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Applications · Chemistry and Drug Discovery

Jingxiang Qu, Wenhan Gao, Ruichen Xu, Yi Liu

Gaussian Probability Path based Generative Models (GPPGMs) generate data by reversing a stochastic process that progressively corrupts samples with Gaussian noise. Despite state-of-the-art results in 3D molecular generation, their deployment is hindered by the high cost of long generative trajectories, often requiring hundreds to thousands of steps during training and sampling. In this work, we propose a principled method, named GAGA, to improve generation efficiency without sacrificing training granularity or inference fidelity of GPPGMs. Our key insight is that different data modalities obtain sufficient Gaussianity at markedly different steps during the forward process. Based on this observation, we analytically identify a characteristic step at which molecular data attains sufficient Gaussianity, after which the trajectory can be replaced by a closed-form Gaussian approximation. Unlike existing accelerators that coarsen or reformulate trajectories, our approach preserves full-resolution learning dynamics while avoiding redundant transport through truncated distributional states. Experiments on 3D molecular generation benchmarks demonstrate that our GAGA achieves substantial improvement on both generation quality and computational efficiency.

General Machine Learning · Representation Learning

Runjian Chen, Hang Zhang, Avinash Ravichandran, Hyoungseob Park, Wenqi Shao, Alex Wong, Ping Luo

Unsupervised 3D representation learning reduces the burden of labeling multimodal 3D data for fusion perception tasks. Among different pre-training paradigms, differentiable-rendering-based methods have shown most promise. However, existing works separately conduct pre-training for each modalities due to computational costs of processing large point clouds with images. As such, mutual benefit of high-level semantics (from image) and 3D structure (from point cloud) has not been exploited. To address this gap, we propose a joint unsupervised differentiable-rendering-based pre-training method for images and point clouds, termed CLAP, short for Curvature sampLing and leArnable Prototype. Specifically, our method overcomes the computational hurdle by Curvature Sampling to select the more informative points/pixels for pre-training. To uncover the performance benefits brought by their complementarity, we propose to use learnable prototypes to represent parts of the 3D scenes in a common feature space and an Expectation-Maximization training scheme to associate embeddings of each modality to prototypes. We further propose a swapping prediction loss that explores their interplay through prototypes along with a Gram Matrix Regularization term to maintain training stability. Experiments on NuScenes and Waymo datasets show that CLAP achieves up to 100% more performance gain as compared to previous SOTA pre-training methods. Codes and models will be released.

Haochen Wang, Yuhao Wang, Tao Zhang, Yikang Zhou, Yanwei Li, Jiacong Wang, Jiani zheng, Ye Tian, Jiahao Meng, Zilong Huang 等

While Multimodal Large Language Models (MLLMs) excel at holistic understanding, they struggle with the dense world, i.e., complex scenes requiring fine-grained analysis of intricate details and object inter-relationships. Region-level MLLMs have been a promising step. However, previous attempts are generally optimized to understand given regions in isolation, neglecting crucial global contexts. To address this, we introduce Grasp Any Region (GAR) for comprehensive region-level visual understanding. Empowered by an effective RoI-aligned feature replay technique, GAR supports (1) precise perception by leveraging necessary global contexts, and (2) modeling interactions between multiple prompts. Together, it then naturally achieves (3) advanced compositional reasoning to answer specific free-form questions about any region, shifting the paradigm from passive description to active dialogue. Moreover, we construct GARBench, which not only provides a more accurate evaluation of single-region comprehension, but also, more importantly, measures interactions and complex reasoning across multiple regions. Empirically, GAR-1B not only maintains the state-of-the-art captioning capabilities, e.g., outperforming DAM-3B +4.5 on DLC-Bench, but also excels at modeling relationships between multiple prompts with advanced comprehension capabilities, even surpassing InternVL3-78B on GARBench-VQA. More importantly, our zero-shot GAR-8B even outperforms in-domain VideoRefer-7B on VideoRefer-BenchQ, indicating its strong comprehension capabilities can be easily transferred to videos. Code and data will be released to the community.

