OpenRaiser/Intern-Atlas huggingface dataset:
Positional Attention: Expressivity and Learnability of Algorithmic Computation
Venue: Conference ICML 2025
Year: 2025

There is a growing interest in the ability of neural networks to execute algorithmic tasks (e.g., arithmetic, summary statistics, and sorting). The goal of this work is to better understand the role of attention in Transformers for algorithmic execution. Its importance for algorithmic execution has been studied theoretically and empirically using parallel computational models. Notably, many parallel algorithms communicate between processors solely using positional information. Inspired by this observation, we investigate how Transformers can execute algorithms using positional attention, where attention weights depend exclusively on positional encodings. We prove that Transformers with positional attention (positional Transformers) maintain the same expressivity of parallel computational models, incurring a logarithmic depth cost relative to the input length. We analyze their in-distribution learnability and explore how parameter norms in positional attention affect sample complexity. Our results show that positional Transformers introduce a learning trade-off: while they exhibit better theoretical dependence on parameter norms, certain tasks may require more layers, which can, in turn, increase sample complexity. Finally, we empirically explore the out-of-distribution performance of positional Transformers and find that they perform well in tasks where their underlying algorithmic solution relies on positional information.
Joint MoE Scaling Laws: Mixture of Experts Can Be Memory Efficient
Venue: Conference ICML 2025
Year: 2025

Mixture of Experts (MoE) architectures have significantly increased computational efficiency in both research and real-world applications of large-scale machine learning models. However, their scalability and efficiency under memory constraints remain relatively underexplored. In this work, we present joint scaling laws for dense and MoE models, incorporating key factors such as the number of active parameters, dataset size, and the number of experts. Our findings provide a principled framework for selecting the optimal MoE configuration under fixed memory and compute budgets. Surprisingly, we show that MoE models can be more memory-efficient than dense models, contradicting conventional wisdom. To derive and validate the theoretical predictions of our scaling laws, we conduct over 280 experiments with up to 2.7B active parameters and up to 5B total parameters. These results offer actionable insights for designing and deploying MoE models in practical large-scale training scenarios.
Bipartite Ranking From Multiple Labels: On Loss Versus Label Aggregation
Venue: Conference ICML 2025
Year: 2025

Bipartite ranking is a fundamental supervised learning problem, with the goal of learning a ranking over instances with maximal Area Under the ROC Curve (AUC) against a single binary target label. However, one may often observe multiple binary target labels, e.g., from distinct human annotators. How can one synthesize such labels into a single coherent ranking? In this work, we formally analyze two approaches to this problem -- loss aggregation and label aggregation -- by characterizing their Bayes-optimal solutions. We show that while both approaches can yield Pareto-optimal solutions, loss aggregation can exhibit label dictatorship: one can inadvertently (and undesirably) favor one label over others. This suggests that label aggregation can be preferable to loss aggregation, which we empirically verify.
Can Classic GNNs Be Strong Baselines for Graph-level Tasks? Simple Architectures Meet Excellence
Venue: Conference ICML 2025
Year: 2025

Message-passing Graph Neural Networks (GNNs) are often criticized for their limited expressiveness, issues like over-smoothing and over-squashing, and challenges in capturing long-range dependencies. Conversely, Graph Transformers (GTs) are regarded as superior due to their employment of global attention mechanisms, which potentially mitigate these challenges. Literature frequently suggests that GTs outperform GNNs in graph-level tasks, especially for graph classification and regression on small molecular graphs. In this study, we explore the untapped potential of GNNs through an enhanced framework, GNN+, which integrates six widely used techniques: edge feature integration, normalization, dropout, residual connections, feed-forward networks, and positional encoding, to effectively tackle graph-level tasks. We conduct a systematic re-evaluation of three classic GNNs (GCN, GIN, and GatedGCN) enhanced by the GNN+ framework across 14 well-known graph-level datasets. Our results reveal that, contrary to prevailing beliefs, these classic GNNs consistently match or surpass the performance of GTs, securing top-three rankings across all datasets and achieving first place in eight. Furthermore, they demonstrate greater efficiency, running several times faster than GTs on many datasets. This highlights the potential of simple GNN architectures, challenging the notion that complex mechanisms in GTs are essential for superior graph-level performance. Our source code is available at https://github.com/LUOyk1999/GNNPlus.
Probing Visual Language Priors in VLMs
Venue: Conference ICML 2025
Year: 2025

