared effects of both attack types from a feature-based homophily perspective, which characterizes local feature consistency between nodes and their neighborhoods. Thorough theoretical and empirical analyses demonstrate that, regardless of trigger mechanisms, backdoors induced by GBAs exhibit lower feature-based homophily than clean nodes, indicating a discrepancy in local feature similarity. Motivated by this insight, we propose to leverage node-level local feature consistency, modeled by a neighbor-aware reconstruction loss, to distinguish backdoors from clean nodes. Then, a robust training strategy is developed to eliminate trigger effects while reducing noise induced by detection uncertainty. Extensive experiments demonstrate that our framework significantly degrades the attack success rate and maintains competitive clean accuracy under both subgraph-based and feature-based attacks.
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All authors Mengting Pan, Fan Li, Chen Chen, Xiaoyang Wang

Machine Learning

Jacobian-Guided Anisotropic Noise Reshaping for Enhancing Representation Utility under Local Differential Privacy

While Local Differential Privacy (LDP) serves as a foundational primitive for distributed data collection, its stringent randomization requirements often lead to severe degradation in data representation utility. This degradation stems from the task-agnostic nature of conventional LDP mechanisms, which perturb all dimensions without accounting for their relative importance to the downstream objective. To address this issue, we propose a novel approach that mitigates noise in task-relevant subspaces of the data representation. Our method identifies task-critical subspaces via the Jacobian of a public downstream model, selectively attenuates noise along these directions, and reshapes the isotropic noise of standard LDP mechanisms into an anisotropic distribution. The resulting mechanism preserves the privacy guarantee of the underlying LDP randomizer while heterogeneously modulating the impact of noise across task directions, thereby substantially enhancing data utility. The approach is applicable to both linear and nonlinear models and can be seamlessly integrated with existing LDP mechanisms. Extensive experiments on CIFAR-10-C under brightness corruption at the highest severity level demonstrate that integrating our approach improves classification accuracy by approximately 8 percentage points for Laplace and 20 percentage points for PrivUnit variants at $\epsilon=7.5$. The source code is available at https://github.com/ymha/jacobian-anr-ldp.
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All authors Youngmok Ha, Viktor Schlegel, Yidan Sun, Anil Anthony Bharath

Machine Learning

Informative Graph Structure Learning

The quality of graph-structured data is fundamental to the success of modern graph analysis techniques such as Graph Neural Networks (GNNs). However, real-world graph data is often suboptimal, suffering from issues such as noise and incomplete connections. Graph Structure Learning (GSL) has emerged as a promising technique that adaptively optimizes node connections. However, we observe that the effectiveness of GSL often comes at the cost of a dramatic expansion in edge count, resulting in significant storage and computational overhead. In this work, we reveal that this limitation stems from the prevalent use of similarity-based edge construction, which predominantly connects highly similar neighbors based on their embeddings, introducing substantial structure redundancy. To address this, we propose a novel Informative Graph Structure Learning method (InGSL), which jointly considers both similarity and diversity in edge construction by incorporating a mutual-information-guided learning strategy. Notably, InGSL serves as a plug-in module that can be seamlessly integrated into existing GSL frameworks. Through extensive experiments on six representative GSL methods, we demonstrate that InGSL achieves significant performance improvements at a reduced number of edges.
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All authors Shen Han, Zhiyao Zhou, Jiawei Chen, Sheng Zhou, Canghong Jin, Hai Lin, Da Zhong Li, Bingde Hu, Can Wang

Machine Learning

Cross-modal Affinity-aligned Multimodal Learning Analytics for Predicting Student Collaboration Satisfaction in Game-Based Learning