Optimization · Everything Else

Kwanhee Lee, Hyeondo Jang, Dongyeop Lee, Dan Alistarh, Namhoon Lee

Neural network pruning is a promising technique to mitigate the excessive computational and memory requirements of large language models (LLMs). Despite its promise, however, progress in this area has diminished, as conventional methods are seemingly unable to surpass moderate sparsity levels (50-60\%) without severely degrading model accuracy. This work breaks through the current impasse, presenting a principled and effective method called $ \text{Elsa}$, which achieves extreme sparsity levels of up to 90\% while retaining high model fidelity. This is done by identifying several limitations in current practice, all of which can be traced back to their reliance on a surrogate objective formulation. $ \text{Elsa}$ tackles this issue directly and effectively via standard and well-established constrained optimization techniques based on ADMM. Our extensive experiments across a wide range of models and scales show that $ \text{Elsa}$ achieves substantial improvements over existing methods; e.g., it achieves 7.8$ \times$ less perplexity than the best existing method on LLaMA-2-7B at 90\% sparsity. Moreover, we show that $ \text{Elsa}$ remains stable even at extreme sparsity (e.g., 95\%), yielding up to $\times$3.98 inference speedup and $\times$7.80 memory compression over its dense counterpart. We also present $ \text{Elsa}_ {-L}$, a quantized variant that scales to extremely large models (27B), and establish its theoretical convergence guarantees. These results highlight meaningful progress in advancing the frontier of LLM sparsity, while promising that significant opportunities for further advancement may remain in directions that have so far attracted limited exploration.

Theory · Everything Else

Fan Wang, Kyle Ritscher, Yik Lun Kei, Xin Ma, OSCAR HERNAN MADRID PADILLA

We study offline change point localization and inference in dynamic multilayer random dot product graphs (D-MRDPGs), where at each time point, a multilayer network is observed with shared node latent positions and time-varying, layer-specific connectivity patterns. We propose a novel two-stage algorithm that combines seeded binary segmentation with low-rank tensor estimation, and establish its consistency in estimating both the number and locations of change points. Furthermore, we derive the limiting distributions of the refined estimators under both vanishing and non-vanishing jump regimes. To the best of our knowledge, this is the first result of its kind in the context of dynamic network data. We also develop a fully data-driven procedure for constructing confidence intervals. Extensive numerical experiments demonstrate the superior performance and practical utility of our methods compared to existing alternatives.

Reinforcement Learning · Online

Seokbin Song, Youngsik Yoon, Siwei Wang, Wei Chen, Jungseul Ok

Combinatorial online learning is a fundamental task for selecting the optimal action (or super arm) as a combination of base arms in sequential interactions with systems providing stochastic rewards. It is applicable to diverse domains such as robotics, social advertising, network routing, and recommendation systems. In many real-world scenarios, we often encounter rising rewards, where playing a base arm not only provides an instantaneous reward but also contributes to the enhancement of future rewards, e.g., robots improving through practice and social influence strengthening in the history of successful recommendations. Crucially, these enhancements may propagate to multiple super arms that share the same base arms, introducing dependencies beyond the scope of existing bandit models. To address this gap, we introduce the Combinatorial Rising Bandit (CRB) framework and propose a provably efficient and empirically effective algorithm, Combinatorial Rising Upper Confidence Bound (CRUCB). We empirically demonstrate the effectiveness of CRUCB in realistic deep reinforcement learning environments and synthetic settings, while our theoretical analysis establishes tight regret bounds. Together, they underscore the practical impact and theoretical rigor of our approach.

