Machine Learning · Cross-listed from stat.ML
Scalable Gaussian process inference via neural feature maps
Anthony Stephenson
We present a theoretically grounded Gaussian process framework that leverages neural feature maps to construct expressive kernels. We show that the learned feature map can be interpreted as an optimal low-rank approximation to a Gram
matrix derived from an implied RKHS, from which we establish consistency of the GP posterior. We further analyse the spectral properties of the induced kernels and introduce product feature-map kernels to address oversmoothing. This simple yet powerful approach enables fast, scalable, and accurate exact GP inference with minimal upfront work. The flexibility of kernel design supports seamless application to both regression and classification tasks across diverse data modalities, including tabular inputs and structured domains such as images. On
benchmark datasets, this approach surpasses pre-existing methods in terms of accuracy and training and prediction efficiency.
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Machine Learning
DeepLog: A Software Framework for Modular Neurosymbolic AI
Robin Manhaeve, Stefano Colamonaco, Vincent Derkinderen et al. (+4 more)
DeepLog is an operational neurosymbolic framework that unifies logic and deep learning within standard PyTorch workflows. While existing neurosymbolic systems focus on a particular paradigm and semantics, DeepLog serves as a universal backend that can emulate many systems in the neurosymbolic alphabet soup. By treating diverse neurosymbolic
languages as high-level specifications, the DeepLog software automatically compiles them into optimized arithmetic
circuits. This design lowers the barrier for machine learning practitioners by treating logic as composable modules, while providing neurosymbolic developers with a shared, high-performance basis for prototyping new integration strategies. The code is available here: https://github.com/ML-KULeuven/deeplog
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All authors Robin Manhaeve, Stefano Colamonaco, Vincent Derkinderen, Rik Adriaensen, Lucas Van Praet, Luc De Raedt, Giuseppe Marra
Machine Learning
Predictive Radiomics for Evaluation of Cancer Immune SignaturE in Glioblastoma: the PRECISE-GBM study
Prajwal Ghimire, Junjie Li, Liu Yaou et al. (+2 more)
Background: Radiogenomics allows identification of radiological biomarkers for genomic phenotypes. In glioblastoma, these biomarkers could potentially complement patient stratification strategies. We aim to develop and analytically validate radiological biomarkers that capture immune
cell signatures within IDH-wildtype glioblastoma microenvironment using radiogenomic analysis. Methods: This was a retrospective multicenter study using curated open-access anonymized imaging and genomic data from TCGA-GBM, CPTAC, IvyGAP, REMBRANDT and CGGA
datasets. Imaging data consisted of MRI-based radiomic features extracted from necrotic core, enhancing and edema regions of deep learning-based auto-segmented tumors. Radiomic feature selections were performed using nested cross-validated LASSO. Support vector machine and ensemble models were trained using seventeen immune and
cell-specific score labels extracted from deconvoluted transcriptomic data using pan-cancer and glioblastoma immune signature
matrices as reference standards. Seventeen classifier models trained in three cross-cohort strategies were validated on three held-out
datasets assessing stability and generalizability. Results: One-hundred-and-seventy-six patients were included in the study. The immune-related radiomic signatures obtained after feature selection were shape, first order and higher order radiomic features. Models predicting macrophage subtype immune signature showed stable mean performance on balanced accuracy (0.67) and precision (0.89) metrics for three independent holdout
datasets with ensemble model outperforming support vector machine model. Conclusion: Radiogenomic models non-invasively predicted the macrophage subtype M0 immune signature in IDH-wildtype glioblastoma. These biomarkers have the potential to stratify patients for immunotherapy within prospective glioblastoma clinical trials.
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All authors Prajwal Ghimire, Junjie Li, Liu Yaou, Marc Modat, Thomas Booth
Machine Learning
Generalization Error Bounds for Picard-Type Operator Learning in Nonlinear Parabolic PDEs
Koichi Taniguchi and Sho Sonoda
Operator learning for partial differential equations (PDEs) aims to learn solution operators on infinite-dimensional function spaces from finite-resolution data. In this setting, it is important for the learned model to be discretization-invariant, or resolution-robust, and to reflect PDE-specific structure. It is therefore natural to ask how such structure should be encoded in the model architecture, hypothesis class, or learning procedure. In this paper, we study operator learning for solution operators of nonlinear
parabolic PDEs based on Duhamel–Picard iteration. We formulate Picard iteration as an abstract state-transition model and present a theoretical framework for Picard-type operator learning. We derive implementation-agnostic generalization error bounds that separate the implementation error from the estimation error associated with the abstract state-transition model induced by Picard iteration. A key consequence is that increasing the Picard depth reduces the Picard truncation error without causing an unbounded growth of the
entropy-based estimation error. We also extend the analysis to long-time prediction by rolling out the same learned local model over successive time blocks. Finally, we illustrate the theory for nonlinear heat equations on the
torus using a Picard-type
Fourier neural operator as a concrete implementation.