Despite recent advances in Vision-Language Models (VLMs), they may over-rely on visual language priors existing in their training data rather than true visual reasoning. To investigate this, we introduce ViLP, a benchmark featuring deliberately out-of-distribution images synthesized via image generation models and out-of-distribution Q&A pairs. Each question in ViLP is coupled with three potential answers and three corresponding images: one that can be resolved by text priors alone and two that demand visual reasoning. Although, humans achieve near-perfect accuracy, modern VLMs falter; for instance, GPT-4 achieves only 66.17% on ViLP. To alleviate this, we propose a self-improving framework in which models generate new VQA data, then apply pixel-level and semantic corruptions to form "good-bad" image pairs for self-training. Our training objectives compel VLMs to focus more on the actual visual inputs, and we demonstrate their effectiveness in boosting the performance of open-source VLMs, including LLaVA-v1.5 and Cambrian.
Vision-Language Models Create Cross-Modal Task Representations
Venue: Conference ICML 2025
Year: 2025

Autoregressive vision-language models (VLMs) can handle many tasks within a single model, yet the representations that enable this capability remain opaque. We find that VLMs align conceptually equivalent inputs into a shared task vector, which is invariant to modality (text, image) and format (examples, instruction), and may simplify VLM processing. We measure this alignment via cross-modal transfer -- the ability of a task vector derived in one modality to trigger the correct generation in another -- on a range of tasks and model architectures. Although the task vector is highly compressed, we find that this single vector outperforms prompting the model with the full task information, unique to this cross-modal case. Furthermore, we show that task vectors can be transferred from a base language model to its fine-tuned vision-language counterpart, and that they can be derived solely from instructions without the need for examples. Taken together, our findings shed light on how VLMs internally process task information, and how they map different modalities into common semantic representations. Project page: https://vlm-cross-modal-reps.github.io.
LLM Enhancers for GNNs: An Analysis from the Perspective of Causal Mechanism Identification
Venue: Conference ICML 2025
Year: 2025

The use of large language models (LLMs) as feature enhancers to optimize node representations, which are then used as inputs for graph neural networks (GNNs), has shown significant potential in graph representation learning. However, the fundamental properties of this approach remain underexplored. To address this issue, we propose conducting a more in-depth analysis of this issue based on the interchange intervention method. First, we construct a synthetic graph dataset with controllable causal relationships, enabling precise manipulation of semantic relationships and causal modeling to provide data for analysis. Using this dataset, we conduct interchange interventions to examine the deeper properties of LLM enhancers and GNNs, uncovering their underlying logic and internal mechanisms. Building on the analytical results, we design a plug-and-play optimization module to improve the information transfer between LLM enhancers and GNNs. Experiments across multiple datasets and models validate the proposed module.
Fast and Low-Cost Genomic Foundation Models via Outlier Removal
Venue: Conference ICML 2025
Year: 2025

To address the challenge of scarce computational resources in genomic modeling, we introduce GERM, a genomic foundation model with strong compression performance and fast adaptability. GERM improves upon models like DNABERT-2 by eliminating outliers that hinder low-rank adaptation and post-training quantization, enhancing both efficiency and robustness. We replace the vanilla attention layer with an outlier-free mechanism inspired by associative memory models. By removing outliers during both pre-training and fine-tuning, this approach accelerates adaptation, reduces computational costs, and enhances quantization robustness within acceptable loss margins. Additionally, we propose GERM-T, a strategy that employs small-step continual learning within the outlier-free framework, leveraging original checkpoints to avoid retraining from scratch. Empirically, GERM improves fine-tuning performance by 37.98% and quantization by 64.34% over the baseline model. It also reduces average kurtosis by 92.14% and maximum infinity norm by 82.77%. Compared to leading methods, GERM consistently delivers superior performance, offering a practical solution for genomic modeling in resource-constrained settings. Code is available at https://github.com/MAGICS-LAB/GERM.
Sparsing Law: Towards Large Language Models with Greater Activation Sparsity
Venue: Conference ICML 2025
Year: 2025

