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Probabilistic Methods · Monte Carlo and Sampling Methods

Minkyu Kim, Kiyoung Seong, Dongyeop Woo, Sungsoo Ahn, Minsu Kim

We address the challenge of training diffusion models to sample from unnormalized energy distributions in the absence of data, the so-called diffusion samplers. Although these approaches have shown promise, they struggle to scale in more demanding scenarios where energy evaluations are expensive and the sampling space is high-dimensional. To address this limitation, we propose a scalable and sample-efficient framework that properly harmonizes the powerful classical sampling method and the diffusion sampler. Specifically, we utilize Monte Carlo Markov chain (MCMC) samplers with a novelty-based auxiliary energy as a Searcher to collect off-policy samples, using an auxiliary energy function to compensate for exploring modes the diffusion sampler rarely visits. These off-policy samples are then combined with on-policy data to train the diffusion sampler, thereby expanding its coverage of the energy landscape. Furthermore, we identify primacy bias, i.e., the preference of samplers for early experience during training, as the main cause of mode collapse during training, and introduce a periodic re-initialization trick to resolve this issue. Our method significantly improves sample efficiency on standard benchmarks for diffusion samplers and also excels at higher-dimensional problems and real-world molecular conformer generation.

Optimization · Neural Network Optimization

Marlon Becker, Frederick Altrock, Benjamin Risse

The recently proposed optimization algorithm for deep neural networks Sharpness Aware Minimization (SAM) suggests perturbing parameters before gradient calculation by a gradient ascent step to guide the optimization into parameter space regions of flat loss. While significant generalization improvements and thus reduction of overfitting could be demonstrated, the computational costs are doubled due to the additionally needed gradient calculation, making SAM unfeasible in case of limited computationally capacities. Motivated by Nesterov Accelerated Gradient (NAG) we propose Momentum-SAM (MSAM), which perturbs parameters in the direction of the accumulated momentum vector to achieve low sharpness without significant computational overhead or memory demands over SGD or Adam. We evaluate MSAM in detail and reveal insights on separable mechanisms of NAG, SAM and MSAM regarding training optimization and generalization.

Reinforcement Learning · Everything Else

Anastasios Manganaris, Vittorio Giammarino, Ahmed Qureshi

Real-world robotic tasks often require agents to achieve sequences of goals while respecting time-varying safety constraints. However, standard Reinforcement Learning (RL) paradigms are fundamentally limited in these settings. A natural approach to these problems is to combine RL with Linear-time Temporal Logic (LTL), a formal language for specifying complex, temporally extended tasks and safety constraints. Yet, existing RL methods for LTL objectives exhibit poor empirical performance in complex and continuous environments. As a result, no scalable methods support both temporally ordered goals and safety simultaneously, making them ill-suited for realistic robotics scenarios. We propose Automaton Constrained Q-Learning (ACQL), an algorithm that addresses this gap by combining goal-conditioned value learning with automaton-guided reinforcement. ACQL supports most LTL task specifications and leverages their automaton representation to explicitly encode stage-wise goal progression and both stationary and non-stationary safety constraints. We show that ACQL outperforms existing methods across a range of continuous control tasks, including cases where prior methods fail to satisfy either goal-reaching or safety constraints. We further validate its real-world applicability by deploying ACQL on a 6-DOF robotic arm performing a goal-reaching task in a cluttered, cabinet-like space with safety constraints. Our results demonstrate that ACQL is a robust and scalable solution for learning robotic behaviors according to rich temporal specifications.

