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Deep Learning · Generative Models and Autoencoders

François Cornet, Federico Bergamin, Arghya Bhowmik, Juan Garcia-Lastra, Jes Frellsen, Mikkel Schmidt

Generative modeling of crystalline materials using diffusion models presents a series of challenges: the data distribution is characterized by inherent symmetries and involves multiple modalities, with some defined on specific manifolds. Notably, the treatment of fractional coordinates representing atomic positions in the unit cell requires careful consideration, as they lie on a hypertorus. In this work, we introduce Kinetic Langevin Diffusion for Materials (KLDM), a novel diffusion model for crystalline materials generation, where the key innovation resides in the modeling of the coordinates. Instead of resorting to Riemannian diffusion on the hypertorus directly, we generalize Trivialized Diffusion Model (TDM) to account for the symmetries inherent to crystals. By coupling coordinates with auxiliary Euclidean variables representing velocities, the diffusion process is now offset to a flat space. This allows us to effectively perform diffusion on the hypertorus while providing a training objective that accounts for the periodic translation symmetry of the true data distribution. We evaluate KLDM on both Crystal Structure Prediction (CSP) and De-novo Generation (DNG) tasks, demonstrating its competitive performance with current state-of-the-art models.

Deep Learning · Graph Neural Networks

Nannan Wu, Yuming Huang, Yiming Zhao, Jie Chen, Wenjun Wang

Subgraph representation learning has attracted growing interest due to its wide applications in various domains. However, existing methods primarily focus on local neighborhood structures while overlooking the significant impact of global structural information, in particular the influence of multi-hop neighbors beyond immediate neighborhoods. This presents two key challenges: how to effectively capture the structural relationships between distant nodes, and how to prevent excessive aggregation of global structural information from weakening the discriminative ability of subgraph representations.To address these challenges, we propose GPEN (Global Position Encoding Network). GPEN leverages a hierarchical tree structure to encode each node's global position based on its path distance to the root node, enabling a systematic way to capture relationships between distant nodes. Furthermore, we introduce a boundary-aware convolution module that selectively integrates global structural information while maintaining the unique structural patterns of each subgraph. Extensive experiments on eight public datasets identify that GPEN significantly outperforms state-of-the-art methods in subgraph representation learning.

Applications · Computer Vision

Hui Nie, Zhao Zhang, Yutao Cheng, Maoke Yang, Gonglei Shi, Qingsong Xie, Jie Shao, Xinglong Wu

We propose Layer Decomposition of Graphic Designs (LDGD), a novel vision task that converts composite graphic design (e.g., posters) into structured representations comprising ordered RGB-A layers and metadata. By transforming visual content into structured data, LDGD facilitates precise image editing and offers significant advantages for digital content creation, management, and reuse. This task presents two core challenges: (1) predicting the attribute information (metadata) of each layer, and (2) recovering the occluded regions within overlapping layers to enable high-fidelity image reconstruction. To address this, we present the Decompose Layer Model (DeaM), a large unified multimodal model that integrates a conjoined visual encoder, a language model, and a condition-aware RGB-A decoder. DeaM adopts a two-stage processing pipeline: first generates layer-specific metadata containing information such as spatial coordinates and quantized encodings, and then reconstructs pixel-accurate layer images using a condition-aware RGB-A decoder. Beyond full decomposition, the model supports interactive decomposition via textual or point-based prompts. Extensive experiments demonstrate the effectiveness of the proposed method. The code is accessed at https://github.com/witnessai/DeaM.

Deep Learning · Large Language Models

Rishabh Tiwari, Haocheng Xi, Aditya Tomar, Coleman Hooper, Sehoon Kim, Maxwell Horton, Mahyar Najibi, Michael Mahoney, Kurt Keutzer, Amir Gholaminejad

Large Language Models (LLMs) are increasingly being deployed on edge devices for long-context settings, creating a growing need for fast and efficient long-context inference. In these scenarios, the Key-Value (KV) cache is the primary bottleneck in terms of both GPU memory and latency, as the full KV cache must be loaded for each decoding step. While speculative decoding is a widely accepted technique to accelerate autoregressive decoding, existing methods often struggle to achieve significant speedups due to inefficient KV cache optimization strategies and result in low acceptance rates. To address these challenges, we propose a novel self-speculative decoding framework, QuantSpec, where the draft model shares the architecture of the target model but employs a hierarchical 4-bit quantized KV cache and 4-bit quantized weights for acceleration. QuantSpec maintains high acceptance rates ($>$90\%) and reliably provides consistent end-to-end speedups upto $\sim2.5\times$, outperforming other self-speculative decoding methods that use sparse KV cache for long-context LLM inference. QuantSpec also reduces the memory requirements by $\sim 1.3\times$ compared to these alternatives.