Applications · Genetics, Cell Biology, Health, etc

Zhao Yang, Yi Duan, Jiwei Zhu, Ying Ba, Chuan Cao, Bing Su

Gene expression prediction, which predicts mRNA expression levels from DNA sequences, presents significant challenges. Previous works often focus on extending input sequence length to locate distal enhancers, which may influence target genes from hundreds of kilobases away. Our work first reveals that for current models, long sequence modeling can decrease performance. Even carefully designed algorithms only mitigate the performance degradation caused by long sequences. Instead, we find that proximal multimodal epigenomic signals near target genes prove more essential. Hence we focus on how to better integrate these signals, which has been overlooked. We find that different signal types serve distinct biological roles, with some directly marking active regulatory elements while others reflect background chromatin patterns that may introduce confounding effects. Simple concatenation may lead models to develop spurious associations with these background patterns. To address this challenge, we propose Prism, a framework that learns multiple combinations of high-dimensional epigenomic features to represent distinct background chromatin states and uses backdoor adjustment to mitigate confounding effects. Our experimental results demonstrate that proper modeling of multimodal epigenomic signals achieves state-of-the-art performance using only short sequences for gene expression prediction.

Theory · Probabilistic Methods

Navid Akhavan Attar, Hesam Asadollahzadeh, Ling Luo, Uwe Aickelin

The merit of Conformal Prediction (CP), as a distribution-free framework for uncertainty quantification, depends on generating prediction sets that are efficient, reflected in small average set sizes, while adaptive, meaning they signal uncertainty by varying in size according to input difficulty. A central limitation for deep conformal classifiers is that the nonconformity scores are derived from softmax outputs, which can be unreliable indicators of how certain the model truly is about a given input, sometimes leading to overconfident misclassifications or undue hesitation. In this work, we argue that this unreliability can be inherited by the prediction sets generated by CP, limiting their capacity for adaptiveness. We propose a new approach that leverages information from the pre-softmax logit space, using the Helmholtz Free Energy as a measure of model uncertainty and sample difficulty. By reweighting nonconformity scores with a monotonic transformation of the energy score of each sample, we improve their sensitivity to input difficulty. Our experiments with four state-of-the-art score functions on multiple datasets and deep architectures show that this energy-based enhancement improves the adaptiveness of the prediction sets, leading to a notable increase in both efficiency and adaptiveness compared to baseline nonconformity scores, without introducing any post-hoc complexity.

Applications · Everything Else

Daniel Paleka, Shashwat Goel, Jonas Geiping, Florian Tramer

Large language models (LLMs) have recently been applied to forecasting tasks, with some works claiming these systems match or exceed human performance. In this paper, we argue that, as a community, we should be careful about such conclusions as evaluating LLM forecasters presents unique challenges. We identify two broad categories of issues: (1) difficulty in trusting evaluation results due to many forms of temporal leakage, and (2) difficulty in extrapolating from evaluation performance to real-world forecasting. Through systematic analysis and concrete examples from prior work, we demonstrate how evaluation flaws can raise concerns about current and future performance claims. We argue that more rigorous evaluation methodologies are needed to confidently assess the forecasting abilities of LLMs.

General Machine Learning · Representation Learning

Jan-Philipp von Bassewitz, Adeel Pervez, Marco Fumero, Matthew Robinson, THEOFANIS KARALETSOS, Francesco Locatello

Modeling the dynamics of cellular differentiation is fundamental to advancing the understanding and treatment of diseases associated with this process, such as cancer. With the rapid growth of single-cell datasets, this has also become a particularly promising and active domain for machine learning. Current state-of-the-art models, however, rely on computationally expensive optimal transport preprocessing and multi-stage training, while also not discovering explicit gene interactions. To address these challenges we propose Cell-Mechanistic Neural Networks (*Cell-MNN*), an encoder-decoder architecture whose latent representation is a *locally linearized ODE* governing the dynamics of cellular evolution from stem to tissue cells. Cell-MNN is fully end-to-end (besides a standard PCA pre-processing) and its ODE representation learns interpretable gene interactions. Empirically, we show that Cell-MNN achieves competitive performance on single-cell benchmarks, surpasses state-of-the-art baselines in scaling to larger datasets and joint training across multiple datasets, while also learning interpretable gene interactions that we validate against the TRRUST database of gene interactions.