Activation sparsity denotes the existence of substantial weakly-contributed elements within activation outputs that can be eliminated, benefiting many important applications concerned with large language models (LLMs). Although promoting greater activation sparsity within LLMs deserves deep studies, existing works lack comprehensive and quantitative research on the correlation between activation sparsity and potentially influential factors. In this paper, we present a comprehensive study on the quantitative scaling properties and influential factors of the activation sparsity within decoder-only Transformer-based LLMs. Specifically, we propose PPL-$p\%$ sparsity, a precise and performance-aware activation sparsity metric that is applicable to any activation function. Through extensive experiments, we find several important phenomena. Firstly, different activation functions exhibit comparable performance but opposite training-time sparsity trends. The activation ratio (i.e., $1-\mathrm{sparsity\ ratio}$) evolves as a convergent increasing power-law and decreasing logspace power-law with the amount of training data for SiLU-activated and ReLU-activated LLMs, respectively. These demonstrate that ReLU is more efficient as the activation function than SiLU and can leverage more training data to improve activation sparsity. Secondly, the activation ratio linearly increases with the width-depth ratio below a certain bottleneck point, indicating the potential advantage of a deeper architecture at a fixed parameter scale. Finally, at similar width-depth ratios, we surprisingly find that the limit value of activation sparsity varies weakly with the parameter scale, i.e., the activation patterns within LLMs are insensitive to the parameter scale. These empirical laws towards LLMs with greater activation sparsity have important implications for making LLMs more efficient and interpretable.
Beyond One-Hot Labels: Semantic Mixing for Model Calibration
Venue: Conference ICML 2025
Year: 2025

Model calibration seeks to ensure that models produce confidence scores that accurately reflect the true likelihood of their predictions being correct. However, existing calibration approaches are fundamentally tied to datasets of one-hot labels implicitly assuming full certainty in all the annotations. Such datasets are effective for classification but provides insufficient knowledge of uncertainty for model calibration, necessitating the curation of datasets with numerically rich ground-truth confidence values. However, due to the scarcity of uncertain visual examples, such samples are not easily available as real datasets. In this paper, we introduce calibration-aware data augmentation to create synthetic datasets of diverse samples and their ground-truth uncertainty. Specifically, we present \textbf{Calibration-aware Semantic Mixing (CSM)}, a novel framework that generates training samples with mixed class characteristics and annotates them with distinct confidence scores via diffusion models. Based on this framework, we propose calibrated reannotation to tackle the misalignment between the annotated confidence score and the mixing ratio during the diffusion reverse process. Besides, we explore the loss functions that better fit the new data representation paradigm. Experimental results demonstrate that CSM achieves superior calibration compared to the state-of-the-art calibration approaches. Our code is \href{https://github.com/E-Galois/CSM}{available here}.
Efficient and Scalable Density Functional Theory Hamiltonian Prediction through Adaptive Sparsity
Venue: Conference ICML 2025
Year: 2025