Applications · Everything Else

Konrad Mundinger, Max Zimmer, Aldo Kiem, Christoph Spiegel, Sebastian Pokutta

We demonstrate how neural networks can drive mathematical discovery through a case study of the Hadwiger-Nelson problem, a long-standing open problem at the intersection of discrete geometry and extremal combinatorics that is concerned with coloring the plane while avoiding monochromatic unit-distance pairs. Using neural networks as approximators, we reformulate this mixed discrete-continuous geometric coloring problem with hard constraints as an optimization task with a probabilistic, differentiable loss function. This enables gradient-based exploration of admissible configurations that most significantly led to the discovery of two novel six-colorings, providing the first improvement in thirty years to the off-diagonal variant of the original problem (Mundinger et al., 2024a). Here, we establish the underlying machine learning approach used to obtain these results and demonstrate its broader applicability through additional numerical insights.

Applications · Computer Vision

Ye Wang, Sipeng Zheng, Bin Cao, Qianshan Wei, Weishuai Zeng, Qin Jin, Zongqing Lu

Inspired by the recent success of LLMs, the field of human motion understanding has increasingly shifted toward developing large motion models. Despite some progress, current efforts remain far from achieving truly generalist models, primarily due to the lack of massive high-quality data. To address this gap, we present MotionLib, the first million-level dataset for motion generation, which is at least 15$\times$ larger than existing counterparts and enriched with hierarchical text descriptions. Using MotionLib, we train a large motion model named Being-M0, demonstrating robust performance across a wide range of human activities, including unseen ones.Through systematic investigation, for the first time, we highlight the importance of scaling both data and model size for advancing motion generation, along with key insights to achieve this goal. To better integrate the motion modality, we propose Motionbook, an innovative motion encoding approach including (1) a compact yet lossless feature to represent motions; (2) a novel 2D lookup-free motion tokenizer that preserves fine-grained motion details while expanding codebook capacity, significantly enhancing the representational power of motion tokens. We believe this work lays the groundwork for developing more versatile and powerful motion generation models in the future. For further details, visit https://beingbeyond.github.io/Being-M0/.

Social Aspects · Safety

Ada Tur, Nicholas Meade, Xing Han Lù, Alejandra Zambrano, Arkil Patel, Esin Durmus, Spandana Gella, Karolina Stanczak, Siva Reddy

LLM-based agents are becoming increasingly proficient at solving web-based tasks. With this capability comes a greater risk of misuse for malicious purposes, such as posting misinformation in an online forum or selling illicit substances on a website. To evaluate these risks, we propose SafeArena, a benchmark focused on the deliberate misuse of web agents. SafeArena comprises 250 safe and 250 harmful tasks across four websites. We classify the harmful tasks into five harm categories---misinformation, illegal activity, harassment, cybercrime, and social bias, designed to assess realistic misuses of web agents. We evaluate leading LLM-based web agents, including GPT-4o, Claude-3.5 Sonnet, Qwen-2-VL 72B, and Llama-3.2 90B, on our benchmark. To systematically assess their susceptibility to harmful tasks, we introduce the Agent Risk Assessment framework that categorizes agent behavior across four risk levels. We find agents are surprisingly compliant with malicious requests, with GPT-4o and Qwen-2 completing 34.7% and 27.3% of harmful requests, respectively. Our findings highlight the urgent need for safety alignment procedures for web agents.

Applications · Health / Medicine

Yishan Shen, Yuyang Ye, Hui Xiong, Yong Chen

Dynamic treatment regimes (DTRs) are critical to precision medicine, optimizing long-term outcomes through personalized, real-time decision-making in evolving clinical contexts, but require careful supervision for unsafe treatment risks. Existing efforts rely primarily on clinician-prescribed gold standards despite the absence of a known optimal strategy, and predominantly using structured EHR data without extracting valuable insights from clinical notes, limiting their reliability for treatment recommendations. In this work, we introduce SAFER, a calibrated risk-aware tabular-language recommendation framework for DTR that integrates both structured EHR and clinical notes, enabling them to learn from each other, and addresses inherent label uncertainty by assuming ambiguous optimal treatment solution for deceased patients. Moreover, SAFER employs conformal prediction to provide statistical guarantees, ensuring safe treatment recommendations while filtering out uncertain predictions. Experiments on two publicly available sepsis datasets demonstrate that SAFER outperforms state-of-the-art baselines across multiple recommendation metrics and counterfactual mortality rate, while offering robust formal assurances. These findings underscore SAFER’s potential as a trustworthy and theoretically grounded solution for high-stakes DTR applications.