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Machine Learning
DP-LAC: Lightweight Adaptive Clipping for Differentially Private Federated Fine-tuning of Language Models
Haaris Mehmood, Jie Xu, Karthikeyan Saravanan et al. (+2 more)
Federated learning (FL) enables the collaborative training of large-scale
language models (LLMs) across edge devices while keeping user data on-device. However, FL still exposes sensitive information through client-provided gradients. Differentially private
stochastic gradient descent (DP-SGD) mitigates this risk by clipping each client's contribution to a threshold $C$ and adding noise proportional to $C$. Existing adaptive clipping techniques dynamically adjust $C$ but demand tedious hyperparameter tuning, which can erode the
privacy budget. In this paper, we introduce DP-LAC, a method that first estimates an initial clipping threshold within an order of magnitude of the optimum using private histogram estimation, and then adapts this threshold during training without consuming additional
privacy budget or introducing new hyperparameters. Empirical results show that DP-LAC outperforms both state-of-the-art adaptive clipping methods and vanilla DP-SGD, achieving an average accuracy gain of $6.6\%$.
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All authors Haaris Mehmood, Jie Xu, Karthikeyan Saravanan, Rogier Van Dalen, Mete Ozay
Machine Learning · Cross-listed from cs.AI
E-TCAV: Formalizing Penultimate Proxies for Efficient Concept Based Interpretability
Hasib Aslam, Muhammad Ali Chattha, Muhammad Taha Mukhtar et al. (+3 more)
TCAV (Testing with Concept Activation Vectors) is an interpretability method that assesses the
alignment between the internal representations of a trained neural network and human-understandable, high-level concepts. Though effective, TCAV suffers from significant computational overhead, inter-layer disagreement of TCAV scores, and statistical instability. This work takes a step toward addressing these challenges by introducing E-TCAV, a framework for efficient approximation of TCAV scores, which is based on extensive investigation into three key aspects of the TCAV methodology: 1) the effect of latent classifiers on the stability of TCAV scores, 2) the inter-layer agreement of TCAV scores, and 3) the use of the penultimate layer as a fast proxy for earlier layers for TCAV computation. To ensure a solid foundation for E-TCAV, we conduct extensive evaluations across four different architectures and five
datasets, encompassing problems from both computer
vision and natural
language domains. Our results show that the layers in the final block of the neural network strongly agree with the penultimate layer in terms of the TCAV scores, and the commonly observed variance of the TCAV scores can be attributed to the choice of the latent classifier. Leveraging this inter-layer agreement and the degeneracy of directional sensitivities at the penultimate layer, E-TCAV guarantees linearly scaling speed-ups with respect to the network's size and the number of evaluation samples, marking a step towards efficient model debugging and real-time concept-guided training.
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All authors Hasib Aslam, Muhammad Ali Chattha, Muhammad Taha Mukhtar, Muhammad Imran Malik, Andreas Dengel, Sheraz Ahmed
Machine Learning
Teaching LLMs to See Graphs: Unifying Text and Structural Reasoning
Dario Vajda
Applying Large
Language Models (LLMs) to graph-structured data usually involves multi-step pipelines in which textual node attributes are compressed into single
tokens and further processed by GNNs, discarding most of their semantic content. We introduce the Graph
Transformer Language Model (GTLM), which enables a pretrained LLM to process graph
topology natively and removes this bottleneck entirely. GTLM injects graph-aware
attention biases directly into the LLM's
attention modules, adding only 0.015% structure-related parameters relative to the base model. Training updates only the structural parameters together with a LoRA adapter on the base model. We prove that our bidirectional
attention prefix is permutation-equivariant over nodes and that GTLM reduces exactly to the pretrained model when no graph is present. Having no global node ordering, GTLM shows no positional degradation and does not get lost in the middle: needle-in-a-graph accuracy stays flat from 1k to 64k
tokens and 4x past the training length, while an identically trained flat-text baseline collapses. Comprehensive evaluations show that a GTLM matches or exceeds domain-specific state-of-the-art models on text-attributed graph
benchmarks, GraphRAG on WebQSP, and molecular
benchmarks, while meaningfully improving over strong baselines on GraphQA. We further show that GTLM's
attention heads implicitly learn to simulate message passing, explaining its strength on algorithmic tasks. Together, these results suggest that a minimally adapted pretrained LLM can serve as a general backbone for graph learning.