Deep Learning · Attention Mechanisms

Patrick Lutz, Aditya Gangrade, Hadi Daneshmand, Venkatesh Saligrama

A transformer is merely a stack of learned data–to–data maps—yet those maps can hide rich algorithms. We train a linear, attention-only transformer on millions of masked-block completion tasks: each prompt is a masked low-rank matrix whose missing block may be (i) a scalar prediction target or (ii) an unseen kernel slice for Nyström extrapolation. The model sees only input–output pairs and a mean-squared loss; it is given no normal equations, no handcrafted iterations, and no hint that the tasks are related. Surprisingly, after training, algebraic unrolling reveals the same parameter-free update rule across all three resource regimes (full visibility, bandwidth-limited heads, rank-limited attention). We prove that this rule achieves second-order convergence on full-batch problems, cuts distributed iteration complexity, and remains accurate with compute-limited attention. Thus, a transformer trained solely to patch missing blocks implicitly discovers a unified, resource-adaptive iterative solver spanning prediction, estimation, and Nyström extrapolation—highlighting a powerful capability of in-context learning.

Navdeep Kumar, Adarsh Gupta, Maxence Mohamed ELFATIHI, Giorgia Ramponi, Kfir Y. Levy, Shie Mannor

Robust policy evaluation for non-rectangular uncertainty set is generally NP-hard, even in approximation. Consequently, existing approaches suffer from either exponential iteration complexity or significant accuracy gaps. Interestingly, we identify a powerful class of $L_p$-bounded uncertainty sets that avoid these complexity barriers due to their structural simplicity. We further show that this class can be decomposed into infinitely many \texttt{sa}-rectangular $L_p$-bounded sets and leverage its structural properties to derive a novel dual formulation for $L_p$ robust Markov Decision Processes (MDPs). This formulation reveals key insights into the adversary’s strategy and leads to the \textbf{first polynomial-time robust policy evaluation algorithm} for $L_1$-normed non-rectangular robust MDPs.

Deep Learning · Generative Models and Autoencoders

Adam Stein, Neelay Velingker, Mayur Naik, Eric Wong

Large language models (LLMs) excel at zero-shot inference but continue to struggle with complex, multi-step reasoning. Recent methods that augment LLMs with intermediate reasoning steps such as Chain of Thought (CoT) and Program of Thought (PoT) improve performance but often produce undesirable solutions, especially in algorithmic domains. We introduce Per-Instance Program Synthesis (PIPS), a method that generates and refines programs at the instance level using structural feedback without relying on task-specific guidance or explicit test cases. To further improve performance, PIPS incorporates a confidence metric that dynamically chooses between direct inference and program synthesis on a per-instance basis. Experiments across three frontier LLMs and 30 benchmarks including all tasks of Big Bench Extra Hard (BBEH), visual question answering tasks, relational reasoning tasks, and mathematical reasoning tasks show that PIPS improves the absolute harmonic mean accuracy by up to 8.6\% and 9.4\% compared to PoT and CoT respectively, and reduces undesirable program generations by 65.1\% on the algorithmic tasks compared to PoT with Gemini-2.0-Flash.

Deep Learning · Attention Mechanisms

Zhihao Zhan, Jianan Zhao, Zhaocheng Zhu, Jian Tang

Efficient long-context modeling remains a critical challenge for natural language processing (NLP), as the time complexity of the predominant Transformer architecture scales quadratically with the sequence length. While state-space models (SSMs) offer alternative sub-quadratic solutions, they struggle to capture long-range dependencies effectively. In this work, we focus on analyzing and improving the long-context modeling capabilities of SSMs. We show that the widely used synthetic task, associative recall, which requires a model to recall a value associated with a single key without context, insufficiently represents the complexities of real-world long-context modeling. To address this limitation, we extend the associative recall to a novel synthetic task, joint recall, which requires a model to recall the value associated with a key given in a specified context. Theoretically, we prove that SSMs do not have the expressiveness to solve multi-query joint recall in sub-quadratic time complexity. To resolve this issue, we propose a solution based on integrating SSMs with Context-Dependent Sparse Attention (CDSA), which has the expressiveness to solve multi-query joint recall with sub-quadratic computation. To bridge the gap between theoretical analysis and real-world applications, we propose locality-sensitive Hashing Attention with sparse Key Selection (HAX), which instantiates the theoretical solution and is further tailored to natural language domains. Extensive experiments on both synthetic and real-world long-context benchmarks show that HAX consistently outperforms SSM baselines and SSMs integrated with context-independent sparse attention (CISA). Our code is available at: https://github.com/DeepGraphLearning/HAX.

