OpenRaiser/Intern-Atlas huggingface dataset:
Enforcing Latent Euclidean Geometry in Single-Cell VAEs for Manifold Interpolation
Venue: Conference ICML 2025
Year: 2025

Latent space interpolations are a powerful tool for navigating deep generative models in applied settings. An example is single-cell RNA sequencing, where existing methods model cellular state transitions as latent space interpolations with variational autoencoders, often assuming linear shifts and Euclidean geometry. However, unless explicitly enforced, linear interpolations in the latent space may not correspond to geodesic paths on the data manifold, limiting methods that assume Euclidean geometry in the data representations. We introduce FlatVI, a novel training framework that regularises the latent manifold of discrete-likelihood variational autoencoders towards Euclidean geometry, specifically tailored for modelling single-cell count data. By encouraging straight lines in the latent space to approximate geodesic interpolations on the decoded single-cell manifold, FlatVI enhances compatibility with downstream approaches that assume Euclidean latent geometry. Experiments on synthetic data support the theoretical soundness of our approach, while applications to time-resolved single-cell RNA sequencing data demonstrate improved trajectory reconstruction and manifold interpolation.
Validating Mechanistic Interpretations: An Axiomatic Approach
Venue: Conference ICML 2025
Year: 2025

Mechanistic interpretability aims to reverse engineer the computation performed by a neural network in terms of its internal components. Although there is a growing body of research on mechanistic interpretation of neural networks, the notion of a mechanistic interpretation itself is often ad-hoc. Inspired by the notion of abstract interpretation from the program analysis literature that aims to develop approximate semantics for programs, we give a set of axioms that formally characterize a mechanistic interpretation as a description that approximately captures the semantics of the neural network under analysis in a compositional manner. We demonstrate the applicability of these axioms for validating mechanistic interpretations on an existing, well-known interpretability study as well as on a new case study involving a Transformer-based model trained to solve the well-known 2-SAT problem.
From Logits to Hierarchies: Hierarchical Clustering made Simple
Venue: Conference ICML 2025
Year: 2025

The hierarchical structure inherent in many real-world datasets makes the modeling of such hierarchies a crucial objective in both unsupervised and supervised machine learning. While recent advancements have introduced deep architectures specifically designed for hierarchical clustering, we adopt a critical perspective on this line of research. Our findings reveal that these methods face significant limitations in scalability and performance when applied to realistic datasets. Given these findings, we present an alternative approach and introduce a lightweight method that builds on pre-trained non-hierarchical clustering models. Remarkably, our approach outperforms specialized deep models for hierarchical clustering, and it is broadly applicable to any pre-trained clustering model that outputs logits, without requiring any fine-tuning. To highlight the generality of our approach, we extend its application to a supervised setting, demonstrating its ability to recover meaningful hierarchies from a pre-trained ImageNet classifier. Our results establish a practical and effective alternative to existing deep hierarchical clustering methods, with significant advantages in efficiency, scalability and performance.
Can Transformers Reason Logically? A Study in SAT Solving
Venue: Conference ICML 2025
Year: 2025

We formally study the logical reasoning capabilities of decoder-only Transformers in the context of the boolean satisfiability (SAT) problem. First, we prove by construction that decoder-only Transformers can decide 3-SAT, in a non-uniform model of computation, using backtracking and deduction via Chain-of-Thought (CoT). %We prove its correctness by showing trace equivalence to the well-known DPLL SAT-solving algorithm. Second, we implement our construction as a PyTorch model with a tool (PARAT) that we designed to empirically demonstrate its correctness and investigate its properties. Third, rather than \textit{programming} a transformer to reason, we evaluate empirically whether it can be \textit{trained} to do so by learning directly from algorithmic traces (``reasoning paths'') from our theoretical construction. The trained models demonstrate strong out-of-distribution generalization on problem sizes seen during training but has limited length generalization, which is consistent with the implications of our theoretical result
Training Software Engineering Agents and Verifiers with SWE-Gym
Venue: Conference ICML 2025
Year: 2025

