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Applications · Chemistry, Physics, and Earth Sciences

Philipp Höllmer, Stefano Martiniani

Continuous-time generative models for crystalline materials enable inverse materials design by learning to predict stable crystal structures, but incorporating explicit target properties into the generative process remains challenging. Policy-gradient reinforcement learning (RL) provides a principled mechanism for aligning generative models with downstream objectives but typically requires access to the score, which has prevented its application to flow-based models that learn only velocity fields. We introduce Open Materials Generation with Inference-time Reinforcement Learning (OMatG-IRL), a policy-gradient RL framework that operates directly on the learned velocity fields and eliminates the need for the explicit computation of the score. OMatG-IRL leverages stochastic perturbations of the underlying generation dynamics preserving the baseline performance of the pretrained generative model while enabling exploration and policy-gradient estimation at inference time. Using OMatG-IRL, we present the first application of RL to crystal structure prediction (CSP). Our method enables effective reinforcement of an energy-based objective while preserving diversity through composition conditioning, and it achieves performance competitive with score-based RL approaches. Finally, we show that OMatG-IRL can learn time-dependent velocity-annealing schedules, enabling accurate CSP with order-of-magnitude improvements in sampling efficiency and, correspondingly, reduction in generation time.

General Machine Learning · Causality

Alpar Turkoglu, Muralikrishnna Guruswamy Sethuraman, Faramarz Fekri

Learning causal relationships between variables from data is a fundamental research area with many applications across disciplines. Most of the existing causal discovery algorithms rely on the assumptions that (i) the underlying system is acyclic, (ii) the exogenous noise variables are Gaussian, and (iii) that the intervention targets for the data generating experiments are known. While these assumptions simplify the analysis, they are violated in real-life systems. Most existing methods that address these issues either assume the underlying model is linear or are constrained to operate in limited interventional settings. To that end, we propose SCOUT, a novel causal discovery framework to learn nonlinear causal cyclic relationships from soft interventional data with unknown targets. Our main approach maximizes the data log-likelihood to recover the graph structure, using two normalizing-flow architectures—contractive residual flows and neural spline flows. By conducting experiments on synthetic and real-world data, we show that SCOUT outperforms state-of-the-art methods in both causal graph and unknown target recovery across various interventional and noise settings.

Deep Learning · Large Language Models

Jie Wu, Haoran Ma, Shisong Tang, Yulin Xu, Xiaoyu Kang, Jiechao Gao

Generating runnable front-end code from UI screenshots is a long-standing goal in automated software engineering. Existing MLLM-based methods predominantly focused on HTML/CSS, leaving multi-framework generation for React/Vue/Angular underexplored. Naively modifying prompts leads to substantial performance gaps across multi-framework and highly framework-specific error modes. To address this, we propose \textbf{MulFCoder}, a framework-conditioned multi-agent method that explicitly encodes framework constraints to bring multi-framework differences into a decidable rule space. MulFCoder orchestrates four agents: Grounder constructs an ElementTable, ContentTable, and macro-layout regions from detected UI elements; Planner builds a DOM-like hierarchical layout tree, produces a task schedule, and derives a framework-specific file Contract; Writer generates structured file writes or patches within a restricted edit window; Judger enforces lightweight, framework-conditioned FastGate constraints to accept or reject updates and trigger bounded repairs, preventing drift and deadlocks without expensive builds. Experiments demonstrate that MulFCoder substantially improves multi-framework compilation success and reduces framework-specific errors, with particularly pronounced gains on constraint-heavy frameworks.

Social Aspects · Privacy

Xutong Mu, Yanbiao Ma, Jia Shi, Xueli Geng, Fengkai Xiang, Tao Zhang, Ke Cheng, Yulong Shen

Federated Learning (FL) faces significant challenges due to domain heterogeneity, where data from different clients exhibit substantial statistical shifts that hinder the generalization of the global model. Although existing methods attempt to mitigate this by exchanging class prototypes, they fall short by representing an entire class's complex distribution with a single point. This oversimplification disregards the rich structural information within the data, especially across diverse domains. To address this limitation, we propose a paradigm shift from point-based representation to structure-based knowledge transfer. We introduce Federated Manifold Learning (FML), a novel framework that leverages perceptual manifolds—the intrinsic geometric structures of classes in the feature space—as rich knowledge carriers. In FML, clients transmit compressed manifolds, which are adaptively fused on the server using an attention-based Manifold Mutual Learning (MML) mechanism. This process enables domain-specific structures to learn from each other, creating a unified yet flexible global convergence target. Manifold-guided local training, enforced by a manifold approximation loss and a separation loss, further aligns local models with this global structure. Extensive experiments on the Digits and Office31 benchmarks demonstrate that FML substantially outperforms state-of-the-art methods, achieving accuracy improvements of up to 6.48%.