Deep Learning · Graph Neural Networks

Zhiqiang Wang, Xiaoyi Wang, Jianqing Liang

Graph Neural Ordinary Differential Equations (GODE) integrate the Variational Autoencoder (VAE) framework with differential equations, effectively modeling latent space uncertainty and continuous dynamics, excelling in graph data evolution and incompleteness. However, existing GODE face challenges in capturing time-varying relationships and nonlinear node state evolution, which limits their ability to model complex dynamic graphs. To address these issues, we propose the ControlSynth Graph ODE (CSG-ODE). In the VAE encoding phase, CSG-ODE introduces an information transmission-based inter-node importance weighting mechanism, integrating it with latent correlations to guide adaptive graph convolutional recurrent networks for temporal node embedding. During decoding, CSG-ODE employs ODE to model node dynamics, capturing nonlinear evolution through sub-networks with nonlinear activations. For scenarios or prediction tasks that require stability, we extend CSG-ODE to stable CSG-ODE (SCSG-ODE) by constraining weight matrices to learnable anti-symmetric forms, theoretically ensuring enhanced stability. Experiments on traffic, motion capture, and simulated physical systems datasets demonstrate that CSG-ODE outperforms state-of-the-art GODE, while SCSG-ODE achieves both superior performance and optimal stability.

Applications · Everything Else

Kai Müller, Martin Wenzel, Tobias Windisch

Many production lines require active control mechanisms, such as adaptive routing, worker reallocation, and rescheduling, to maintain optimal performance. However, designing these control systems is challenging for various reasons, and while reinforcement learning (RL) has shown promise in addressing these challenges, a standardized and general framework is still lacking. In this work, we introduce LineFlow, an extensible, open-source Python framework for simulating production lines of arbitrary complexity and training RL agents to control them. To demonstrate the capabilities and to validate the underlying theoretical assumptions of LineFlow, we formulate core subproblems of active line control in ways that facilitate mathematical analysis. For each problem, we provide optimal solutions for comparison. We benchmark state-of-the-art RL algorithms and show that the learned policies approach optimal performance in well-understood scenarios. However, for more complex, industrial-scale production lines, RL still faces significant challenges, highlighting the need for further research in areas such as reward shaping, curriculum learning, and hierarchical control.

Applications · Neuroscience, Cognitive Science

Yi Xie, Jaedong Hwang, Carlos Brody, David Tank, Ila R. Fiete

Brains excel at robust decision-making and data-efficient learning. Understanding the architectures and dynamics underlying these capabilities can inform inductive biases for deep learning. We present a multi-region brain model that explores the normative role of structured memory circuits in a spatially embedded binary decision-making task from neuroscience.We counterfactually compare the learning performance and neural representations of reinforcement learning (RL) agents with brain models of different interaction architectures between grid and place cells in the entorhinal cortex and hippocampus, coupled with an action-selection cortical recurrent neural network. We demonstrate that a specific architecture--where grid cells receive and jointly encode self-movement velocity signals and decision evidence increments--optimizes learning efficiency while best reproducing experimental observations relative to alternative architectures.Our findings thus suggest brain-inspired structured architectures for efficient RL. Importantly, the models make novel, testable predictions about organization and information flow within the entorhinal-hippocampal-neocortical circuit: we predict that grid cells must conjunctively encode position and evidence for effective spatial decision-making, directly motivating new neurophysiological experiments.

Social Aspects · Security

Ankit Pratap Singh, Ahmed Abbasi, Namrata Vaswani

This work has two contributions. First, we introduce a provably secure (Byzantine-resilient) sample- and communication-efficient alternating gradient descent (GD) and minimization based algorithms for solving the federated low rank matrix completion (LRMC) problem. This involves learning a low rank (LR) matrix from a small subset of its entries. Second, we extend our ideas to show how a special case of our algorithms also solves another partly-decoupled vertically federated LR matrix learning problem, that is LR column-wise sensing (LRCS), also referred to as multi-task linear representation learning in the literature. Finally, we also show how our results can be extended for the LR phase retrieval problem. In all problems, we consider column-wise or vertical federation, i.e. each node observes a small subset of entries of a disjoint column sub-matrix of the entire LR matrix. For the LRMC problem, horizontal federation is equivalent since it is symmetric across rows and columns; while for the other two it is not. In all problems, the data at different nodes is heterogeneous (not identically distributed), making it harder to obtain provable guarantees.