Collaborative game-based learning environments offer rich opportunities for small-group knowledge construction, yet automatically predicting student collaboration satisfaction remains challenging. A critical barrier is modality degradation: in educational deployments, individual modalities such as eye gaze exhibit inconsistent informativeness across student cohorts, causing implicit attention-based fusion to produce brittle multimodal representations. We propose the Affinity-Aligned Multimodal Learning Analytics (AAMLA) framework, whose core contribution is the Cross-modal Affinity-guided Modality Alignment (CAMA) module, which explicitly models inter-modal relationships via affinity matrices and enforces cross-modal consistency through contrastive learning, enabling adaptive suppression of uninformative modalities without discarding them. AAMLA further applies modality-specific projection layers to map heterogeneous features, including facial action units, head pose, eye gaze, and interaction trace logs, into a unified semantic space prior to alignment. Experiments on 50 middle school students in the EcoJourneys collaborative learning environment demonstrate consistent improvements over unimodal baselines and prior cross-attention approaches under standard and modality degradation conditions, with SHAP and t-SNE analyses confirming that CAMA produces robust, interpretable cross-modal representations for student collaboration modeling.
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Machine Learning

FIM-LoRA: Task-Informative Rank Allocation for LoRA via Calibration-Time Gradient-Variance Estimation

Low-rank adaptation (LoRA) assigns a uniform rank to every adapted weight matrix - a practical convenience that ignores a fundamental reality: different layers contribute unequally to task adaptation. We address this with a lightweight engineering solution: before fine-tuning begins, run eight calibration backward passes, compute the gradient variance of each LoRA-B matrix as a proxy for layer informativeness, and redistribute the rank budget proportionally. The resulting adapter is a standard LoRA with a per-layer rank pattern - no new parameters, no training overhead, no changes to serving infrastructure. We implement this via an efficient approximation of the empirical Fisher Information Matrix (eFIM) diagonal, restricted to LoRA adapter matrices only, which reduces memory cost by approximately 256x compared to full-model Fisher estimation. On GLUE with DeBERTa-v3-base, FIM-LoRA matches LoRA (88.6 vs. 88.7) at the same parameter budget, and on commonsense reasoning with LLaMA-3-8B reaches 68.5 vs. 68.7 for LoRA. The per-layer rank maps are interpretable: value projections and early-to-middle layers consistently receive higher rank, consistent with established findings on transformer layer roles.
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Machine Learning

Cross-Domain Molecular Relational Learning: Leveraging Chemical Structure-Activity Analysis

Recent advances in molecular representation integrates molecular topological and visual modalities, opening new avenues for precise Molecular Relational Learning (MRL). Existing MRL methods focus on intra-domain modeling, and their inherent domain-closed effect limits applicability to molecular science, particularly in elucidating cross-domain interaction mechanisms. Consequently, the imperative for Cross-Domain Molecular Relational Learning has become increasingly pressing. Benefiting from structure-activity analysis, we propose the Domain Adversarial Training Network with Structural-Semantic Transfer Discrepancy (DisTrans) to optimize cross-domain adaptive representation for molecular structures and visual images. 1) We employ the gradient reversal strategy based on substructure topological discrepancies between domains to learn the domain dependence of molecular structures. This strategy guides the model to adapt to the structural adjacency patterns in the target domain, generating domain-separable structural representations. 2) We apply the cross-domain representation guidance mechanism to align the functional-group semantic information between the source and target domains, learning cross-domain consistency information. The experimental results in two typical cross-domain strategies demonstrate that DisTrans outperforms 16 baseline methods, maintaining satisfactory performance even under pronounced inter-domain discrepancy.
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All authors Peiliang Zhang, Jingling Yuan, Shiqing Wu, Mengqing Hu, Chao Che, Yongjun Zhu, Lin Li

Machine Learning

PULSE: Generative Phase Evolution for Non-Stationary Time Series Forecasting

Time series forecasting under non-stationarity faces a fundamental tension between capturing stable representations and adapting to distribution shifts. Existing methods implicitly rely on static historical assumptions, leading to a critical failure mode we term Phase Amnesia, where models become blind to the evolving global context. To resolve this, we formalize non-stationary dynamics through three physical hypotheses: wold decomposition, dynamical phase evolution, and heteroscedastic manifold generation. These principles inspire PULSE, a physics-informed, plug-and-play framework adopting a Disentangle–Evolve–Simulate design philosophy. Specifically, PULSE utilizes phase-anchored disentanglement to resolve optimization interference caused by dominant trends, employs a Phase Router to actively generate future trajectories, and introduces Statistic-Aware Mixup (SAM) to ensure robustness against out-of-distribution volatility. Empirically, PULSE enables a simple MLP backbone to achieve state-of-the-art or highly competitive performance across 12 real-world benchmarks. This validates that a correct physics-informed inductive bias is far more critical than raw architectural complexity for non-stationary forecasting. The code is available at: https://github.com/Gemost/PULSE.
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All authors Yangyou Liu, Zezhi Shao, Xinyu Chen, Hu Chen, Fei Wang, Yuankai Wu