Deep Learning · Large Language Models

Shawn Im, Federico Danieli, Skyler Seto, Barry-John Theobald, Katherine Metcalf

Direct Alignment Algorithms (DAAs) such as DPO have become a common way to post-train and align LLMs with human preferences. However, DAAs have been observed to over-optimize their implicit reward model and decrease the likelihood of preferred responses. This results in a decrease in the total likelihood assigned to responses seen in the preference dataset, potentially resulting in undesirable behavior. To counteract this undesired side-effect of DAAs, we examine the effect of using objectives that add a regularization term to maintain the total length-normalized probabilities of the chosen and rejected responses. To better understand over-optimization, we investigate how response likelihood changes are distributed over the tokens with and without regularization. We find that a significant portion of the likelihood changes are due to a small set of outlier tokens, which explains how DAAs improve generation quality despite decreasing the likelihoods of chosen responses. We apply the proposed regularization to reference-based (DPO) and reference-free (SimPO) methods and find (1) improved trade-offs between generation quality and general benchmark capability and (2) improvements in reward modeling across datasets. For example, on Llama-3.1-8B-Instruct, we see both a >20\% relative increase in AlpacaEval2 scores and >9\% relative performance gains on general benchmarks. Additionally, we find that the added regularization term effectively mitigates the amount of displacement within preferred responses overall, and for the outlier tokens specifically, by utilizing low-likelihood tokens.

Deep Learning · Robustness

Xin Wei, Qin Yang, Hongji Zhao, Fei Gao, Mingrui Zhu, Nannan Wang, Xinbo Gao

While data augmentation is essential for robust point cloud recognition, conventional spatial mixup strategies often compromise geometric integrity by generating physically unrealistic samples. To overcome this limitation, we propose PSMix, which shifts the mixing paradigm to the spectral domain via the Spherical Harmonic Transform. Instead of simple coordinate interpolation, PSMix performs a rotation-aware hierarchical mixing on spectral coefficients. This approach explicitly preserves global structural properties while diversifying local details, achieving a balance that spatial methods struggle to maintain. Complementing this, we introduce an adversarial rotation optimization strategy to enforce invariance against challenging orientations. Extensive experiments on ModelNet-C and ScanObjectNN-C demonstrate that PSMix achieves state-of-the-art robustness, while also serving as an orthogonal plug-in that further boosts the performance of existing spatial strategies.

Deep Learning · Large Language Models

Hyungjoo Chae, Jungsoo Park, Alan Ritter

Training autonomous web agents is fundamentally limited by the environments they learn from: real-world websites are unsafe to explore, hard to reset, and rarely provide verifiable feedback. We propose VeriEnv, a framework that treats language models as environment creators, automatically cloning real-world websites into fully executable, verifiable synthetic environments. By exposing controlled internal access via a Python SDK, VeriEnv enables agents to self-generate tasks with deterministic, programmatically verifiable rewards, eliminating reliance on heuristic or LLM-based judges. This design decouples agent learning from unsafe real-world interaction while enabling scalable self-evolution through environment expansion. Through experiments on web agent benchmarks, we show that agents trained with VeriEnv generalize to unseen websites, achieve site-specific mastery through self-evolving training, and benefit from scaling the number of training environments.

Deep Learning · Large Language Models

Yao Guan, Lin Wang, Zhihui Lu, Ziyi Wang, Wenzhu Yan, Qiang Duan

Despite the remarkable progress of Large Language Model (LLM) based Multi-Agent Systems, most research focuses on optimizing coordination topology while largely underexploring the equally critical problem: how to transmit and optimize messages among agents effectively? Current communication schemes typically rely on the direct concatenation of first-order neighbor responses, which induces a restricted evidence receptive field and leads to the dilution of crucial insights over multi-hop paths. To address these limitations, we propose the Multi-Order Communication (MOC) scheme, which reconstructs the inter-agent communication to capture multi-hop dependencies and incorporates a structural message consolidation strategy to ensure efficiency. Specifically, we formalize the communication mechanism to construct a structured multi-order evidence stream, and subsequently design a Semantic-Topological Merging algorithm to optimize semantic fidelity within token constraints. Extensive experiments across six diverse datasets and LLM backbones of varying parameter scales demonstrate that MOC consistently improves task performance and reduces communication costs.