Hamiltonian matrix prediction is pivotal in computational chemistry, serving as the foundation for determining a wide range of molecular properties. While SE(3) equivariant graph neural networks have achieved remarkable success in this domain, their substantial computational cost--driven by high-order tensor product (TP) operations--restricts their scalability to large molecular systems with extensive basis sets. To address this challenge, we introduce SPHNet, an efficient and scalable equivariant network, that incorporates adaptive SParsity into Hamiltonian prediction. SPHNet employs two innovative sparse gates to selectively constrain non-critical interaction combinations, significantly reducing tensor product computations while maintaining accuracy. To optimize the sparse representation, we develop a Three-phase Sparsity Scheduler, ensuring stable convergence and achieving high performance at sparsity rates of up to 70%. Extensive evaluations on QH9 and PubchemQH datasets demonstrate that SPHNet achieves state-of-the-art accuracy while providing up to a 7x speedup over existing models. Beyond Hamiltonian prediction, the proposed sparsification techniques also hold significant potential for improving the efficiency and scalability of other SE(3) equivariant networks, further broadening their applicability and impact. Our code can be found at https://github.com/microsoft/SPHNet.
Locality Preserving Markovian Transition for Instance Retrieval
Venue: Conference ICML 2025
Year: 2025

Diffusion-based re-ranking methods are effective in modeling the data manifolds through similarity propagation in affinity graphs. However, positive signals tend to diminish over several steps away from the source, reducing discriminative power beyond local regions. To address this issue, we introduce the Locality Preserving Markovian Transition (LPMT) framework, which employs a long-term thermodynamic transition process with multiple states for accurate manifold distance measurement. The proposed LPMT first integrates diffusion processes across separate graphs using Bidirectional Collaborative Diffusion (BCD) to establish strong similarity relationships. Afterwards, Locality State Embedding (LSE) encodes each instance into a distribution for enhanced local consistency. These distributions are interconnected via the Thermodynamic Markovian Transition (TMT) process, enabling efficient global retrieval while maintaining local effectiveness. Experimental results across diverse tasks confirm the effectiveness of LPMT for instance retrieval.
Transolver++: An Accurate Neural Solver for PDEs on Million-Scale Geometries
Venue: Conference ICML 2025
Year: 2025

Although deep models have been widely explored in solving partial differential equations (PDEs), previous works are primarily limited to data only with up to tens of thousands of mesh points, far from the million-point scale required by industrial simulations that involve complex geometries. In the spirit of advancing neural PDE solvers to real industrial applications, we present Transolver++, a highly parallel and efficient neural solver that can accurately solve PDEs on million-scale geometries. Building upon previous advancements in solving PDEs by learning physical states via Transolver, Transolver++ is further equipped with an extremely optimized parallelism framework and a local adaptive mechanism to efficiently capture eidetic physical states from massive mesh points, successfully tackling the thorny challenges in computation and physics learning when scaling up input mesh size. Transolver++ increases the single-GPU input capacity to million-scale points for the first time and is capable of continuously scaling input size in linear complexity by increasing GPUs. Experimentally, Transolver++ yields 13% relative promotion across six standard PDE benchmarks and achieves over 20% performance gain in million-scale high-fidelity industrial simulations, whose sizes are 100$\times$ larger than previous benchmarks, covering car and 3D aircraft designs.
Learning to Trust Bellman Updates: Selective State-Adaptive Regularization for Offline RL
Venue: Conference ICML 2025
Year: 2025

Offline reinforcement learning (RL) aims to learn an effective policy from a static dataset. To alleviate extrapolation errors, existing studies often uniformly regularize the value function or policy updates across all states. However, due to substantial variations in data quality, the fixed regularization strength often leads to a dilemma: Weak regularization strength fails to address extrapolation errors and value overestimation, while strong regularization strength shifts policy learning toward behavior cloning, impeding potential performance enabled by Bellman updates. To address this issue, we propose the selective state-adaptive regularization method for offline RL. Specifically, we introduce state-adaptive regularization coefficients to trust state-level Bellman-driven results, while selectively applying regularization on high-quality actions, aiming to avoid performance degradation caused by tight constraints on low-quality actions. By establishing a connection between the representative value regularization method, CQL, and explicit policy constraint methods, we effectively extend selective state-adaptive regularization to these two mainstream offline RL approaches. Extensive experiments demonstrate that the proposed method significantly outperforms the state-of-the-art approaches in both offline and offline-to-online settings on the D4RL benchmark.
LADA: Scalable Label-Specific CLIP Adapter for Continual Learning
Venue: Conference ICML 2025
Year: 2025