We present SWE-Gym, the first environment for training real-world software engineering (SWE) agents. SWE-Gym contains 2,438 real-world Python task instances, each comprising a codebase with an executable runtime environment, unit tests, and a task specified in natural language. We use SWE-Gym to train language model based SWE agents, achieving up to 19% absolute gains in resolve rate on the popular SWE-Bench Verified and Lite test sets. We also experiment with inference-time scaling through verifiers trained on agent trajectories sampled from SWE-Gym. When combined with our fine-tuned SWE agents, we achieve 32.0% and 26.0% on SWE-Bench Verified and Lite, respectively, reflecting a new state-of-the-art for open-weight SWE agents. To facilitate further research, we publicly release SWE-Gym, models, and agent trajectories.
How Do Images Align and Complement LiDAR? Towards a Harmonized Multi-modal 3D Panoptic Segmentation
Venue: Conference ICML 2025
Year: 2025

LiDAR-based 3D panoptic segmentation often struggles with the inherent sparsity of data from LiDAR sensors, which makes it challenging to accurately recognize distant or small objects. Recently, a few studies have sought to overcome this challenge by integrating LiDAR inputs with camera images, leveraging the rich and dense texture information provided by the latter. While these approaches have shown promising results, they still face challenges, such as misalignment during data augmentation and the reliance on post-processing steps. To address these issues, we propose Image-Assists-LiDAR (IAL), a novel multi-modal 3D panoptic segmentation framework. In IAL, we first introduce a modality-synchronized data augmentation strategy, PieAug, to ensure alignment between LiDAR and image inputs from the start. Next, we adopt a transformer decoder to directly predict panoptic segmentation results. To effectively fuse LiDAR and image features into tokens for the decoder, we design a Geometric-guided Token Fusion (GTF) module. Additionally, we leverage the complementary strengths of each modality as priors for query initialization through a Prior-based Query Generation (PQG) module, enhancing the decoder's ability to generate accurate instance masks. Our IAL framework achieves state-of-the-art performance compared to previous multi-modal 3D panoptic segmentation methods on two widely used benchmarks. Code and models are publicly available at <https://github.com/IMPL-Lab/IAL.git>.
Commute Graph Neural Networks
Venue: Conference ICML 2025
Year: 2025

Graph Neural Networks (GNNs) have shown remarkable success in learning from graph-structured data. However, their application to directed graphs (digraphs) presents unique challenges, primarily due to the inherent asymmetry in node relationships. Traditional GNNs are adept at capturing unidirectional relations but fall short in encoding the mutual path dependencies between nodes, such as asymmetrical shortest paths typically found in digraphs. Recognizing this gap, we introduce Commute Graph Neural Networks (CGNN), an approach that seamlessly integrates node-wise commute time into the message passing scheme. The cornerstone of CGNN is an efficient method for computing commute time using a newly formulated digraph Laplacian. Commute time is then integrated into the neighborhood aggregation process, with neighbor contributions weighted according to their respective commute time to the central node in each layer. It enables CGNN to directly capture the mutual, asymmetric relationships in digraphs. Extensive experiments on 8 benchmarking datasets confirm the superiority of CGNN against 13 state-of-the-art methods.
The Hidden Dimensions of LLM Alignment: A Multi-Dimensional Analysis of Orthogonal Safety Directions
Venue: Conference ICML 2025
Year: 2025

Large Language Models' safety-aligned behaviors, such as refusing harmful queries, can be represented by linear directions in activation space. Previous research modeled safety behavior with a single direction, limiting mechanistic understanding to an isolated safety feature. In this work, we discover that safety-aligned behavior is jointly controlled by multi-dimensional directions. Namely, we study the vector space of representation shifts during safety fine-tuning on Llama 3 8B for refusing jailbreaks. By studying orthogonal directions in the space, we first find that a dominant direction governs the model's refusal behavior, while multiple smaller directions represent distinct and interpretable features like hypothetical narrative and role-playing. We then measure how different directions promote or suppress the dominant direction, showing the important role of secondary directions in shaping the model's refusal representation. Finally, we demonstrate that removing certain trigger tokens in harmful queries can mitigate these directions to bypass the learned safety capability, providing new insights on understanding safety alignment vulnerability from a multi-dimensional perspective. Code and artifacts are available at https://github.com/BMPixel/safety-residual-space.
Preference Optimization for Combinatorial Optimization Problems
Venue: Conference ICML 2025
Year: 2025