Theory · Learning Theory

Doron Cohen, Aryeh Kontorovich, Yonatan Livshitz

We present improved bounds for estimating discrete probability distributions under the $\ell_{\infty}$ norm. These include minimax bounds in expectation and high-probability tail bounds. We resolve some of the open questions posed in Kontorovich and Painsky (JMLR, 2025) --- including a fully empirical version of the tightest risk bound they presented and identifying the form of the worst-case extremal distribution. Encouraging empirical results are reported as well.

Applications · Chemistry, Physics, and Earth Sciences

Zhang Yiyuan, Cailong Hua, Vinitendra Singh, Joseph Muretta, James Ervasti, Murti Salapaka

Many fundamental biological processes are governed by mechanical forces, with proteins acting as the key molecular mediators. Elucidating how protein unfolding responds to force is critical for understanding the mechano-pathologies, such as cardiomyopathy and muscular dystrophy. While the unfolding trajectories measured by Single-Molecule Force Spectroscopy (SMFS) map the instantaneous force response against molecular extension, its broader application is limited by time-consuming data collection and high operational costs. Here, we present the first scalable generative diffusion framework for full unfolding trajectory prediction, which integrates protein encoders for multi-scale conditioning. Beyond establishing the field's first systematic benchmark using existing models, we propose GenUnfold, a novel physics-guided diffusion model that combines global coevolutionary context with a local mechanical representation of the protein. The representation is derived from a novel physics-biased attention mechanism, which steers the generative diffusion process by modeling dynamic residue dependencies as a function of both structural topology and interaction stiffness. The benchmark for this task is built upon the biomolecule stretching database and several representative baseline models. Empirical results demonstrate that GenUnfold achieves state-of-the-art performance, reducing distributional error (FID) by 30\% and 54\% compared to pretrained Evolutionary Scale Model (ESM)-2 and standard transformer, respectively. Beyond statistical curve similarity, GenUnfold demonstrates superior physical consistency; in downstream mechanical property prediction, it reduces prediction errors for unfolding force and energy distributions by 6\% and 36\% over the ESM-2 baseline. These results indicate that while existing generative AI approaches can alleviate the need for predicting representative force curves, GenUnfold further improves performance by leveraging the synergy between protein structure and evolutionary information. By enabling proteome-wide screening to identify mechanical candidates before costly physical validation, our approach is promising to accelerate the discovery of force-targeted therapeutics.

Deep Learning · Large Language Models

Amit Dhurandhar, Vijil Chenthamarakshan, Dennis Wei, Tejaswini Pedapati, Karthikeyan Natesan Ramamurthy, Rahul Nair

Transformers are arguably the preferred architecture for language generation. In this paper, inspired by continued fractions, we introduce a new function class for generative modeling. The architecture family implementing this function class is named CoFrGeNets - Continued Fraction Generative Networks. We design novel architectural components based on this function class that can replace Multi-head Attention and Feed-Forward Networks in Transformer blocks while requiring much fewer parameters. We derive custom gradient formulations to optimize the proposed components more accurately and efficiently than using standard PyTorch-based gradients. Our components are a plug-in replacement requiring little change in training or inference procedures that have already been put in place for Transformer-based models thus making our approach easy to incorporate in large industrial workflows. We experiment on two very different transformer architectures GPT2-xl (1.5B) and Llama3 (3.2B), where the former we pre-train on OpenWebText and GneissWeb, while the latter we pre-train on the docling data mix which consists of nine different datasets. Results show that the performance on downstream classification, Q\& A, reasoning and text understanding tasks of our models is competitive and sometimes even superior to the original models with two thirds to half the parameters and shorter pre-training time. We believe that future implementations customized to hardware will further bring out the true potential of our architectures.

Social Aspects · Accountability, Transparency, and Interpretability

Shichang Zhang, Hongzhe Du, Jiaqi Ma, Himabindu Lakkaraju

Modern AI systems are typically developed through multiple stages-pretraining, fine-tuning rounds, and subsequent adaptation or alignment, where each stage builds on the previous ones and updates the model in distinct ways. This raises a critical question of accountability: when a deployed model succeeds or fails, which stage is responsible, and to what extent? We pose the accountability attribution problem for tracing model behavior back to specific stages of the model development process. To address this challenge, we propose a general framework that answers counterfactual questions about stage effects: how would the model's behavior have changed if the updates from a particular stage had not occurred? Within this framework, we introduce estimators that efficiently quantify stage effects without retraining the model, accounting for both the data and key aspects of model optimization dynamics, including learning rate schedules, momentum, and weight decay. We demonstrate that our approach successfully quantifies the accountability of each stage to the model's behavior. Based on the attribution results, our method can identify and remove spurious correlations learned during image classification and text toxicity detection tasks that were developed across multiple stages. Our approach provides a practical tool for model analysis and represents a significant step toward more accountable AI development.