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Machine Learning
When Normality Shifts: Risk-Aware Test-Time Adaptation for Unsupervised Tabular Anomaly Detection
Wei Huang, Hezhe Qiao, Kailai Zhang et al. (+3 more)
Unsupervised tabular anomaly detection methods typically learn feature patterns from normal samples during training and subsequently identify samples that deviate from these patterns as anomalies during testing. However, in practical scenarios, the limited scale and diversity of training data often lead to an incomplete characterization of normal patterns. While test-time adaptation offers a remedy, its isolated focus on test-time optimization ignores the critical synergy with training-phase learning. Furthermore, indiscriminate adaptation to unlabeled test data inevitably triggers anomaly contamination, preventing the model from fully realizing its discriminative capability between normal and anomalous samples. To address these issues, we propose RTTAD, a Risk-aware Test-time adaptation method for unsupervised Tabular Anomaly Detection. RTTAD holistically tackles normality shifts via a synergistic two-stage mechanism. During training, collaborative dual-task learning captures multi-level representations to establish a robust normal prior. During testing, a Test-Time Contrastive Learning (TTCL) module explicitly accounts for adaptation risk by selectively updating the model using high-confidence pseudo-normal samples while constraining anomalous ones. Additionally, TTCL incorporates a k-nearest neighbor-based contrastive objective to refine
embedding distributions, thereby further enhancing the model's discriminative capacity. Extensive experiments on 15 tabular
datasets demonstrate that RTTAD achieves state-of-the-art overall detection performance.
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All authors Wei Huang, Hezhe Qiao, Kailai Zhang, Zaisheng Ye, Yu-Ming Shang, Xiangling Fu
Machine Learning · Cross-listed from cs.CL
Building Korean linguistic resource for NLU data generation of banking app CS dialog system
Jeongwoo Yoon, On-yu Park, Changhoe Hwang et al. (+3 more)
Natural
language understanding (NLU) is integral to task-oriented dialog systems, but demands a considerable amount of annotated training data to increase the coverage of diverse utterances. In this study, we report the construction of a linguistic resource named FIAD (Financial Annotated
Dataset) and its use to generate a Korean annotated training data for NLU in the banking customer service (CS) domain. By an empirical examination of a corpus of banking app reviews, we identified three linguistic patterns occurring in Korean request utterances: TOPIC (ENTITY, FEATURE), EVENT, and DISCOURSE MARKER. We represented them in LGGs (Local Grammar Graphs) to generate annotated data covering diverse intents and entities. To assess the practicality of the resource, we evaluate the performances of DIET-only (Intent: 0.91 /Topic [entity+feature]: 0.83), DIET+ HANBERT (I:0.94/T:0.85), DIET+ KoBERT (I:0.94/T:0.86), and DIET+ KorBERT (I:0.95/T:0.84) models trained on FIAD-generated data to extract various types of semantic items.
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All authors Jeongwoo Yoon, On-yu Park, Changhoe Hwang, Gwanghoon Yoo, Eric Laporte, Jeesun Nam
Machine Learning · Cross-listed from cs.SE
MARGIN: Margin-Aware Regularized Geometry for Imbalanced Vulnerability Detection
Yuteng Zhang, Huifang Ma, Jiahui Wei et al. (+2 more)
Software vulnerability detection is critical for ensuring software security and reliability. Despite recent advances in deep learning, real-world vulnerability
datasets suffer from two severe challenges: frequency imbalance and difficulty imbalance. We reinterpret these challenges from an
embedding geometry perspective, observing that such imbalances induce
geometric distortions in hyperspherical representation space. To address this issue, we propose MARGIN, a metric-based framework that learns discriminative vulnerability representations through adaptive margin metric learning and hyperspherical prototype modeling. MARGIN dynamically adjusts
geometric regularization according to the distribution structure estimated by the von Mises-Fisher concentration, aligning the probability mass of
embedding distributions with their corresponding Voronoi
cells, thereby reducing
geometric distortion and yielding more stable decision boundaries. Extensive experiments on public vulnerability
datasets show that MARGIN consistently outperforms strong baselines, achieving notable improvements in classification and detection, especially on challenging, imbalanced
datasets. Further analysis demonstrates that MARGIN produces more structured
embedding geometries, improving robustness, interpretability, and generalization.
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All authors Yuteng Zhang, Huifang Ma, Jiahui Wei, Qingqing Li, Yafei Yang
Machine Learning
The Benefits of Temporal Correlations: SGD Learns k-Juntas from Random Walks Efficiently
Elisabetta Cornacchia, Dan Mikulincer and Elchanan Mossel
We study how temporal correlations in the data can make certain sparse learning problems efficiently learnable by gradient-based methods. Our focus is on Boolean k-juntas, a canonical sparse learning problem known to pose barriers for gradient-based methods under independent uniform samples. We show that this picture changes when the samples are generated by a lazy random walk on the hypercube. In this setting, the temporal dependencies can be exploited by a two-layer ReLU network trained using stylized-SGD with a temporal-difference loss, which compares target and predicted increments across consecutive samples. For every fixed k, the resulting sample complexity is essentially linear in the ambient dimension d. By contrast, we show that for large-batch gradient methods using standard convex pointwise losses, temporal correlations do not provide the same advantage.
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Machine Learning
When Does Non-Uniform Replay Matter in Reinforcement Learning?