Continual learning with vision-language models like CLIP offers a pathway toward scalable machine learning systems by leveraging its transferable representations. Existing CLIP-based methods adapt the pre-trained image encoder by adding multiple sets of learnable parameters, with each task using a partial set of parameters. This requires selecting the expected parameters for input images during inference, which is prone to error that degrades performance. To address this problem, we introduce LADA (Label-specific ADApter). Instead of partitioning parameters across tasks, LADA appends lightweight, label-specific memory units to the frozen CLIP image encoder, enabling discriminative feature generation by aggregating task-agnostic knowledge. To prevent catastrophic forgetting, LADA employs feature distillation for seen classes, preventing their features from being interfered with by new classes. Positioned after the image encoder, LADA prevents gradient flow to the frozen CLIP parameters, ensuring efficient training. Extensive results show that LADA achieves state-of-the-art performance in continual learning settings. The implementation code is available at https://github.com/MaolinLuo/LADA.
Graph-constrained Reasoning: Faithful Reasoning on Knowledge Graphs with Large Language Models
Venue: Conference ICML 2025
Year: 2025

Large language models (LLMs) have demonstrated impressive reasoning abilities, but they still struggle with faithful reasoning due to knowledge gaps and hallucinations. To address these issues, knowledge graphs (KGs) have been utilized to enhance LLM reasoning through their structured knowledge. However, existing KG-enhanced methods, either retrieval-based or agent-based, encounter difficulties in accurately retrieving knowledge and efficiently traversing KGs at scale. In this work, we introduce graph-constrained reasoning (GCR), a novel framework that bridges structured knowledge in KGs with unstructured reasoning in LLMs. To eliminate hallucinations, GCR ensures faithful KG-grounded reasoning by integrating KG structure into the LLM decoding process through KG-Trie, a trie-based index that encodes KG reasoning paths. KG-Trie constrains the decoding process, allowing LLMs to directly reason on graphs and generate faithful reasoning paths grounded in KGs. Additionally, GCR leverages a lightweight KG-specialized LLM for graph-constrained reasoning alongside a powerful general LLM for inductive reasoning over multiple reasoning paths, resulting in accurate reasoning with zero reasoning hallucination. Extensive experiments on several KGQA benchmarks demonstrate that GCR achieves state-of-the-art performance and exhibits strong zero-shot generalizability to unseen KGs without additional training.
MERIT: Maximum-normalized Element-wise Ratio for Language Model Large-batch Training
Venue: Conference ICML 2025
Year: 2025

Large-batch training has become a cornerstone in accelerating the training of deep neural networks, yet it poses challenges in optimization and generalization. Existing optimizers like AdamW present performance degradation during language models' large-batch training, due to the information bottleneck in attention layers caused by the sharp increase of max attention logit. While the LAMB optimizer partially addresses this issue, some attention layers still face this issue. The reason is that $l_2$-norm-based trust ratios in LAMB are less effective in directly influencing the max value of query/key weights. Furthermore, the weight-wise trust ratio in LAMB is error-prone as it overlooks relationships of weight values within rows or columns. Building on these observations, we propose a novel optimizer, MERIT, which leverages the max-norm to calculate the trust ratio to constrain the max attention logit more effectively. Moreover, we further construct element-wise trust ratios to provide more robust update scaling by focusing on local weight structures. Extensive experiments of large-batch training across various sizes of GPT-2 models demonstrate the superior performance of MERIT. Notably, during the training of GPT-2 Medium, MERIT enables a 6k batch size without any performance degradation compared to the standard batch size (480) with 48B training tokens. This work highlights the importance of considering the max attention logit and finer-granularity trust ratio in large-batch training. It successfully improves the training stability and paves the way for larger batch usage, enabling faster development and iteration of large language models. Code is available at https://github.com/NUS-HPC-AI-Lab/MERIT.