Reinforcement Learning (RL) has emerged as a powerful tool for neural combinatorial optimization, enabling models to learn heuristics that solve complex problems without requiring expert knowledge. Despite significant progress, existing RL approaches face challenges such as diminishing reward signals and inefficient exploration in vast combinatorial action spaces, leading to inefficiency. In this paper, we propose Preference Optimization, a novel method that transforms quantitative reward signals into qualitative preference signals via statistical comparison modeling, emphasizing the superiority among sampled solutions. Methodologically, by reparameterizing the reward function in terms of policy and utilizing preference models, we formulate an entropy-regularized RL objective that aligns the policy directly with preferences while avoiding intractable computations. Furthermore, we integrate local search techniques into the fine-tuning rather than post-processing to generate high-quality preference pairs, helping the policy escape local optima. Empirical results on various benchmarks, such as the Traveling Salesman Problem (TSP), the Capacitated Vehicle Routing Problem (CVRP) and the Flexible Flow Shop Problem (FFSP), demonstrate that our method significantly outperforms existing RL algorithms, achieving superior convergence efficiency and solution quality.
Video-Enhanced Offline Reinforcement Learning: A Model-Based Approach
Venue: Conference ICML 2025
Year: 2025

Offline reinforcement learning (RL) enables policy optimization using static datasets, avoiding the risks and costs of extensive real-world exploration. However, it struggles with suboptimal offline behaviors and inaccurate value estimation due to the lack of environmental interaction. We present Video-Enhanced Offline RL (VeoRL), a model-based method that constructs an interactive world model from diverse, unlabeled video data readily available online. Leveraging model-based behavior guidance, our approach transfers commonsense knowledge of control policy and physical dynamics from natural videos to the RL agent within the target domain. VeoRL achieves substantial performance gains (over 100% in some cases) across visual control tasks in robotic manipulation, autonomous driving, and open-world video games.
Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation
Venue: Conference ICML 2025
Year: 2025

Generative Flow Networks (GFlowNets) have recently emerged as a suitable framework for generating diverse and high-quality molecular structures by learning from rewards treated as unnormalized distributions. Previous works in this framework often restrict exploration by using predefined molecular fragments as building blocks, limiting the chemical space that can be accessed. In this work, we introduce Atomic GFlowNets (A-GFNs), a foundational generative model leveraging individual atoms as building blocks to explore drug-like chemical space more comprehensively. We propose an unsupervised pre-training approach using drug-like molecule datasets, which teaches A-GFNs about inexpensive yet informative molecular descriptors such as drug-likeliness, topological polar surface area, and synthetic accessibility scores. These properties serve as proxy rewards, guiding A-GFNs towards regions of chemical space that exhibit desirable pharmacological properties. We further implement a goal-conditioned finetuning process, which adapts A-GFNs to optimize for specific target properties. In this work, we pretrain A-GFN on a subset of ZINC dataset, and by employing robust evaluation metrics we show the effectiveness of our approach when compared to other relevant baseline methods for a wide range of drug design tasks. The code is accessible at https://github.com/diamondspark/AGFN.
Variational Control for Guidance in Diffusion Models
Venue: Conference ICML 2025
Year: 2025

Diffusion models exhibit excellent sample quality, but existing guidance methods often require additional model training or are limited to specific tasks. We revisit guidance in diffusion models from the perspective of variational inference and control, introducing Diffusion Trajectory Matching (DTM) that enables guiding pretrained diffusion trajectories to satisfy a terminal cost. DTM unifies a broad class of guidance methods and enables novel instantiations. We introduce a new method within this framework that achieves state-of-the-art results on several linear, non-linear, and blind inverse problems without requiring additional model training or specificity to pixel or latent space diffusion models. Our code will be available at https://github.com/czi-ai/oc-guidance
QuEST: Stable Training of LLMs with 1-Bit Weights and Activations
Venue: Conference ICML 2025
Year: 2025