Machine Learning

TIER: Trajectory-Invariant Execution Rewards for Multi-Step Tool Composition

Tool use enables large language models to solve complex tasks through sequences of API calls, yet existing reinforcement learning approaches fail to scale to multi-step composition settings. Outcome-based rewards provide only sparse feedback, while trajectory-supervised rewards depend on annotated reference solutions, penalizing valid alternatives and limiting scalability. We propose TIER: Trajectory-Invariant Execution Rewards, a reward framework that derives supervision directly from function schemas and runtime execution, rather than from reference trajectories. The reward decomposes into format validity, schema adherence, execution success, and answer correctness, providing dense, interpretable sequence-level feedback derived from fine-grained verification of individual steps of tool use. This design allows any valid execution path to receive credit, naturally supporting multiple solution strategies and adapting to evolving tool interfaces. On DepthBench, a compositional benchmark stratified by depth (1 to 6 steps), TIER achieves >90% accuracy across steps, where trajectory-supervised rewards collapse beyond step-4. We further demonstrate consistent gains on benchmarks like BFCL v3 and NestFUL. Ablation studies confirm that all reward components are necessary, highlighting the importance of multi-level supervision for compositional reasoning.
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All authors Anay Kulkarni, ChiaEn Lu, Dheeraj Mekala, Jayanth Srinivasa, Gaowen Liu, Jingbo Shang

Machine Learning

The Unlearnability Phenomenon in RLVR for Language Models

Reinforcement Learning with Verifiable Reward (RLVR) has proven effective in improving Large Language Model's (LLM) reasoning ability. However, the learning dynamics of RLVR remain underexplored. In this paper, we reveal a counterintuitive phenomenon: among hard examples that the model initially struggles with, a substantial subset remains unlearnable even when correct rollouts are present. To understand the phenomenon, we first demonstrate that existing optimization and sampling techniques fail to resolve unlearnability. With cross-example gradient analysis, we show that unlearnable examples have fundamental representation issue, characterized by low gradient similarity with the rest of the examples and ungeneralizable reasoning patterns. We further show that representation flaws are difficult to mitigate in RL, as data augmentation does not improve gradient similarity. Our study provides the first systematic characterization of unlearnable data in RLVR training and reveals fundamental limitations in current RL approaches for reasoning tasks. Code and data are available at \url{https://github.com/yulinchen99/unlearnability-rlvr}.
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Machine Learning

Lever: Speculative LLM Inference on Smartphones

Large language models (LLMs) are increasingly needed for interactive mobile applications, but high-quality models exceed the limited DRAM available on smartphones. Flash storage can hold larger models, yet flash-backed inference is slow because autoregressive decoding repeatedly invokes the target model and incurs costly I/O. We observe that speculative decoding is a natural fit for this setting: a small draft model can remain in DRAM, while a larger flash-resident target model verifies multiple candidate tokens per invocation. However, existing methods assume server-class accelerators and fail to account for prolonged I/O latency, limited computation parallelism, and irregular speculation execution. We present Lever, an end-to-end system for efficient flash-backed LLM inference on smartphones. Lever jointly optimizes the three stages of speculative decoding under mobile constraints. For drafting, it builds token trees using an I/O- and compute-aware gain-cost objective. For verification, it prunes low-value branches through early-exit prediction to reduce target-model computation. For execution, it maps speculation efficiently across mobile CPU-NPU hardware to improve utilization. Comprehensive evaluations show that Lever reduces inference latency by an average of 2.93x over baseline flash-offloaded inference and 1.50x over conventional speculative decoding, narrowing the latency gap between flash-backed and memory-resident LLM inference.
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All authors Tuowei Wang, Fengzu Li, Yanfan Sun, Wei Gao, Ju Ren