arXiv subjects

Muhan Zhang

Publications and source records attributed to Muhan Zhang.

At least 73 records · Page 4Linked to original sources

arXiv2025

Masked Language Models are Good Heterogeneous Graph Generalizers

Heterogeneous graph neural networks (HGNNs) excel at capturing structural and semantic information in heterogeneous graphs (HGs), while struggling to generalize across domains and tasks. With the rapid advancement of large language models (LLMs), a recent study explored the integration of HGNNs with LLMs for generalizable heterogeneous graph learning. However, this approach typically encodes structural information as HG tokens using HGNNs, and disparities in embedding spaces between HGNNs and LLMs have been shown to bias the LLM's comprehension of HGs. Moreover, since these HG tokens are often derived from node-level tasks, the model's ability to generalize across tasks remains limited. To this end, we propose a simple yet effective Masked Language Modeling-based method, called MLM4HG. MLM4HG introduces metapath-based textual sequences instead of HG tokens to extract structural and semantic information inherent in HGs, and designs customized textual templates to unify different graph tasks into a coherent cloze-style 'mask' token prediction paradigm. Specifically,MLM4HG first converts HGs from various domains to texts based on metapaths, and subsequently combines them with the unified task texts to form a HG-based corpus. Moreover, the corpus is fed into a pretrained LM for fine-tuning with a constrained target vocabulary, enabling the fine-tuned LM to generalize to unseen target HGs. Extensive cross-domain and multi-task experiments on four real-world datasets demonstrate the superior generalization performance of MLM4HG over state-of-the-art methods in both few-shot and zero-shot scenarios. Our code is available at https://github.com/BUPT-GAMMA/MLM4HG.

cs.SI↗

arXiv2025

Geometric Representation Condition Improves Equivariant Molecule Generation

Recent advances in molecular generative models have demonstrated great promise for accelerating scientific discovery, particularly in drug design. However, these models often struggle to generate high-quality molecules, especially in conditional scenarios where specific molecular properties must be satisfied. In this work, we introduce GeoRCG, a general framework to improve molecular generative models by integrating geometric representation conditions with provable theoretical guarantees. We decompose the generation process into two stages: first, generating an informative geometric representation; second, generating a molecule conditioned on the representation. Compared with single-stage generation, the easy-to-generate representation in the first stage guides the second stage generation toward a high-quality molecule in a goal-oriented way. Leveraging EDM and SemlaFlow as base generators, we observe significant quality improvements in unconditional molecule generation on the widely used QM9 and GEOM-DRUG datasets. More notably, in the challenging conditional molecular generation task, our framework achieves an average 50\% performance improvement over state-of-the-art approaches, highlighting the superiority of conditioning on semantically rich geometric representations. Furthermore, with such representation guidance, the number of diffusion steps can be reduced to as small as 100 while largely preserving the generation quality achieved with 1,000 steps, thereby significantly reducing the generation iterations needed. Code is available at https://github.com/GraphPKU/GeoRCG.

cs.LG↗

arXiv2025

On the Completeness of Invariant Geometric Deep Learning Models

Invariant models, one important class of geometric deep learning models, are capable of generating meaningful geometric representations by leveraging informative geometric features in point clouds. These models are characterized by their simplicity, good experimental results and computational efficiency. However, their theoretical expressive power still remains unclear, restricting a deeper understanding of the potential of such models. In this work, we concentrate on characterizing the theoretical expressiveness of a wide range of invariant models under fully-connected conditions. We first rigorously characterize the expressiveness of the most classic invariant model, message-passing neural networks incorporating distance (DisGNN), restricting its unidentifiable cases to be only highly symmetric point clouds. We then prove that GeoNGNN, the geometric counterpart of one of the simplest subgraph graph neural networks, can effectively break these corner cases' symmetry and thus achieve E(3)-completeness. By leveraging GeoNGNN as a theoretical tool, we further prove that: 1) most subgraph GNNs developed in traditional graph learning can be seamlessly extended to geometric scenarios with E(3)-completeness; 2) DimeNet, GemNet and SphereNet, three well-established invariant models, are also all capable of achieving E(3)-completeness. Our theoretical results fill the gap in the expressive power of invariant models, contributing to a rigorous and comprehensive understanding of their capabilities.