Deep Learning · Large Language Models

Ren-Biao Liu, Anqi Li, ChaodingYang, Hui Sun, Ming Li

Large Language Models (LLMs) have demonstrated exceptional performance in code generation, becoming increasingly vital for software engineering and development. Recently, Chain-of-Thought (CoT) has proven effective for complex tasks by prompting LLMs to reason step-by-step and provide a final answer.However, research on *how LLMs learn to reason with CoT data for code generation* remains limited.In this work, we revisit classic CoT training, which typically learns reasoning steps before the final answer.We synthesize a dataset to separate the CoT process from code solutions and then conduct extensive experiments to study how CoT works in code generation empirically.We observe counterintuitive phenomena, suggesting that the traditional training paradigm may not yield benefits for code generation. Instead, training LLMs to generate code first and then output the CoT to explain reasoning steps for code generation is more effective.Specifically, our results indicate that a 9.86% relative performance improvement can be achieved simply by changing the order between CoT and code. Our findings provide valuable insights into leveraging CoT to enhance the reasoning capabilities of CodeLLMs and improve code generation.

Deep Learning · Large Language Models

Han Zhong, Zikang Shan, Guhao Feng, Wei Xiong, Xinle Cheng, Li Zhao, Di He, Jiang Bian, Liwei Wang

In the classical Reinforcement Learning from Human Feedback (RLHF) framework, Proximal Policy Optimization (PPO) is employed to learn from sparse, sentence-level rewards---a challenging scenario in traditional deep reinforcement learning. Despite the great successes of PPO in the alignment of state-of-the-art closed-source large language models (LLMs), its open-source implementation is still largely sub-optimal, as widely reported by numerous research studies. To address these issues, we introduce a framework that models RLHF problems as a Markov decision process (MDP), enabling the capture of fine-grained token-wise information. Furthermore, we provide theoretical insights that demonstrate the superiority of our MDP framework over the previous sentence-level bandit formulation. Under this framework, we introduce an algorithm, dubbed as Reinforced Token Optimization (\texttt{RTO}), which learns the token-wise reward function from preference data and performs policy optimization based on this learned token-wise reward signal. Theoretically, \texttt{RTO} is proven to have the capability of finding the near-optimal policy sample-efficiently. For its practical implementation, \texttt{RTO} innovatively integrates Direct Preference Optimization (DPO) and PPO. DPO, originally derived from sparse sentence rewards, surprisingly provides us with a token-wise characterization of response quality, which is seamlessly incorporated into our subsequent PPO training stage. We conduct extensive experiments to evaluate \texttt{RTO} against PPO and other direct preference learning algorithms. The results highlight the effectiveness of RTO, with the algorithm outperforming PPO by 7.5 points on the AlpacaEval 2 benchmark and by 4.1 points on Arena-Hard. Our code and models are available at \href{https://github.com/zkshan2002/RTO}{https://github.com/zkshan2002/RTO}.

Theory · Game Theory

Yi Feng, Kaito Fujii, EFSTRATIOS PANTELEIMON SKOULAKIS, Xiao Wang, Volkan Cevher

Since Polyak's pioneering work, heavy ball (HB) momentum has been widely studied in minimization. However, its role in min-max games remains largely unexplored. As a key component of practical min-max algorithms like Adam, this gap limits their effectiveness. In this paper, we present a continuous-time analysis for HB with simultaneous and alternating update schemes in min-max games. Locally, we prove *smaller* momentum enhances algorithmic stability by enabling local convergence across a wider range of step sizes, with alternating updates generally converging faster. Globally, we study the implicit regularization of HB, and find *smaller* momentum guides algorithms trajectories towards shallower slope regions of the loss landscapes, with alternating updates amplifying this effect. Surprisingly, all these phenomena differ from those observed in minimization, where *larger* momentum yields similar effects. Our results reveal fundamental differences between HB in min-max games and minimization, and numerical experiments further validate our theoretical results.