General Machine Learning · Representation Learning

Miranda Anna Christ, Adrián Csiszárik, Gergely Becsó, Dániel Varga

This paper investigates the structure of linear operators introduced in Hernandez et al. [2023] that decode specific relational facts in transformer language models. We extend their single-relation findings to a collection of relations and systematically chart their organization. We show that such collections of relation decoders can be highly compressed by simple order-3 tensor networks without significant loss in decoding accuracy. To explain this surprising redundancy, we develop a cross-evaluation protocol, in which we apply each linear decoder operator to the subjects of every other relation. Our results reveal that these linear maps do not encode distinct relations, but extract recurring, coarse-grained semantic properties (e.g., country of capital city and country of food are both in the country-of-X property). This property-centric structure clarifies both the operators' compressibility and highlights why they generalize only to new relations that are semantically close. Our findings thus interpret linear relational decoding in transformer language models as primarily property-based, rather than relation-specific.

Ilias Diakonikolas, Chao Gao, Daniel Kane, John Lafferty, Ankit Pensia

We study the task of noiseless linear regression under Gaussian covariates in the presence of additive oblivious contamination. Specifically, we are given i.i.d.\ samples from a distribution $(x, y)$ on $\mathbb R^d \times \mathbb R$ with $x \sim \mathcal N(0,I_d)$ and $y = x^\top \beta + z$, where $z$ is drawn from an unknown distribution that is independent of $x$. Moreover, $z$ satisfies $\mathbb P[z = 0] = \alpha>0$. The goal is to accurately recover the regressor $\beta$ to small $\ell_2$-error. Ignoring computational considerations, this problem is known to be solvable using $O(d/\alpha)$ samples. On the other hand, the best known polynomial-time algorithms require $\Omega(d/\alpha^2)$ samples. Here we provide formal evidence that the quadratic dependence in $1/\alpha$ is inherent for efficient algorithms. Specifically, we show that any efficient Statistical Query algorithm for this task requires VSTAT complexity at least $\tilde{\Omega}(d^{1/2}/\alpha^2)$.

Zhiheng Xi, Guanyu Li, Yutao Fan, Honglin Guo, Yufang Liu, Xiaoran Fan, Jiaqi Liu, dingjinchao, Wangmeng Zuo, Zhenfei Yin 等

In this paper, we introduce BMMR, a large-scale bilingual, multimodal, multi-disciplinary reasoning dataset for the community to develop and evaluate large multimodal models (LMMs). BMMR comprises 100k university-level questions drawn from 300 UNESCO-defined subjects, spanning diverse formats—multiple-choice, fill-in-the-blank, and open-ended QA—and sourced from both print and digital media such as books, exams, and quizzes. All data are curated and filtered via a human-in-the-loop, automated, and scalable framework, and each instance is paired with a high-quality reasoning path. The dataset is organized into two parts: BMMR-Eval that comprises 20k high-quality instances to comprehensively assess LMMs’ knowledge and reasoning across multiple disciplines in both Chinese and English; and BMMR-Train that contains 80k instances to support further research and development, extending the current focus on mathematical reasoning to diverse disciplines and domains. In addition, we propose the process-based multi-discipline BMMR-Verifier for accurate and fine-grained evaluation of LMMs’ reasoning. Extensive experiments reveal that (i) even SOTA models leave substantial headroom on BMMR-Eval; (ii) reasoning models exhibit discipline bias and outperform LMMs only on specific subjects; (iii) open-source models still trail their proprietary counterparts; and (iv) fine-tuning on BMMR-Train narrows this gap. Additionally, we conduct reasoning-chain analyses using BMMR-Verifier and other in-depth studies, uncovering the challenges LMMs currently face in multidisciplinary reasoning. We will release the data and models, and we believe our work can offers valuable insights and contributions to the community.