One approach to reducing the massive costs of large language models (LLMs) is the use of quantized or sparse representations for training or deployment. While post-training compression methods are very popular, the question of obtaining even more accurate compressed models by directly training over such representations, i.e., Quantization-Aware Training (QAT), is still open: for example, a recent study (arXiv:2411.04330) put the "optimal" bit-width at which models can be trained using QAT, while staying accuracy-competitive with standard FP16/BF16 precision, at 8-bits weights and activations. We advance this state-of-the-art via a new method called QuEST, for which we demonstrate optimality at 4-bits and stable convergence as low as 1-bit weights and activations. QuEST achieves this by improving two key aspects of QAT methods: (1) accurate and fast quantization of the (continuous) distributions of weights and activations via Hadamard normalization and MSE-optimal fitting; (2) a new trust gradient estimator based on the idea of explicitly minimizing the error between the noisy gradient computed over quantized states and the "true" (but unknown) full-precision gradient. Experiments on Llama-type architectures show that QuEST induces stable scaling laws across the entire range of hardware-supported precisions, and can be extended to sparse representations. We provide GPU kernel support showing that models produced by QuEST can be executed efficiently. Our code is available at https://github.com/IST-DASLab/QuEST.
Geometric Generative Modeling with Noise-Conditioned Graph Networks
Venue: Conference ICML 2025
Year: 2025

Generative modeling of graphs with spatial structure is essential across many applications from computer graphics to spatial genomics. Recent flow-based generative models have achieved impressive results by gradually adding and then learning to remove noise from these graphs. Existing models, however, use graph neural network architectures that are independent of the noise level, limiting their expressiveness. To address this issue, we introduce \textit{Noise-Conditioned Graph Networks} (NCGNs), a class of graph neural networks that dynamically modify their architecture according to the noise level during generation. Our theoretical and empirical analysis reveals that as noise increases, (1) graphs require information from increasingly distant neighbors and (2) graphs can be effectively represented at lower resolutions. Based on these insights, we develop Dynamic Message Passing (DMP), a specific instantiation of NCGNs that adapts both the range and resolution of message passing to the noise level. DMP consistently outperforms noise-independent architectures on a variety of domains including $3$D point clouds, spatiotemporal transcriptomics, and images. Code is available at https://github.com/peterpaohuang/ncgn.
The Price of Freedom: Exploring Expressivity and Runtime Tradeoffs in Equivariant Tensor Products
Venue: Conference ICML 2025
Year: 2025

$E(3)$-equivariant neural networks have demonstrated success across a wide range of 3D modelling tasks. A fundamental operation in these networks is the tensor product, which interacts two geometric features in an equivariant manner to create new features. Due to the high computational complexity of the tensor product, significant effort has been invested to optimize the runtime of this operation. For example, Luo et al. (2024) recently proposed the Gaunt tensor product (GTP) which promises a significant speedup. In this work, we provide a careful, systematic analysis of a number of tensor product operations. In particular, we emphasize that different tensor products are not performing the same operation. The reported speedups typically come at the cost of expressivity. We introduce measures of expressivity and interactability to characterize these differences. In addition, we realized the original implementation of GTP can be greatly simplified by directly using a spherical grid at no cost in asymptotic runtime. This spherical grid approach is faster on our benchmarks and in actual training of the MACE interatomic potential by 30%. Finally, we provide the first systematic microbenchmarks of the various tensor product operations. We find that the theoretical runtime guarantees can differ wildly from empirical performance, demonstrating the need for careful application-specific benchmarking. Code is available at https://github.com/atomicarchitects/PriceofFreedom.
Enhancing Diversity In Parallel Agents: A Maximum State Entropy Exploration Story
Venue: Conference ICML 2025
Year: 2025