Deep Learning · Large Language Models

Xingwu Sun, Shuaipeng Li, Ruobing Xie, Weidong Han, Kan Wu, Zhen Yang, Yixing Li, An Wang, SHUAI LI, Jinbao Xue 等

Low-precision training is considered an effective strategy for reducing both training and downstream inference costs. Previous scaling laws for precision mainly focus on integer quantization, which pay less attention to the constituents in floating-point (FP) quantization, and thus cannot well fit the LLM losses in this scenario. In contrast, while FP quantization training is more commonly implemented in production, it's research has been relatively superficial. In this paper, we thoroughly explore the effects of FP quantization targets, exponent bits, mantissa bits, and the calculation granularity of the scaling factor in FP quantization training performance of LLM models.In addition to an accurate FP quantization unified scaling law, we also provide valuable suggestions for the community: (1) Exponent bits contribute slightly more to the model performance than mantissa bits. We provide the optimal exponent-mantissa bit ratio for different bit numbers, which is available for future reference by hardware manufacturers; (2) We discover the formation of the critical data size in low-precision LLM training. Too much training data exceeding the critical data size will inversely bring in degradation of LLM performance; (3) The optimal FP quantization precision is directly proportional to the computational power, but within a wide computational power range. We estimate that the best cost-performance precision should lie between 4-8 bits.

Optimization

Lisa Jin, Jianhao Ma, Zechun Liu, Andrey Gromov, Aaron Defazio, Lin Xiao

We develop a novel optimization method for quantization-aware training (QAT). Specifically, we show that convex, piecewise-affine regularization (PAR) can effectively induce neural network weights to cluster towards discrete values. We minimize PAR-regularized loss functions using an aggregate proximal stochastic gradient method (AProx) and prove that it enjoys last-iterate convergence. Our approach provides an interpretation of the straight-through estimator (STE), a widely used heuristic for QAT, as the asymptotic form of PARQ. We conduct experiments to demonstrate that PARQ obtains competitive performance on convolution- and transformer-based vision tasks.

Applications · Chemistry, Physics, and Earth Sciences

Haoyang Jiang, Jindong Wang, Xingquan Zhu, Yi He

Graph Neural Networks (GNNs) often struggle in preserving high-frequency components of nodal signals when dealing with directed graphs. Such components are crucial for modeling flow dynamics, without which a traditional GNN tends to treat a graph with forward and reverse topologies equal. To make GNNs sensitive to those high-frequency components thereby being capable to capture detailed topological differences, this paper proposes a novel framework that combines 1) explicit difference matrices that model directional gradients and 2) implicit physical constraints that enforce messages passing within GNNs to be consistent with natural laws. Evaluations on two real-world directed graph data, namely, water flux network and urban traffic flow network, demonstrate the effectiveness of our proposal.

Deep Learning · Large Language Models

Shiwei Li, Xiandi Luo, Xing Tang, Haozhao Wang, Hao Chen, weihongluo, Yuhua Li, xiuqiang He, Ruixuan Li

Low-rank adaptation (LoRA) is a widely used parameter-efficient fine-tuning method. In standard LoRA layers, one of the matrices, $A$ or $B$, is initialized to zero, ensuring that fine-tuning starts from the pretrained model. However, there is no theoretical support for this practice.In this paper, we investigate the impact of non-zero initialization on LoRA's fine-tuning dynamics from an infinite-width perspective. Our analysis reveals that, compared to zero initialization, simultaneously initializing $A$ and $B$ to non-zero values improves LoRA's robustness to suboptimal learning rates, particularly smaller ones. Further analysis indicates that although the non-zero initialization of $AB$ introduces random noise into the pretrained weight, it generally does not affect fine-tuning performance. In other words, fine-tuning does not need to strictly start from the pretrained model.The validity of our findings is confirmed through extensive experiments across various models and datasets. The code is available at https://github.com/Leopold1423/non_zero_lora-icml25.

Deep Learning · Generative Models and Autoencoders

Charles O'Neill, Alim Gumran, David Klindt

A recent line of work has shown promise in using sparse autoencoders (SAEs) to uncover interpretable features in neural network representations. However, the simple linear-nonlinear encoding mechanism in SAEs limits their ability to perform accurate sparse inference. Using compressed sensing theory, we prove that an SAE encoder is inherently insufficient for accurate sparse inference, even in solvable cases. We then decouple encoding and decoding processes to empirically explore conditions where more sophisticated sparse inference methods outperform traditional SAE encoders. Our results reveal substantial performance gains with minimal compute increases in correct inference of sparse codes. We demonstrate this generalises to SAEs applied to large language models, where more expressive encoders achieve greater interpretability. This work opens new avenues for understanding neural network representations and analysing large language model activations.