Applications · Physics

Tai Hoang, Alessandro Trenta, Alessio Gravina, Niklas Freymuth, Philipp Becker, Davide Bacciu, Gerhard Neumann

Learning to simulate complex physical systems from data has emerged as a promising way to overcome the limitations of traditional numerical solvers, which often require prohibitive computational costs for high-fidelity solutions. Recent Graph Neural Simulators (GNSs) accelerate simulations by learning dynamics on graph-structured data, yet often struggle to capture long-range interactions and suffer from error accumulation under autoregressive rollouts. To address these challenges, we propose Information-preserving Graph Neural Simulators (IGNS), a graph-based neural simulator built on the principles of Hamiltonian dynamics. This structure guarantees preservation of information across the graph, while extending to port-Hamiltonian systems allows the model to capture a broader class of dynamics, including non-conservative effects. IGNS further incorporates a warmup phase to initialize global context, geometric encoding to handle irregular meshes, and a multi-step training objective that facilitates PDE matching, where the trajectory produced by integrating the port-Hamiltonian core aligns with the ground-truth trajectory, thereby reducing rollout error. To evaluate these properties systematically, we introduce new benchmarks that target long-range dependencies and challenging external forcing scenarios. Across all tasks, IGNS consistently outperforms state-of-the-art GNSs, achieving higher accuracy and stability under challenging and complex dynamical systems. Our project page: https://thobotics.github.io/neural_pde_matching.

General Machine Learning · Representation Learning

Seongtae Hong, Youngjoon Jang, Jungseob Lee, Hyeonseok Moon, Heuiseok Lim

With the increasing accessibility and utilization of multilingual documents, Cross-Lingual Information Retrieval (CLIR) has emerged as an important research area. Conventionally, CLIR tasks have been conducted under settings where the language of documents differs from that of queries, and typically, the documents are composed in a single coherent language. In this paper, we highlight that in such a setting, the cross-lingual alignment capability may not be evaluated adequately. Specifically, we observe that, in a document pool where English documents coexist with another language, most multilingual retrievers tend to prioritize unrelated English documents over the related document written in the same language as the query. To rigorously analyze and quantify this phenomenon, we introduce various scenarios and metrics designed to evaluate the cross-lingual alignment performance of multilingual retrieval models. Furthermore, to improve cross-lingual performance under these challenging conditions, we propose a novel training strategy aimed at enhancing cross-lingual alignment. Using only a small dataset consisting of 2.8k samples, our method significantly improves the cross-lingual retrieval performance while simultaneously mitigating the English inclination problem. Extensive analyses demonstrate that the proposed method substantially enhances the cross-lingual alignment capabilities of most multilingual embedding models.

John Hewitt, Oyvind Tafjord, Robert Geirhos, Been Kim

Humans invent new words when there is a rising demand for a new useful concept (e.g., doomscrolling). We explore and validate a similar idea in our communication with LLMs: introducing new words to better understand and control the models, expanding on the recently introduced neologism learning. This method introduces a new word by adding a new word embedding and training with examples that exhibit the concept with no other changes in model parameters. We show that adding a new word allows for control of concepts such as flattery, incorrect answers, text length, as well as more complex concepts in AxBench. We discover that neologisms can also further our understanding of the model via self-verbalization: models can describe what each new word means to them in natural language, like explaining that a word that represents a concept of incorrect answers means “a lack of complete, coherent, or meaningful answers. . . ” To validate self-verbalizations, we introduce plug-in evaluation: we insert the verbalization into the context of a model and measure whether it controls the target concept. In some self-verbalizations, we find machine-only synonyms: words that seem unrelated to humans but cause similar behavior in machines. Finally, we show how neologism learning can jointly learn multiple concepts in multiple words.