cs.LG↗

arXiv2025

TransMLA: Multi-Head Latent Attention Is All You Need

In this paper, we present TransMLA, a framework that seamlessly converts any GQA-based pre-trained model into an MLA-based model. Our approach enables direct compatibility with DeepSeek's codebase, allowing these models to fully leverage DeepSeek-specific optimizations such as vLLM and SGlang. By compressing 93% of the KV cache in LLaMA-2-7B, TransMLA achieves a 10.6x inference speedup at an 8K context length while preserving meaningful output quality. Additionally, the model requires only 6 billion tokens for fine-tuning to regain performance on par with the original across multiple benchmarks. TransMLA offers a practical solution for migrating GQA-based models to the MLA structure. When combined with DeepSeek's advanced features, such as FP8 quantization and Multi-Token Prediction, even greater inference acceleration can be realized.

cs.LG↗

arXiv2025

Griffin: Towards a Graph-Centric Relational Database Foundation Model

We introduce Griffin, the first foundation model attemptation designed specifically for Relational Databases (RDBs). Unlike previous smaller models focused on single RDB tasks, Griffin unifies the data encoder and task decoder to handle diverse tasks. Additionally, we enhance the architecture by incorporating a cross-attention module and a novel aggregator. Griffin utilizes pretraining on both single-table and RDB datasets, employing advanced encoders for categorical, numerical, and metadata features, along with innovative components such as cross-attention modules and enhanced message-passing neural networks (MPNNs) to capture the complexities of relational data. Evaluated on large-scale, heterogeneous, and temporal graphs extracted from RDBs across various domains (spanning over 150 million nodes), Griffin demonstrates superior or comparable performance to individually trained models, excels in low-data scenarios, and shows strong transferability with similarity and diversity in pretraining across new datasets and tasks, highlighting its potential as a universally applicable foundation model for RDBs. Code available at https://github.com/yanxwb/Griffin.

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arXiv2025

Beyond Single-Task: Robust Multi-Task Length Generalization for LLMs

Length generalization, the ability to solve problems longer than those seen during training, remains a critical challenge for large language models (LLMs). Previous work modifies positional encodings (PEs) and data formats to improve length generalization on specific symbolic tasks such as addition and sorting. However, these approaches are fundamentally limited to special tasks, often degrading general language performance. Furthermore, they are typically evaluated on small transformers trained from scratch on single tasks and can cause performance drop when applied during post-training stage of practical LLMs with general capabilities. Hu et al., (2024) proposed Rule-Following Fine-Tuning (RFFT) to improve length generalization in the post-training stage of LLMs. Despite its compatibility with practical models and strong performance, RFFT is proposed for single tasks too, requiring re-training for each individual task with extensive examples. In this paper, we study length generalization in multi-task settings and propose Meta Rule-Following Fine-Tuning (Meta-RFFT), the first framework enabling robust cross-task length generalization. As our first contribution, we construct a large length generalization dataset containing 86 tasks spanning code execution, number processing, symbolic and logical reasoning tasks, beyond the common addition or multiplication tasks. Secondly, we show that cross-task length generalization is possible with Meta-RFFT. After training on a large number of tasks and instances, the models achieve remarkable length generalization ability on unseen tasks with minimal fine-tuning or one-shot prompting. For example, after fine-tuning on 1 to 5 digit addition, our 32B model achieves 95% accuracy on 30 digit addition, significantly outperforming the state-of-the-art reasoning models (DeepSeek-R1-671B: 72%), despite never seeing this task during RF-pretraining.

cs.CL↗

arXiv2025

PHYBench: Holistic Evaluation of Physical Perception and Reasoning in Large Language Models

Current benchmarks for evaluating the reasoning capabilities of Large Language Models (LLMs) face significant limitations: task oversimplification, data contamination, and flawed evaluation items. These deficiencies necessitate more rigorous assessment methods. To address these limitations, we introduce PHYBench, a benchmark of 500 original physics problems ranging from high school to Physics Olympiad difficulty. PHYBench addresses data contamination through original content and employs a systematic curation pipeline to eliminate flawed items. Evaluations show that PHYBench activates more tokens and provides stronger differentiation between reasoning models compared to other baselines like AIME 2024, OlympiadBench and GPQA. Even the best-performing model, Gemini 2.5 Pro, achieves only 36.9% accuracy compared to human experts' 61.9%. To further enhance evaluation precision, we introduce the Expression Edit Distance (EED) Score for mathematical expression assessment, which improves sample efficiency by 204% over binary scoring. Moreover, PHYBench effectively elicits multi-step and multi-condition reasoning, providing a platform for examining models' reasoning robustness, preferences, and deficiencies. The benchmark results and dataset are publicly available at https://www.phybench.cn/.