Applications · Neuroscience, Cognitive Science

Yu Duan, Hamza Chaudhry, Misha B Ahrens, Christopher Harvey, Matthew G Perich, Karl Deisseroth, Kanaka Rajan

Predicting future neural activity is a core challenge in modeling brain dynamics, with applications ranging from scientific investigation to closed-loop neurotechnology. While recent models of population activity emphasize interpretability and behavioral decoding, neural forecasting—particularly across multi-session, spontaneous recordings—remains underexplored. We introduce POCO, a unified forecasting model that combines a lightweight univariate forecaster with a population-level encoder to capture both neuron-specific and brain-wide dynamics. Trained across five calcium imaging datasets spanning zebrafish, mice, and *C. elegans*, POCO achieves state-of-the-art accuracy at cellular resolution in spontaneous behaviors. After pre-training, POCO rapidly adapts to new recordings with minimal fine-tuning. Notably, POCO's learned unit embeddings recover biologically meaningful structure—such as brain region clustering—without any anatomical labels. Our comprehensive analysis reveals several key factors influencing performance, including context length, session diversity, and preprocessing. Together, these results position POCO as a scalable and adaptable approach for cross-session neural forecasting and offer actionable insights for future model design. By enabling accurate, generalizable forecasting models of neural dynamics across individuals and species, POCO lays the groundwork for adaptive neurotechnologies and large-scale efforts for neural foundation models. Code is available at [https://github.com/yuvenduan/POCO](https://github.com/yuvenduan/POCO).

Applications · Chemistry and Drug Discovery

Giannis Daras, Jeffrey Ouyang-Zhang, Krithika Ravishankar, Constantinos Daskalakis, Adam Klivans, Daniel Diaz

We present Ambient Protein Diffusion, a framework for training protein diffusion models that generates structures with unprecedented diversity and quality. State-of-the-art generative models are trained on computationally derived structures from AlphaFold2 (AF), as experimentally determined structures are relatively scarce. The resulting models are therefore limited by the quality of synthetic datasets. Since the accuracy of AF predictions degrades with increasing protein length and complexity, de novo generation of long, complex proteins remains challenging. Ambient Protein Diffusion overcomes this problem by treating low-confidence AF structures as corrupted data. Rather than simply filtering out low-quality AF structures, our method adjusts the diffusion objective for each structure based on its corruption level, allowing the model to learn from both high and low quality structures. Empirically, ambient protein diffusion yields major improvements: on proteins with 700 residues, diversity increases from 45% to 85% from the previous state-of-the-art, and designability improves from 70% to 88%.

Data-centric AI · Everything Else

Seong Hyeon Park, Jinwoo Shin

Understanding the 3D world from 2D monocular videos is a crucial ability for AI. Recently, to tackle this underdetermined task, end-to-end 3D geometry priors have been sought after, such as pre-trained point map models at scale. These models enable robust 3D understanding from casually taken videos, providing accurate object shapes disentangled from uncertain camera parameters. However, they still struggle when affected by object deformation and dynamics, failing to establish consistent correspondence over the frames. Furthermore, their architectures are typically limited to pairwise frame processing, which is insufficient for capturing complex motion dynamics over extended sequences. To address these limitations, we introduce Track3R, a novel framework that integrates a new architecture and task to jointly predict point map and motion trajectories across multiple frames from video input. Specifically, our key idea is modeling two disentangled trajectories for each point: one representing object motion and the other camera poses. This design not only can enable understanding of the 3D object dynamics, but also facilitates the learning of more robust priors for 3D shapes in dynamic scenes. In our experiments, Track3R demonstrates significant improvements in a joint point mapping and 3D motion estimation task for dynamic scenes, such as 25.8% improvements in the motion estimation, and 15.7% in the point mapping accuracy.