Philipp Becker, Niklas Freymuth, Serge Thilges, Fabian Otto, Gerhard Neumann

Reinforcement Learning (RL) with PPO-like clip objectives has become the standard choice for reward-based fine-tuning of large language models (LLMs). Although recent work has explored improved estimators of advantages and normalization, the clipping mechanism itself has remained untouched. Originally introduced as a proxy for principled KL-based trust regions, clipping is a crude approximation that often causes unstable updates and suboptimal performance. We replace the clip objective with a novel discrete differentiable trust region projection, which provides principled token-level KL constraints. The projection operates on a sparse subset of the model’s most important token logits to balance computational cost and projection effectiveness. Our approach, Trust Region Optimization for Large Language Models (TROLL), serves as a direct replacement for PPO-like clipping during training and does not alter the model’s inference behavior. Across mathematical reasoning and code generation tasks, model families, as well as advantage-estimation methods, TROLL consistently outperforms PPO-like clipping in terms of training speed, stability, and final success rates.

General Machine Learning · Everything Else

Anna Beer, Lena Krieger, Pascal Weber, Martin Ritzert, Ira Assent, Claudia Plant

Evaluating the quality of a clustering result without access to ground truth labels is fundamental for research in data mining. However, most cluster validation indices (CVIs) do not consider the noise assignments by density-based clustering methods like DBSCAN or HDBSCAN, even though the ability to correctly determine noise is paramount to successful clustering. In this paper, we propose DISCO, a **D**ensity-based **I**nternal **S**core for **C**lusterings with n**O**ise, the first CVI to explicitly assess the *quality* of noise assignments rather than merely counting them. DISCO is based on the Silhouette Coefficient, but adopts density-connectivity to evaluate clusters of arbitrary shapes, and proposes explicit noise evaluation: it rewards correctly assigned noise labels and penalizes noise labels where a cluster label would have been more appropriate. The pointwise definition of DISCO allows for the seamless integration of noise evaluation into the final clustering evaluation, while also enabling explainable evaluations of the clustered data. In contrast to most state-of-the-art methods, DISCO is well-defined and also covers edge cases that regularly appear as output from clustering algorithms, such as singleton clusters or a single cluster plus noise.

Deep Learning · Generative Models and Autoencoders

Chenru Wang, Beier Zhu, Chi Zhang

Rectified-Flow (RF)-based generative models have recently emerged as strong alternatives to traditional diffusion models, demonstrating state-of-the-art performance across various tasks. By learning a continuous velocity field that transforms simple noise into complex data, RF-based models not only enable high-quality generation, but also support training-free inversion, which facilitates downstream tasks such as reconstruction and editing. However, existing inversion methods, such as vanilla RF-based inversion, suffer from approximation errors that accumulate across timesteps, leading to unstable velocity fields and degraded reconstruction and editing quality. To address this challenge, we propose Proximal-Mean Inversion (PMI), a training-free gradient correction method that stabilizes the velocity field by guiding it toward a running average of past velocities, constrained within a theoretically derived spherical Gaussian. Furthermore, we introduce mimic-CFG, a lightweight velocity correction scheme for editing tasks, which interpolates between the current velocity and its projection onto the historical average, balancing editing effectiveness and structural consistency. Extensive experiments on PIE-Bench demonstrate that our methods significantly improve inversion stability, image reconstruction quality, and editing fidelity, while reducing the required number of neural function evaluations. Our approach achieves state-of-the-art performance on the PIE-Bench with enhanced efficiency and theoretical soundness.

Applications · Time Series

Akash Pandey, Payal Mohapatra, Wei Chen, Qi Zhu, Sinan Keten

Identifying the extent to which every temporal segment influences a model’s predictions is essential for explaining model decisions and increasing transparency. While post-hoc explainable methods based on gradients and feature-based attributions have been popular, they suffer from reference state sensitivity and struggle to generalize across time-series datasets, as they treat time points independently and ignore sequential dependencies. Another perspective on explainable time-series classification is through interpretable components of the model, for instance, leveraging self-attention mechanisms to estimate temporal attribution; however, recent findings indicate that these attention weights often fail to provide faithful measures of temporal importance. In this work, we advance this perspective and present a novel explainability-driven deep learning framework, TimeSliver, which jointly utilizes raw time-series data and its symbolic abstraction to construct a representation that maintains the original temporal structure. Each element in this representation linearly encodes the contribution of each temporal segment to the final prediction, allowing us to assign a meaningful importance score to every time point. For time-series classification, TimeSliver outperforms other temporal attribution methods by 11\% on 7 distinct synthetic and real-world multivariate time-series datasets. TimeSliver also achieves predictive performance within 2\% of state-of-the-art baselines across 26 UEA benchmark datasets, positioning it as a strong and explainable framework for general time-series classification.