Michal Korniak, Mikołaj Czarnecki, Yarden As et al. (+3 more)
Modern off-policy reinforcement learning
algorithms often rely on simple uniform replay sampling and it remains unclear when and why non-uniform replay improves over this strong baseline. Across diverse RL settings, we show that the effectiveness of non-uniform replay is governed by three factors: replay volume, the number of replayed transitions per environment step; expected recency, how recent sampled transitions are; and the
entropy of the replay sampling distribution. Our main contribution is clarifying when non-uniform replay is beneficial and providing practical guidance for replay design in modern off-policy RL. Namely, we find that non-uniform replay is most beneficial when replay volume is low, and that high-
entropy sampling is important even at comparable expected recency. Motivated by these findings, we adopt a simple Truncated
Geometric replay that biases sampling toward recent experience while preserving high
entropy and incurring negligible computational overhead. Across large-scale parallel simulation, single-task, and multi-task settings, including three modern
algorithms evaluated on five RL
benchmark suites, this replay sampling strategy improves sample efficiency in low-volume regimes while remaining competitive when replay volume is high.
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All authors Michal Korniak, Mikołaj Czarnecki, Yarden As, Piotr Miłoś, Pieter Abbeel, Michal Nauman
Machine Learning
FORGE: Fragment-Oriented Ranking and Generation for Context-Aware Molecular Optimization
Qingchuan Zhang, He Cao, Hao Li et al. (+6 more)
Molecular optimization seeks to improve a molecule through small structural edits while preserving similarity to the starting compound. Recent
language-model approaches typically treat this task as
prompt-conditioned sequence generation. However, relying on natural
language introduces an inherent data-scaling bottleneck, often leads to chemical
hallucinations, and ignores the strong context dependence of fragment effects. We present FORGE, a two-stage framework that reformulates molecular optimization as context-aware local editing. By utilizing automatically mined, verified low-to-high edit pairs instead of expensive human text annotations, Stage 1 ranks candidate fragments by their property contribution under the full molecular context to inject chemical prior, and Stage 2 generates explicit fragment replacements. Built on a compact 0.6B
language model, FORGE further adapts to unseen black-box objectives through in-context demonstrations. Across
Prompt-MolOpt, PMO-1k and ChemCoTBench, FORGE consistently outperforms prior methods, including substantially larger
language models and graph methods. These results highlight the value of explicit fragment-level supervision as a more easily obtainable, scalable, and
hallucination-less alternative to natural
language training.
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All authors Qingchuan Zhang, He Cao, Hao Li, Yanjun Shao, Zhiyuan Liu, Shihang Wang, Shufang Xie, Shenghua Gao, Xinwu Ye
Machine Learning · Cross-listed from astro-ph.GA
Stellar Age Compression Reshapes Interpretations of the Milky Way Thick-Disk Formation History
Zhipeng Zhang
The formation timescale of the Milky Way thick disk is one of the central debates in
Galactic archaeology. The age-
metallicity relation (AMR), formation timescale, and chemical
evolution gradients are frequently used to infer a rapid assembly, short-timescale enrichment, and bursty formation history of the thick disk. However,
stellar ages are not directly observable, introducing the potential risk that inferred ages may harbor a systematic compression tied to observational quality. In this paper, we use the same
stellar sample and identical physical
covariate matching conditions, but two independent age scales–spectroscopic inferred ages (astroNN) and asteroseismic ages (APOKASC-3)–to compare the observable signatures of the thick-disk formation history. We find that several key observables previously supporting a rapid thick-disk formation are systematically weakened under seismic anchoring: the AMR slope flattens from -3.29 to -1.86 Gyr dex-1 (Delta a = +1.43), the formation timescale widens from 3.04 to 3.55 Gyr, and the peak formation age shifts from 9.1 to 6.0 Gyr. Through transport inversion experiments, we further show that additive noise can only broaden the age distribution and cannot reproduce the above pattern, whereas a compressive transport map (lambda < 1) simultaneously reproduces a narrower age distribution, a steeper AMR, and rapid-formation-like observables. This result indicates that the compression transformation itself is sufficient to generate rapid-formation-friendly observables without requiring an intrinsically bursty formation history. Our findings reveal that statistical interpretations of the Milky Way formation history may depend sensitively on the
stellar age definition itself.
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Machine Learning · Cross-listed from math.OC
Parameterized Complexity of Stationarity Testing for Piecewise-Affine Functions and Shallow CNN Losses
Yuhan Ye
We study the parameterized complexity of testing approximate first-order stationarity at a prescribed point for continuous piecewise-affine (PA) functions, a basic task in nonsmooth optimization. PA functions form a canonical model for nonsmooth stationarity testing and capture the local polyhedral geometry that appears in ReLU-type training losses. Recent work of Tian and So (2025) shows that testing approximate stationarity notions for PA functions is computationally intractable in the worst case, and identifies fixed-dimensional tractability as an open direction. We address this direction from the viewpoint of parameterized complexity, with the ambient dimension $d$ as the parameter. In this paper, we give XP
algorithms in fixed dimension for the tractable sides, and prove W[1]-hardness for the complementary sides. Moreover, lower bounds under the parameterized $k$-Clique hypothesis rule out deterministic
algorithms running in time $\rho(d)s^{o(d)}$ for any computable function $\rho$, where $s$ denotes the total binary encoding length of the instance. As a further consequence, our results yield the corresponding parameterized complexity picture for testing local minimality of continuous PA functions. We also extend our hardness results to a family of shallow ReLU CNN training losses, tested in the trainable weight space. Thus, the same parameterized-complexity picture also appears for simple CNN training losses. Notably, our lower bounds assume that $k$-Clique on $N$-vertex graphs admits no deterministic $\rho(k)N^{o(k)}$-time
algorithm for any computable function $\rho$. The recent refutations of the Exponential Time Hypothesis (ETH) (OpenAI, 2026) and the stronger fine-grained $k$-Clique hypothesis (Vassilevska Williams and Zamir, 2026) do not contradict this assumption.