Deep Learning · Graph Neural Networks

Yeonjun In, Kanghoon Yoon, Sukwon Yun, Kibum Kim, Sungchul Kim, Chanyoung Park

In real-world applications, node features in graphs often contain noise from various sources, leading to significant performance degradation in GNNs. Although several methods have been developed to enhance robustness, they rely on the unrealistic assumption that noise in node features is independent of the graph structure and node labels, thereby limiting their applicability. To this end, we introduce a more realistic noise scenario, dependency-aware noise on graphs (DANG), where noise in node features create a chain of noise dependencies that propagates to the graph structure and node labels. We propose a novel robust GNN, DA-GNN, which captures the causal relationships among variables in the data generating process (DGP) of DANG using variational inference. In addition, we present new benchmark datasets that simulate DANG in real-world applications, enabling more practical research on robust GNNs. Extensive experiments demonstrate that DA-GNN consistently outperforms existing baselines across various noise scenarios, including both DANG and conventional noise models commonly considered in this field.

Probabilistic Methods · Monte Carlo and Sampling Methods

Zijing Ou, Ruixiang Zhang, Yingzhen Li

Sampling from unnormalised discrete distributions is a fundamental problem across various domains. While Markov chain Monte Carlo offers a principled approach, it often suffers from slow mixing and poor convergence. In this paper, we propose Discrete Neural Flow Samplers (DNFS), a trainable and efficient framework for discrete sampling. DNFS learns the rate matrix of a continuous-time Markov chain such that the resulting dynamics satisfy the Kolmogorov equation. As this objective involves the intractable partition function, we then employ control variates to reduce the variance of its Monte Carlo estimation, leading to a coordinate descent learning algorithm. To further facilitate computational efficiency, we propose locally equivaraint Transformer, a novel parameterisation of the rate matrix that significantly improves training efficiency while preserving powerful network expressiveness. Empirically, we demonstrate the efficacy of DNFS in a wide range of applications, including sampling from unnormalised distributions, training discrete energy-based models, and solving combinatorial optimisation problems.

Deep Learning · Generative Models and Autoencoders

Yuanpei Gao, Qi Yan, Yan Leng, Renjie Liao

While deep learning methods have achieved strong performance in time series prediction, their black-box nature and inability to explicitly model underlying stochastic processes often limit their robustness handling non-stationary data, especially in the presence of abrupt changes. In this work, we introduce Neural MJD, a neural network based non-stationary Merton jump diffusion (MJD) model. Our model explicitly formulates forecasting as a stochastic differential equation (SDE) simulation problem, combining a time-inhomogeneous Itô diffusion to capture non-stationary stochastic dynamics with a time-inhomogeneous compound Poisson process to model abrupt jumps. To enable tractable learning, we introduce a likelihood truncation mechanism that caps the number of jumps within small time intervals and provide a theoretical error bound for this approximation. Additionally, we propose an Euler-Maruyama with restart solver, which achieves a provably lower error bound in estimating expected states and reduced variance compared to the standard solver. Experiments on both synthetic and real-world datasets demonstrate that Neural MJD consistently outperforms state-of-the-art deep learning and statistical learning methods. Our code is available at https://github.com/DSL-Lab/neural-MJD.

Applications · Language, Speech and Dialog

Tongyao Zhu, Qian Liu, Haonan Wang, Shiqi Chen, Xiangming Gu, Tianyu Pang, Min-Yen Kan

Recent advancements in LLM pretraining have featured ever-expanding context windows to process longer sequences. However, our controlled study reveals that models pretrained with shorter context windows consistently outperform their long-context counterparts under a fixed token budget. This finding motivates us to explore an optimal context window scheduling strategy to better balance long-context capability with pretraining efficiency. To this end, we propose SkyLadder, a simple yet effective approach that implements a short-to-long context window transition. SkyLadder preserves strong standard benchmark performance, while matching or exceeding baseline results on long-context tasks. Through extensive experiments, we pretrain 1B-parameter models (up to 32K context) and 3B-parameter models (8K context) on 100B tokens, demonstrating that SkyLadder yields consistent gains of up to 3.7% on common benchmarks, while achieving up to 22% faster training speeds compared to baselines.