cs.CL↗

arXiv2025

LoRASuite: Efficient LoRA Adaptation Across Large Language Model Upgrades

As Large Language Models (LLMs) are frequently updated, LoRA weights trained on earlier versions quickly become obsolete. The conventional practice of retraining LoRA weights from scratch on the latest model is costly, time-consuming, and environmentally detrimental, particularly as the diversity of LLMs and downstream tasks expands. This motivates a critical question: "How can we efficiently leverage existing LoRA weights to adapt to newer model versions?" To address this, we propose LoRASuite, a modular approach tailored specifically to various types of LLM updates. First, we compute a transfer matrix utilizing known parameters from both old and new LLMs. Next, we allocate corresponding layers and attention heads based on centered kernel alignment and cosine similarity metrics, respectively. A subsequent small-scale, skillful fine-tuning step ensures numerical stability. Experimental evaluations demonstrate that LoRASuite consistently surpasses small-scale vanilla LoRA methods. Notably, on backbone LLMs such as MiniCPM and Qwen, LoRASuite even exceeds the performance of full-scale LoRA retraining, with average improvements of +1.4 and +6.6 points on math tasks, respectively. Additionally, LoRASuite significantly reduces memory consumption by 5.5 GB and computational time by 78.23%.

cs.LG↗

arXiv2025

GOFA: A Generative One-For-All Model for Joint Graph Language Modeling

Foundation models, such as Large Language Models (LLMs) or Large Vision Models (LVMs), have emerged as one of the most powerful tools in the respective fields. However, unlike text and image data, graph data do not have a definitive structure, posing great challenges to developing a Graph Foundation Model (GFM). For example, current attempts at designing general graph models either transform graph data into a language format for LLM-based prediction or still train a GNN model with LLM as an assistant. The former can handle unlimited tasks, while the latter captures graph structure much better -- yet, no existing work can achieve both simultaneously. In this paper, we identify three key desirable properties of a GFM: self-supervised pretraining, fluidity in tasks, and graph awareness. To account for these properties, we extend the conventional language modeling to the graph domain and propose a novel generative graph language model GOFA to solve the problem. The model interleaves randomly initialized GNN layers into a frozen pre-trained LLM so that the semantic and structural modeling abilities are organically combined. GOFA is pre-trained on newly proposed graph-level next-word prediction, question-answering, and structural tasks to obtain the above GFM properties. The pre-trained model is further fine-tuned on downstream tasks to obtain task-solving ability. The fine-tuned model is evaluated on various downstream tasks, demonstrating a strong ability to solve structural and contextual problems in zero-shot scenarios. The code is available at https://github.com/JiaruiFeng/GOFA.

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arXiv2025

VACT: A Video Automatic Causal Testing System and a Benchmark

With the rapid advancement of text-conditioned Video Generation Models (VGMs), the quality of generated videos has significantly improved, bringing these models closer to functioning as ``*world simulators*'' and making real-world-level video generation more accessible and cost-effective. However, the generated videos often contain factual inaccuracies and lack understanding of fundamental physical laws. While some previous studies have highlighted this issue in limited domains through manual analysis, a comprehensive solution has not yet been established, primarily due to the absence of a generalized, automated approach for modeling and assessing the causal reasoning of these models across diverse scenarios. To address this gap, we propose VACT: an **automated** framework for modeling, evaluating, and measuring the causal understanding of VGMs in real-world scenarios. By combining causal analysis techniques with a carefully designed large language model assistant, our system can assess the causal behavior of models in various contexts without human annotation, which offers strong generalization and scalability. Additionally, we introduce multi-level causal evaluation metrics to provide a detailed analysis of the causal performance of VGMs. As a demonstration, we use our framework to benchmark several prevailing VGMs, offering insight into their causal reasoning capabilities. Our work lays the foundation for systematically addressing the causal understanding deficiencies in VGMs and contributes to advancing their reliability and real-world applicability.

cs.AI↗

arXiv2025

PiSSA: Principal Singular Values and Singular Vectors Adaptation of Large Language Models