Parallel data collection has redefined Reinforcement Learning (RL), unlocking unprecedented efficiency and powering breakthroughs in large-scale real-world applications. In this paradigm, $N$ identical agents operate in $N$ replicas of an environment simulator, accelerating data collection by a factor of $N$. A critical question arises: \textit{Does specializing the policies of the parallel agents hold the key to surpass the $N$ factor acceleration?} In this paper, we introduce a novel learning framework that maximizes the entropy of collected data in a parallel setting. Our approach carefully balances the entropy of individual agents with inter-agent diversity, effectively minimizing redundancies. The latter idea is implemented with a centralized policy gradient method, which shows promise when evaluated empirically against systems of identical agents, as well as synergy with batch RL techniques that can exploit data diversity. Finally, we provide an original concentration analysis that shows faster rates for specialized parallel sampling distributions, which supports our methodology and may be of independent interest.
Understanding High-Dimensional Bayesian Optimization
Venue: Conference ICML 2025
Year: 2025

Recent work reported that simple Bayesian optimization (BO) methods perform well for high-dimensional real-world tasks, seemingly contradicting prior work and tribal knowledge. This paper investigates why. We identify underlying challenges that arise in high-dimensional BO and explain why recent methods succeed. Our empirical analysis shows that vanishing gradients caused by Gaussian process (GP) initialization schemes play a major role in the failures of high-dimensional Bayesian optimization (HDBO) and that methods that promote local search behaviors are better suited for the task. We find that maximum likelihood estimation (MLE) of GP length scales suffices for state-of-the-art performance. Based on this, we propose a simple variant of MLE called MSR that leverages these findings to achieve state-of-the-art performance on a comprehensive set of real-world applications. We present targeted experiments to illustrate and confirm our findings.
TopoTune: A Framework for Generalized Combinatorial Complex Neural Networks
Venue: Conference ICML 2025
Year: 2025

Graph Neural Networks (GNNs) effectively learn from relational data by leveraging graph symmetries. However, many real-world systems -- such as biological or social networks -- feature multi-way interactions that GNNs fail to capture. Topological Deep Learning (TDL) addresses this by modeling and leveraging higher-order structures, with Combinatorial Complex Neural Networks (CCNNs) offering a general and expressive approach that has been shown to outperform GNNs. However, TDL lacks the principled and standardized frameworks that underpin GNN development, restricting its accessibility and applicability. To address this issue, we introduce Generalized CCNNs (GCCNs), a simple yet powerful family of TDL models that can be used to systematically transform any (graph) neural network into its TDL counterpart. We prove that GCCNs generalize and subsume CCNNs, while extensive experiments on a diverse class of GCCNs show that these architectures consistently match or outperform CCNNs, often with less model complexity. In an effort to accelerate and democratize TDL, we introduce TopoTune, a lightweight software for defining, building, and training GCCNs with unprecedented flexibility and ease.
Optimization Proxies using Limited Labeled Data and Training Time - A Semi-Supervised Bayesian Neural Network Approach
Venue: Conference ICML 2025
Year: 2025

Constrained optimization problems arise in various engineering systems such as inventory management and power grids. Standard deep neural network (DNN) based machine learning proxies are ineffective in practical settings where labeled data is scarce and training times are limited. We propose a semi-supervised Bayesian Neural Networks (BNNs) based optimization proxy for this complex regime, wherein training commences in a sandwiched fashion, alternating between a supervised learning step for minimizing cost, and an unsupervised learning step for enforcing constraint feasibility. We show that the proposed semi-supervised BNN outperforms DNN architectures on important non-convex constrained optimization problems from energy network operations, achieving up to a tenfold reduction in expected maximum equality gap and halving the inequality gaps. Further, the BNN's ability to provide posterior samples is leveraged to construct practically meaningful probabilistic confidence bounds on performance using a limited validation data, unlike prior methods. The implementation code for this study is available at: https://github.com/kaarthiksundar/BNN-OPF/.