Deep Learning · Algorithms

Felix Dangel, Tim Siebert, Marius Zeinhofer, Andrea Walther

Computing partial differential equation (PDE) operators via nested backpropagation is expensive, yet popular, and severely restricts their utility for scientific machine learning. Recent advances, like the forward Laplacian and randomizing Taylor mode automatic differentiation (AD), propose forward schemes to address this. We introduce an optimization technique for Taylor mode that 'collapses' derivatives by rewriting the computational graph, and demonstrate how to apply it to general linear PDE operators, and randomized Taylor mode. The modifications simply require propagating a sum up the computational graph, which could---or should---be done by a machine learning compiler, without exposing complexity to users. We implement our collapsing procedure and evaluate it on popular PDE operators, confirming it accelerates Taylor mode and outperforms nested backpropagation.

Applications

Mingwei Zhan, Ruijie Zhao, Xianwen Deng, Zhi Xue, Qi Li, Zhuotao Liu, Guang Cheng, Ke Xu

Network traffic classification is essential for network management and security. In recent years, deep learning (DL) algorithms have emerged as essential tools for classifying complex traffic. However, they rely heavily on high-quality labeled training data. In practice, traffic data is often noisy due to human error or inaccurate automated labeling, which could render classification unreliable and lead to severe consequences. Although some studies have alleviated the label noise issue in specific scenarios, they are difficult to generalize to general traffic classification tasks due to the inherent semantic complexity of traffic data. In this paper, we propose FlowRefiner, a robust and general traffic classification framework against label noise. FlowRefiner consists of three core components: a traffic semantics-driven noise detector, a confidence-guided label correction mechanism, and a cross-granularity robust classifier. First, the noise detector utilizes traffic semantics extracted from a pre-trained encoder to identify mislabeled flows. Next, the confidence-guided label correction module fine-tunes a label predictor to correct noisy labels and construct refined flows. Finally, the cross-granularity robust classifier learns generalized patterns of both flow-level and packet-level, improving classification robustness against noisy labels. We evaluate our method on four traffic datasets with various classification scenarios across varying noise ratios. Experimental results demonstrate that FlowRefiner mitigates the impact of label noise and consistently outperforms state-of-the-art baselines by a large margin. The code is available at https://github.com/NSSL-SJTU/FlowRefiner.

Computer Vision · Everything Else

Yangshi Ge, Yiwei Bao, Feng Lu

In recent years, face-based deep-learning gaze estimation methods have achieved significant advancements. However, while face images provide supplementary information beneficial for gaze inference, the substantial extraneous information they contain also increases the risk of overfitting during model training and compromises generalization capability. To alleviate this problem, we propose the 3DPE-Gaze framework, explicitly modeling 3D facial priors for feature decoupling and generalized gaze estimation. The 3DPE-Gaze framework consists of two core modules: the 3D Geometric Prior Module (3DGP) incorporating the FLAME model to parameterize facial structures and gaze-irrelevant facial appearances while extracting gaze features; the Semantic Concept Alignment Module (SCAM) separates gaze-related and unrelated concepts through CLIP-guided contrastive learning. Finally, the 3DPE-Gaze framework combines 3D facial landmark as prior for generalized gaze estimation. Experimental results show that 3DPE-Gaze outperforms existing state-of-the-art methods on four major cross-domain tasks, with particularly outstanding performance in challenging scenarios such as lighting variations, extreme head poses, and glasses occlusion.