To parameter-efficiently fine-tune (PEFT) large language models (LLMs), the low-rank adaptation (LoRA) method approximates the model changes $ΔW \in \mathbb{R}^{m \times n}$ through the product of two matrices $A \in \mathbb{R}^{m \times r}$ and $B \in \mathbb{R}^{r \times n}$, where $r \ll \min(m, n)$, $A$ is initialized with Gaussian noise, and $B$ with zeros. LoRA freezes the original model $W$ and updates the "Noise & Zero" adapter, which may lead to slow convergence. To overcome this limitation, we introduce Principal Singular values and Singular vectors Adaptation (PiSSA). PiSSA shares the same architecture as LoRA, but initializes the adaptor matrices $A$ and $B$ with the principal components of the original matrix $W$, and put the remaining components into a residual matrix $W^{res} \in \mathbb{R}^{m \times n}$ which is frozen during fine-tuning. Compared to LoRA, PiSSA updates the principal components while freezing the "residual" parts, allowing faster convergence and enhanced performance. Comparative experiments of PiSSA and LoRA across 12 different models, ranging from 184M to 70B, encompassing 5 NLG and 8 NLU tasks, reveal that PiSSA consistently outperforms LoRA under identical experimental setups. On the GSM8K benchmark, Mistral-7B fine-tuned with PiSSA achieves an accuracy of 72.86%, surpassing LoRA's 67.7% by 5.16%. Due to the same architecture, PiSSA is also compatible with quantization to further reduce the memory requirement of fine-tuning. Compared to QLoRA, QPiSSA exhibits smaller quantization errors in the initial stages. Fine-tuning LLaMA-3-70B on GSM8K, QPiSSA attains an accuracy of 86.05%, exceeding the performances of QLoRA at 81.73%. Leveraging a fast SVD technique, PiSSA can be initialized in only a few seconds, presenting a negligible cost for transitioning from LoRA to PiSSA. Code is available at https://github.com/GraphPKU/PiSSA.

cs.LG↗

arXiv2025

GNNs as Predictors of Agentic Workflow Performances

Agentic workflows invoked by Large Language Models (LLMs) have achieved remarkable success in handling complex tasks. However, optimizing such workflows is costly and inefficient in real-world applications due to extensive invocations of LLMs. To fill this gap, this position paper formulates agentic workflows as computational graphs and advocates Graph Neural Networks (GNNs) as efficient predictors of agentic workflow performances, avoiding repeated LLM invocations for evaluation. To empirically ground this position, we construct FLORA-Bench, a unified platform for benchmarking GNNs for predicting agentic workflow performances. With extensive experiments, we arrive at the following conclusion: GNNs are simple yet effective predictors. This conclusion supports new applications of GNNs and a novel direction towards automating agentic workflow optimization. All codes, models, and data are available at https://github.com/youngsoul0731/Flora-Bench.

cs.CL↗

arXiv2025

Improving Graph Neural Networks on Multi-node Tasks with the Labeling Trick

In this paper, we study using graph neural networks (GNNs) for \textit{multi-node representation learning}, where a representation for a set of more than one node (such as a link) is to be learned. Existing GNNs are mainly designed to learn single-node representations. When used for multi-node representation learning, a common practice is to directly aggregate the single-node representations obtained by a GNN. In this paper, we show a fundamental limitation of such an approach, namely the inability to capture the dependence among multiple nodes in the node set. A straightforward solution is to distinguish target nodes from others. Formalizing this idea, we propose \text{labeling trick}, which first labels nodes in the graph according to their relationships with the target node set before applying a GNN and then aggregates node representations obtained in the labeled graph for multi-node representations. Besides node sets in graphs, we also extend labeling tricks to posets, subsets and hypergraphs. Experiments verify that the labeling trick technique can boost GNNs on various tasks, including undirected link prediction, directed link prediction, hyperedge prediction, and subgraph prediction. Our work explains the superior performance of previous node-labeling-based methods and establishes a theoretical foundation for using GNNs for multi-node representation learning.

cs.LG↗

arXiv2025

Number Cookbook: Number Understanding of Language Models and How to Improve It

Large language models (LLMs) can solve an increasing number of complex reasoning tasks while making surprising mistakes in basic numerical understanding and processing (such as 9.11 > 9.9). The latter ability is essential for tackling complex arithmetic and mathematical problems and serves as a foundation for most reasoning tasks, but previous work paid little attention to it or only discussed several restricted tasks (like integer addition). In this paper, we comprehensively investigate the numerical understanding and processing ability (NUPA) of LLMs. Firstly, we introduce a benchmark covering four common numerical representations and 17 distinct numerical tasks in four major categories, resulting in 41 meaningful combinations in total. These tasks are derived from primary and secondary education curricula, encompassing nearly all everyday numerical understanding and processing scenarios, and the rules of these tasks are very simple and clear. Through the benchmark, we find that current LLMs fail frequently in many of the tasks. To study the problem, we train small models with existing and potential techniques for enhancing NUPA (such as tokenizers, PEs, and number formats), comprehensively evaluating their effectiveness using our testbed. We also finetune practical-scale LLMs on our proposed NUPA tasks and find that 1) naive finetuning can improve NUPA a lot on many but not all tasks, and 2) surprisingly, techniques designed to enhance NUPA prove ineffective for finetuning pretrained models. We further explore the impact of chain-of-thought techniques on NUPA. Our work provides a more detailed and comprehensive understanding of NUPA in LLMs. Our benchmark and code are released at https://github.com/GraphPKU/number_cookbook.