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Machine Learning · Cross-listed from math.ST
Extended Wasserstein-GAN Approach to Causal Distribution Learning: Density-Free Estimation and Minimax Optimality
Shu Tamano and Masaaki Imaizumi
Distributional causal inference requires estimating not only average treatment effects but also interventional outcome distributions, including
quantiles, tail risks, and policy-dependent uncertainty. As a method for distributional causal inference, generative
adversarial network (GAN)-based counterfactual methods are flexible tools for this task. However, these methods have several limitations. First, the objectives of certain techniques do not coincide with the statistical risk of the identifiable causal target, and therefore provide limited theoretical guarantees regarding estimable counterfactual distributions or optimality. Second, implementing target-design risks under observational sampling can require density-ratio estimation. In this paper, we propose GANICE (GAN for Interventional Conditional Estimation) with several advantages: it (i) specifies the conditional interventional distribution for each treatment–
covariate state as the causal estimation target; (ii) estimates the conditional distribution such that its averaged Wasserstein risk is minimized; (iii) attains minimax optimality. GANICE achieves these advantages through the extended Wasserstein distance and
cell-normalized estimation, with minimax bounds based on Wasserstein GAN oracle inequalities and an anisotropic Assouad construction; Besov theory characterizes the cellwise critics. Our experiments show that GANICE outperforms existing methods on most
benchmarks.
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Machine Learning
Unveiling High-Probability Generalization in Decentralized SGD
Jiahuan Wang, Ping Luo, Ziqing Wen et al. (+2 more)
Decentralized
stochastic gradient descent (D-SGD) is an efficient method for large-scale distributed learning. Existing generalization studies mainly address expected results, achieving rates limited to $\mathcal{O}\left(\frac{1}{\delta \sqrt{mn}}\right)$, where $\delta$ is the confidence parameter, $m$ the number of workers, and $n$ the sample size. When $m=1$, D-SGD reduces to traditional SGD, whose optimal high-probability generalization bound is $\mathcal{O}\left(\frac{1}{\sqrt{n}}\log (1/\delta)\right)$. This discrepancy reveals a gap between high-probability guarantees for SGD and those for D-SGD. To close this, we develop a high-probability learning theory for D-SGD, aiming for the optimal $\mathcal{O}\left(\frac{1}{\sqrt{mn}}\log (1/\delta)\right)$ rate. We refine bounds for D-SGD using pointwise uniform stability in distributed learning-a weaker notion than uniform stability-and analyze them across convex, strongly convex, and non-convex settings. We also provide high-probability results for gradient-based measures in non-convex cases where only local minima exist, and derive optimization error and excess risk bounds. Finally, accounting for communication overhead, we analyze generalization bounds for local models within time-varying frameworks.
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All authors Jiahuan Wang, Ping Luo, Ziqing Wen, Dongsheng Li, Tao Sun
Machine Learning
Task-Aware Calibration: Provably Optimal Decoding in LLMs
Tim Tomov, Dominik Fuchsgruber, Rajeev Verma et al. (+1 more)
LLM decoding often relies on the model's predictive distribution to generate an output. Consequently, misalignment with respect to the true generating distribution leads to suboptimal decisions in practice. While a natural solution is to calibrate the model's output distribution, for LLMs, this is ill-posed at the combinatorially vast level of free-form
language. We address this by building on the insight that in many tasks, these free-form outputs can be interpreted in a semantically meaningful latent structure, for example, discrete class labels, integers, or sets. We introduce task calibration as a paradigm to calibrate the model's predictive distribution in the task-induced latent space. We apply a decision-theoretic result to show that Minimum Bayes Risk (MBR) decoding on the task-calibrated latent distribution is the optimal decoding strategy on latent model beliefs. Empirically, it consistently improves generation quality across different tasks and baselines. We also introduce Task Calibration Error (TCE), an application-aware calibration metric that quantifies the excess loss due to miscalibration. Our work demonstrates that task calibration enables more reliable model decisions across various tasks and applications.