Reinforcement Learning · Planning

Yao Zhang, Shijie Tang, Zeyu Li, Zhen Han, Volker Tresp

Web agents hold great potential for automating complex computer tasks, yet their interactions involve long-horizon, sequential decision-making with irreversible actions. In such settings, outcome-based supervision is sparse and delayed, often rewarding incorrect trajectories and failing to support inference-time scaling. This motivates the use of Process Reward Models (WebPRMs) for web navigation, but existing approaches remain limited: scalar WebPRMs collapse progress into coarse, weakly grounded signals, while checklist-based WebPRMs rely on brittle template matching that fails under layout or semantic changes and often mislabels superficially correct actions as successful, providing little insight or interpretability. To address these challenges, we introduce WebArbiter, a reasoning-first, principle-inducing WebPRM that formulates reward modeling as text generation, producing structured justifications that conclude with a preference verdict and identify the action most conducive to task completion under the current context. Training follows a two-stage pipeline: reasoning distillation equips the model with coherent principle-guided reasoning, and reinforcement learning corrects teacher biases by directly aligning verdicts with correctness, enabling stronger generalization. To support systematic evaluation, we release WebPRMBench, a comprehensive benchmark spanning four diverse web environments with rich tasks and high-quality preference annotations. On WebPRMBench, WebArbiter-7B outperforms the strongest baseline, GPT-5, by 9.1 points. In reward-guided trajectory search on WebArena-Lite, it surpasses the best prior WebPRM by up to 7.2 points, underscoring its robustness and practical value in complex web tasks.

Applications · Genetics, Cell Biology, Health, etc

Zhijian Wei, Runze Ma, Zichen Wang, Zhongmin Li, Shuotong Song, Shuangjia Zheng

Virtual cell modeling aims to predict cellular responses to perturbations. Existing virtual cell models rely heavily on large-scale single-cell datasets, learning explicit mappings between gene expression and perturbations. Although recent models attempt to incorporate multi-source biological information, their generalization remains constrained by data quality, coverage, and batch effects. More critically, these models often function as black boxes, offering predictions without interpretability or consistency with biological principles, which undermines their credibility in scientific research. To address these challenges, we present VCWorld, a cell-level white-box simulator that integrates structured biological knowledge with the iterative reasoning capabilities of large language models to instantiate a biological world model. VCWorld operates in a data-efficient manner to reproduce perturbation-induced signaling cascades and generates interpretable, stepwise predictions alongside explicit mechanistic hypotheses. In drug perturbation benchmarks, VCWorld achieves state-of-the-art predictive performance, and the inferred mechanistic pathways are consistent with publicly available biological evidence. Our code is publicly available at https://anonymous.4open.science/r/VCWorld-B970.

Deep Learning · Generative Models and Autoencoders

Philipp Becker, Niklas Freymuth, Serge Thilges, Fabian Otto, Gerhard Neumann

Reinforcement Learning (RL) with PPO-like clip objectives has become the standard choice for reward-based fine-tuning of large language models (LLMs). Although recent work has explored improved estimators of advantages and normalization, the clipping mechanism itself has remained untouched. Originally introduced as a proxy for principled KL-based trust regions, clipping is a crude approximation that often causes unstable updates and suboptimal performance. We replace the clip objective with a novel discrete differentiable trust region projection, which provides principled token-level KL constraints. The projection operates on a sparse subset of the model’s most important token logits to balance computational cost and projection effectiveness. Our approach, Trust Region Optimization for Large Language Models (TROLL), serves as a direct replacement for PPO-like clipping during training and does not alter the model’s inference behavior. Across mathematical reasoning and code generation tasks, model families, as well as advantage-estimation methods, TROLL consistently outperforms PPO-like clipping in terms of training speed, stability, and final success rates.