Applications · Chemistry, Physics, and Earth Sciences

Montgomery Bohde, Hongxuan Liu, Mrunali Manjrekar, Magdalena Lederbauer, Shuiwang Ji, Runzhong Wang, Connor Coley

Tandem mass spectrometry is prominent in scientific discovery workflows for identifying unknown small molecules, yet high-throughput structural elucidation remains challenging. While recent autoregressive and graph diffusion models have shown promise in *de novo* elucidation, performance remains limited by poor scalability during both training and inference time. In this work, we present FRIGID, a framework with a novel diffusion language model that generates molecular structures conditioned on mass spectra via intermediate fingerprint representations and determined chemical formulae, training at the scale of hundreds of millions of unlabeled structures. We then demonstrate how forward fragmentation models enable inference-time scaling by identifying spectrum-inconsistent fragments and refining them through targeted remasking and denoising. While FRIGID already achieves strong performance with its diffusion base, inference-time scaling significantly improves its accuracy, surpassing 15% Top-1 accuracy on the challenging MassSpecGym benchmark and more than doubling the Top-1 accuracy of the leading methods on NPLIB1. Further empirical analyses show that FRIGID exhibits log-linear performance scaling with increasing inference-time compute, opening a promising new direction for continued improvements in *de novo* structural elucidation.

Theory · Learning Theory

Benjamin Dupuis, Tyler Farghly, Maxime Haddouche, Alain Oliviero Durmus, Umut Simsekli

Diffusion models (DMs) are a state-of-the-art generative method to approximately sample from an unknown distribution. Their training and evaluation primarily rely on an Evidence Lower Bound (ELBO), which relates the Kullback-Leibler (KL) divergence of model samples to the score matching loss along the path, which serves as a tractable surrogate. The difference between sample quality and the score matching loss produced by this bound leads to the score matching gap, which is known to be tight in the worst-case but not descriptive of sample quality in general. In this work, we provide a theoretical analysis of this gap, developing tighter bounds for three metrics: KL divergence, reverse KL divergence, and Wasserstein distance, effectively exploiting the regularity of the class of score estimators. Our results suggest that the quality of the score approximation has more impact on closing the score matching gap for low noise scales. To obtain these bounds, our key technical insight is to exploit the contraction properties of the backward processes. In particular, we rely on entropy flows, logarithmic Sobolev inequalities and reflection couplings, rigorously linking the ergodicity of the Langevin diffusion to the score matching gap problem.

Deep Learning · Generative Models and Autoencoders

Zehua Chen, Yucheng Yang, Binjie Yuan, Kaiwen Zheng, Jun Liu, Jun Zhu

Guidance methods, e.g., classifier-free guidance (CFG) and auto-guidance (AG), have distinctively improved noise-to-data diffusion generation results. Recently, bridge models have been proposed, which present a data-to-data sampling process to exploit instructive information from clean prior representation, showing advantages on the tasks such as image-to-image translation. In this work, we design a custom guidance method for bridge models, named prior guidance (PG). Different from highlighting condition alignment (CFG) or score accuracy (AG), we training-freely construct an additional weak prior for the pre-trained bridge models, and extrapolate the estimation results to further encourage prior exploitation. Then, we analyze the underlying mechanism of prior exploitation in bridge process and design frequency-modulated prior guidance (FMPG), which tailors the guidance scale to low- and high-frequency bands coherent with bridge generative dynamics. Finally, considering the challenge of bridge models on image in-painting, we develop a cascaded guidance framework, CFG-FMPG, that first generates a coarse prior under global semantic condition and then refines it with FMPG, naturally fulfilling their complementary advantages along sampling trajectory. Experiments conducted on strong pre-trained bridge models, DDBM and DBIM, valid the consistent improvement achieved by our training-free design.