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All authors Tim Tomov, Dominik Fuchsgruber, Rajeev Verma, Stephan Günnemann
Machine Learning
Empty SPACE: Cross-Attention Sparsity for Concept Erasure in Diffusion Models
Nicola Novello and Andrea M. Tonello
Erasing specific concepts from text-to-image
diffusion models is essential for avoiding the generation of copyrighted and explicit content. Closed-form concept erasure methods offer a fast alternative to backpropagation-based techniques, but they become less effective when scaling from smaller models such as Stable
Diffusion 1.5 to larger models like Stable
Diffusion XL. To maintain erasure effectiveness in these larger-scale architectures, we propose SParse cross-
Attention-based Concept Erasure (SPACE). SPACE iteratively modifies the cross-
attention parameters of a model with a closed-form update that jointly induces sparsity and erases target concepts. By concentrating the concept mapping to a lower-dimensional subspace, SPACE achieves superior erasure efficacy compared to dense baselines. Extensive experimental results show improvements in erasure effectiveness and robustness against
adversarial prompts. Furthermore, SPACE achieves 80%-90% cross-
attention sparsity, reducing the storage requirements for saving the modified parameters by 70%, demonstrating its
memory efficiency.
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Machine Learning
Many Needles in a Haystack: Active Hit Discovery for Perturbation Experiments
Andrea Rubbi, Arpit Merchant, Samuel Ogden et al. (+4 more)
High-throughput gene perturbation experiments can test several genetic interventions in parallel, yet experimental budgets remain limited. A central goal is hit discovery: identifying as many perturbations as possible whose phenotypic effect exceeds a predefined threshold. Pure exploration strategies are statistically inefficient, wasting budget on low-value regions.
Bayesian optimization methods offer a principled alternative but target a single global optimum, over-exploiting dominant modes while neglecting other high-value regions. We formalize hit discovery as a sequential experimental design problem and propose Probability-of-Hit, an acquisition function that directly targets threshold exceedance by ranking candidates according to their posterior probability of being a hit. We prove asymptotic optimality of this approach and demonstrate strong empirical performance on both synthetic
benchmarks and real biological immunology
datasets, including up to 6.4% improvement over baselines on the Schmidt IL-2
dataset.
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All authors Andrea Rubbi, Arpit Merchant, Samuel Ogden, Amir Akbarnejad, Pietro Liò, Sattar Vakili, Mo Lotfollahi
Machine Learning
Breaking the Reward Barrier: Accelerating Tree-of-Thought Reasoning via Speculative Exploration
Shuzhang Zhong, Haochen Huang, Shengxuan Qiu et al. (+3 more)
Tree-of-Thought (ToT)
reasoning structures Large
Language Model (LLM) inference as a tree-based search, demonstrating strong potential for solving complex mathematical and programming tasks. However, its efficiency is constrained by the reward dependency barrier – a synchronization bottleneck caused by sequential reward-guided exploration that limits search parallelism and introduces substantial latency. Prior system optimizations, mainly designed for linear Chain-of-Thought (CoT)
reasoning, cannot address these challenges, leaving the efficiency of ToT underexplored. To enhance ToT
reasoning efficiency, we observe that the
reasoning paths can be explored speculatively to break the reward synchronization barrier. Therefore, in this paper, we propose SPEX and introduce three key techniques: (i) intra-query speculative path selection to predict and expand high-potential branches of ToT, (ii) inter-query budget allocation to balance speculative resource allocation across queries dynamically, and (iii) adaptive early termination to prune deep and redundant branches for a skewed search tree. We implement SPEX on top of the SGLang framework and evaluate it across diverse ToT
algorithms and LLMs. Extensive experiments show that SPEX achieves $1.2 \sim 3 \times$ speedup for different ToT
reasoning algorithms. Moreover, SPEX synergizes with
token-level speculative decoding, achieving cumulative speedups of up to $4.1\times$. Ablation studies further confirm the contributions of each technique. Overall, SPEX represents a significant step toward efficient and scalable ToT
reasoning, unlocking the parallelism required for high-performance inference-time scaling for LLMs.
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All authors Shuzhang Zhong, Haochen Huang, Shengxuan Qiu, Pengfei Zuo, Runsheng Wang, Meng Li
Machine Learning · Cross-listed from cs.AI
Jiaxuan Wang, Xuan Ouyang, Zhiyu Chen et al. (+2 more)
On-policy self-
distillation (OPSD) uses a model as its own teacher under privileged context, providing
token-level supervision on the model's own
reasoning trajectories. However, persistent all-
token guidance can degrade training in our math RL setting. Such guidance may unnecessarily constrain non-critical
tokens and reinforce biases induced by privileged information unavailable at inference. Motivated by these risks, we propose STEPS, a selective OPSD framework that controls the location, direction, and duration of
distillation. STEPS identifies critical spans in student rollouts, applies forward KL to key spans or reverse KL to error spans, and gradually transitions to pure GRPO after a short
distillation phase. Across four models from three families, STEPS improves mean accuracy over GRPO. On Qwen3-8B, it raises average accuracy across four math
benchmarks and GPQA-Diamond by an absolute 2.76% with a strong annotator. Using the training policy as its own annotator yields an absolute mean gain of 1.90%, with an estimated 2.7% training-time overhead amortized over 300 steps. Controlled ablations support semantic span selection, class-specific KL directions, and the hand-off to GRPO. Together, these results support brief, targeted self-
distillation as an efficient complement to reward-driven
reasoning training.
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All authors Jiaxuan Wang, Xuan Ouyang, Zhiyu Chen, Yulan Hu, Lan-Zhe Guo
Machine Learning
ProteinOPD: Towards Effective and Efficient Preference Alignment for Protein Design
Yulin Zhang, He Cao, Zihao Jiang et al. (+6 more)
Designing
proteins with desired functions or properties represents a core goal in synthetic biology and drug discovery. Recent advances in
protein language models (PLMs) have enabled the generation of highly designable
protein sequences, while preference
alignment provides a promising way to steer designs toward desired functions and properties. Nevertheless, they often trigger catastrophic forgetting of pretrained knowledge, degrading basic designability and failing to balance multiple competing objectives. To address these issues, we draw inspiration from On-Policy
Distillation (OPD), an advanced post-training method renowned for mitigating catastrophic forgetting through its mode-seeking nature. In this work, we propose ProteinOPD, a multi-objective preference
alignment framework that can effectively balance multiple preference objectives while maintaining the inherent designability of PLMs. ProteinOPD adapts a pretrained PLM into preference-specific teachers and distills their knowledge into a shared student via
token-level OPD on the student's own trajectories. During this process, the student is aligned to a unique normalized
geometric consensus of weighted teachers while ensuring bounded optimization under conflicts. This bridges the gap for OPD in multi-objective/teacher
alignment. Extensive experiments show that ProteinOPD achieves substantial gains on target preference objectives without compromising the designability, with an 8x training speedup over RL-based
alignment competitors.
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All authors Yulin Zhang, He Cao, Zihao Jiang, Chenyi Zi, Zhipeng Zhou, Zijing Liu, Yu Li, Jia Li, Ziqi Gao
Machine Learning
Fix the Loss, Not the Radius: Rethinking the Adversarial Perturbation of Sharpness-Aware Minimization
Jinping Wang, Qinhan Liu, Zhiwu Xie et al. (+1 more)
Sharpness-Aware Minimization (SAM) improves generalization by minimizing the worst-case loss within a fixed parameter-space radius neighborhood. SAM and its variants mainly rely on a first-order linearized surrogate, while flat minima are inherently a second-order (
curvature) notion.We revisit this mismatch and propose Loss-Equated SAM (LE-SAM), which inverts the traditional SAM mechanism that fixed perturbation radius with a fixed loss-space budget,effectively removing gradient-norm-dominated learning signals and shifting optimization toward
curvature-dominated terms. Extensive experiments across diverse
benchmarks and tasks demonstrate the strong generalization ability of LESAM that consistently outperforms SAM and even its variants, achieving the state-of-the-art performance.
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All authors Jinping Wang, Qinhan Liu, Zhiwu Xie, Zhiqiang Gao
Machine Learning
One-Step Graph-Structured Neural Flows for Irregular Multivariate Time Series Classification
Mengzhou Gao, Kaiwei Wang and Pengfei Jiao
Neural Flows efficiently model irregular multivariate time series by directly learning ODE solution trajectories with neural networks, bypassing step-by-step numerical solvers. Despite their efficiency, many existing approaches treat variables independently, leaving inter-variable interactions underexplored. Moreover, their one-step mapping makes interaction modeling inherently challenging, as it removes the iterative refinement of interactions during learning. To address this challenge, we propose one-step Graph-Structured Neural Flows (GSNF), which introduce two auxiliary-trajectory self-supervision strategies to strengthen interaction learning: (i) interaction-aware trajectory generation via re-initialization, which induces trajectory divergence to expose graph-induced interactions, with a theoretically derived lower bound on divergence; and (ii) reverse-time trajectory generation, which enforces forward-backward consistency to regularize graph learning, enabled by flow invertibility. Experiments on five real-world
datasets show that GSNF achieves state-of-the-art classification performance with highly competitive training time and
memory usage.
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Machine Learning · Cross-listed from q-bio.NC
Joint sparse coding and temporal dynamics support context reconfiguration
Qianqian Shi, Yue Che, Faqiang Liu et al. (+6 more)
Adaptive behavior requires the
brain to transition between distinct contexts while maintaining representations of prior experience. The ability to reconfigure neural representations without erasing previously acquired knowledge is central to learning in dynamic environments, yet the neural mechanisms that support this balance remain unclear. Understanding these mechanisms is also critical for addressing catastrophic forgetting in artificial systems designed for lifelong learning. Here, we identify joint sparse coding and temporal dynamics in both the mouse medial prefrontal cortex (mPFC) and computational networks as mechanisms that help preserve prior representations during context transitions. Specifically, sparsity in context-dependent representations reduces cross-context interference, whereas temporal dynamics within the network activity further enhance context separability across time. Strikingly, networks endowed with both properties, such as spiking neural networks, exhibit improved retention during lifelong learning without auxiliary heuristics. These findings establish joint sparse coding and temporal dynamics as a core mechanism supporting flexible context reconfiguration in lifelong learning and, through their activity constraining nature, as an energy-efficient architectural principle for stable adaptation. Together, they provide a mechanistic framework for understanding how the
brain preserves prior knowledge while flexibly adapting to new contexts.