Applications · Everything Else

Hinal Jajal, Michał Mucha, Charles Sweat, Chris Pulman, Charlie Flanagan, Peter Anderson

Prior work on judgmental forecasting with large language models (LLMs) has focused on broad, mixed‑topic question banks and shallow context (e.g., short news snippets). We study a specialized, high‑stakes financial setting: forecasting M\&A outcomes for merger arbitrage. Using rich textual evidence, with context engineering informed by veteran merger-arb specialists, we construct an LLM‑based forecasting system and finetune the model using outcome-conditioned gold reasoning traces. The system outputs probabilistic forecasts over closing at announced terms, higher bid, and deal termination. On an out-of-sample set of more than 400 large deals spanning 42 countries, our finetuned system outperforms a variety of frontier models and market-based baselines, using a Brier score weighted by the P\&L impact of each deal.

Applications · Everything Else

Shuai Xiao, Weijun Fang, Qiaosheng Zhang

While Transformer-based architectures have revolutionized neural decoding, existing models often treat codes as generic sequences, ignoring their inherent algebraic properties. In this paper, we take a step toward bridging these two domains by proposing a novel decoding approach that integrates the algebraic structure of cyclic codes into Transformer-based decoders. Leveraging the inherent cyclic properties, we introduce interpretable error correction patterns and inter-node relationship hypotheses that link the structural characteristics of the codes to the model parameters. Building on these insights, we design a plug-and-play, flexibly deployable decoding method tailored for cyclic codes. Experimental results show that our method achieves an average reduction in bit error rate (BER) by an order of magnitude, while also reducing the total number of parameters by approximately 97%. Additional comparative experiments validate our proposed conjectures and highlight a promising pathway for bridging classical coding theory and modern Transformer-based decoding architectures.

Deep Learning · Generative Models and Autoencoders

Ganggui Ding, Xiaogang Xu, Hao Chen, Chunhua Shen

Generative video diffusion models have shown strong robustness to large motion and occlusions for video frame interpolation (VFI). However, their inference efficiency lags significantly behind learning-based methods due to the structural redundancy of pairwise inference and the procedural latency of multi-step iterative denoising. To address these limitations, we propose SpeedVFI, a one-step diffusion framework that achieves dual efficiency improvements by interpolating the entire video sequence in a single forward pass to eliminate pairwise overhead, and distilling the generation trajectory into a one-step denoising process to bypass iterative latency. To support this high-efficiency architecture, we introduce temporal RoPE alignment to ensure temporal consistency across the unified sequence, and noise-centric partial attention to reduce computational overhead while preserving global context. Extensive experiments demonstrate that SpeedVFI accelerates diffusion-based VFI by orders of magnitude while maintaining competitive quantitative and visual quality.

General Machine Learning · Representation Learning

Viktoria Schuster, Sana Tonekaboni, Caroline Uhler

Determining the complexity, or Intrinsic Dimension (ID), of data is fundamental to efficient and interpretable representation learning. This is particularly challenging in multi-modal settings when trying to learn disentangled representations for shared and private information. Existing techniques leave a critical gap: they are often static, uni-modal, or in the case of contrastive methods, adapt only to the shared ID implicitly. We introduce Fidelity-Guided Rank Optimization (FiGuRO), a framework for learning the complete ID structure of uni- and multi-modal data. FiGuRO learns the dimensions of low-rank projections using truncated singular value decomposition and an algorithm that determines when to reduce or increase dimensionalities and in which latent spaces. Disentanglement of shared and private information arises as an emergent property of this optimization, eliminating the need for complex auxiliary loss functions. We demonstrate that FiGuRO outperforms existing ID estimation techniques and is more robust to hyperparameter changes. Across simulations and real-world data, FiGuRO captures distinct ID scales and varying subspace ratios, and decomposes shared and private information successfully. Furthermore, we show that FiGuRO can be applied to modern uni-modal pretrained models, enabling efficient, post-hoc disentanglement of multi-modal representations.

Theory · Deep Learning

Xingyu Lyu, Qianqian Xu, zhiyong yang, Peisong Wen, Qingming Huang

Gated Linear Units (GLU) and their variants are widely adopted in modern open-source large language model architectures and consistently outperform their non-gated counterparts, yet the underlying reasons for this advantage remain unclear. In this work, we study GLU by analyzing two-layer networks in the neural tangent kernel (NTK) regime. Our analysis reveals that the GLU structure reshapes the NTK spectrum, leading to a smaller condition number and a more compact eigenvalue distribution. Building on this finding, we further analyze the resulting training dynamics and show how the reshaped spectrum leads to faster convergence of GLU models, including a characteristic loss-crossing phenomenon observed between GLU and non-GLU models. Finally, we empirically observe that GLU has limited impact in reducing the stochastic error on various models, including ViT and GPT-2, suggesting that its primary benefit lies in accelerating optimization rather than reducing the stochastic error.