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All authors Qianqian Shi, Yue Che, Faqiang Liu, Hongyi Li, Mingkun Xu, Sandra Reinert, Pieter M. Goltstein, Rong Zhao, Luping Shi
Machine Learning
Balancing Efficiency and Fairness in Traffic Light Control through Deep Reinforcement Learning
Matteo Cederle, Giacomo Scatto and Gian Antonio Susto
Urban traffic congestion presents a significant challenge for modern cities, which impacts mobility and sustainability. Traditional traffic light control systems often fail to adapt to dynamic conditions, leading to inefficiencies. This paper proposes a novel deep reinforcement learning
agent for traffic light control that addresses this limitation by explicitly integrating
fairness considerations for both vehicular and pedestrian traffic. Unlike prior work, our approach dynamically balances these flows based on real-time demand, moving beyond systems focused solely on vehicles. Experimental results demonstrate that our
agent effectively reduces congestion while ensuring equitable service for both the categories of road users. This research contributes to a practical and adaptable solution for intelligent traffic management within the framework of smart cities, paving the way for more efficient and inclusive urban mobility.
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Machine Learning
Hyperparameter Transfer for Dense Associative Memories
Roi Holtzman, Dmitry Krotov and Boris Hanin
Dense Associative
Memory (DenseAM) is a promising family of AI architectures that is represented by a neural network performing temporal dynamics on an energy landscape. While hyperparameter transfer methods are well-studied for feed-forward networks, these methods have not been developed for settings in which weights are shared across layers and within the layer, which is common in DenseAMs. Additionally, DenseAMs utilize rapidly peaking activation functions that are rarely used in feed-forward architectures. The confluence of these aspects makes DenseAM a challenging framework for using existing methods for hyperparameter transfer. Our work initiates the development of hyperparameter transfer methods for this class of models. We derive explicit prescriptions for how the hyperparameters tuned on small models can be transferred to models trained at scale. We demonstrate excellent agreement between these theoretical findings and empirical results.
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Machine Learning · Cross-listed from stat.ML
Coarsening Linear Non-Gaussian Causal Models with Cycles
Francisco Madaleno, Francisco C. Pereira and Alex Markham
Recent work on causal abstraction, in particular graphical approaches focusing on causal structure between clusters of variables, aims to summarize a high-dimensional causal structure in terms of a low-dimensional one. Existing methods for learning such summaries from data assume that both structures are acyclic. Acyclicity is helpful for causal effect identification and
reasoning, but it excludes the many systems of scientific interest that contain feedback loops. We show that in the linear non-Gaussian (LiNG) setting, the acyclicity assumption on the high-dimensional structure can be relaxed while still allowing recovery of a low-dimensional causal directed acyclic graph (DAG). LiNG models with cycles are observationally identifiable only up to an equivalence class whose members differ only within their feedback loops. Our low-dimensional DAG, which is invariant across all members of this class, is therefore identifiable from observational data alone. While existing approaches for learning this equivalence class have exponential time complexity, our low-dimensional summary is learned in worst-case cubic time and comes with finite-sample guarantees. We provide open source code and experiments on synthetic data to corroborate our theoretical results.
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Machine Learning
OUIDecay: Adaptive Layer-wise Weight Decay for CNNs Using Online Activation Patterns
Alberto Fernández-Hernández, Jose I. Mestre, Cristian Pérez-Corral et al. (+3 more)
Weight decay remains one of the most widely used regularization mechanisms for training convolutional neural networks, yet it is still commonly applied as a fixed coefficient shared by all layers throughout training. This uniform treatment ignores that different layers may follow different structural dynamics and therefore may require different regularization strengths. In this work, we propose OUIDecay, an adaptive layer-wise and time-dependent weight decay scheduler for CNNs driven by the Overfitting-Underfitting Indicator (OUI), an activation-based metric previously shown to provide early information about regularization quality. OUIDecay uses a lightweight batch-based formulation of OUI to monitor the structural behavior of each layer online and periodically rescales its weight decay relative to the other layers in the network. Unlike gradient-based adaptive decay methods, our approach relies on functional information extracted from activation patterns and does not require validation data. Experiments on EfficientNet-B0 with Stanford Cars, ResNet50 with Food101, DenseNet121 with CIFAR100, and MobileNetV2 with CIFAR10 show that OUIDecay achieves the best mean best-validation-loss in 7 out of 8 evaluated settings. These results indicate that activation-driven weight decay adaptation is a practical and effective alternative to fixed decay and gradient-based adaptive decay, while keeping the method lightweight and suitable for online use.
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All authors Alberto Fernández-Hernández, Jose I. Mestre, Cristian Pérez-Corral, Manuel F. Dolz, Jose Duato, Enrique S. Quintana-Ortí