cs.CL↗

arXiv2025

Using Random Noise Equivariantly to Boost Graph Neural Networks Universally

Recent advances in Graph Neural Networks (GNNs) have explored the potential of random noise as an input feature to enhance expressivity across diverse tasks. However, naively incorporating noise can degrade performance, while architectures tailored to exploit noise for specific tasks excel yet lack broad applicability. This paper tackles these issues by laying down a theoretical framework that elucidates the increased sample complexity when introducing random noise into GNNs without careful design. We further propose Equivariant Noise GNN (ENGNN), a novel architecture that harnesses the symmetrical properties of noise to mitigate sample complexity and bolster generalization. Our experiments demonstrate that using noise equivariantly significantly enhances performance on node-level, link-level, subgraph, and graph-level tasks and achieves comparable performance to models designed for specific tasks, thereby offering a general method to boost expressivity across various graph tasks.

cs.LG↗

arXiv2025

Do Graph Diffusion Models Accurately Capture and Generate Substructure Distributions?

Diffusion models have gained popularity in graph generation tasks; however, the extent of their expressivity concerning the graph distributions they can learn is not fully understood. Unlike models in other domains, popular backbones for graph diffusion models, such as Graph Transformers, do not possess universal expressivity to accurately model the distribution scores of complex graph data. Our work addresses this limitation by focusing on the frequency of specific substructures as a key characteristic of target graph distributions. When evaluating existing models using this metric, we find that they fail to maintain the distribution of substructure counts observed in the training set when generating new graphs. To address this issue, we establish a theoretical connection between the expressivity of Graph Neural Networks (GNNs) and the overall performance of graph diffusion models, demonstrating that more expressive GNN backbones can better capture complex distribution patterns. By integrating advanced GNNs into the backbone architecture, we achieve significant improvements in substructure generation.

cs.LG↗

arXiv2025

CLOVER: Cross-Layer Orthogonal Vectors Pruning and Fine-Tuning

Decoder-only models generate tokens autoregressively by caching key/value vectors, but as the cache grows, inference becomes memory-bound. To address this issue, we introduce CLOVER (Cross-Layer Orthogonal Vectors), a novel approach that treats pairs of attention layers as a set of low-rank decompositions. CLOVER applies Singular Value Decomposition (SVD) to the $ Q $-$ K $ and $ V $-$ O $ pairs within each attention head. The resulting singular values can either guide pruning or serve as trainable parameters for efficient fine-tuning of all orthogonal vectors. After pruning or fine-tuning, these values are reintegrated into the model without increasing its parameter count. We apply CLOVER to various models, including GPT-2 XL, DeepSeek-V2-Lite, Whisper-Large-v3, Stable Diffusion XL, and LLaMA-3.2-11B-Vision. Our results demonstrate that CLOVER significantly improves pruning efficiency. For instance, the perplexity of pruning 70\% of the $ Q $-$ K $ pairs in GPT-2 XL is similar to that of pruning just 8\% with vanilla methods. Fine-tuning the singular values further results in a full-rank update, outperforming state-of-the-art methods (LoRA, DoRA, HiRA, and PiSSA) by 7.6\%, 5.5\%, 3.8\%, and 0.7\%, respectively, on eight commonsense tasks for LLaMA-2 7B.

cs.LG↗

arXiv2025

RedStar: Does Scaling Long-CoT Data Unlock Better Slow-Reasoning Systems?

Can scaling transform reasoning? In this work, we explore the untapped potential of scaling Long Chain-of-Thought (Long-CoT) data to 1000k samples, pioneering the development of a slow-thinking model, RedStar. Through extensive experiments with various LLMs and different sizes, we uncover the ingredients for specialization and scale for Long-CoT training. Surprisingly, even smaller models show significant performance gains with limited data, revealing the sample efficiency of Long-CoT and the critical role of sample difficulty in the learning process. Our findings demonstrate that Long-CoT reasoning can be effectively triggered with just a few thousand examples, while larger models achieve unparalleled improvements. We also introduce reinforcement learning (RL)-scale training as a promising direction for advancing slow-thinking systems. RedStar shines across domains: on the MATH-Hard benchmark, RedStar-code-math boosts performance from 66.2\% to 81.6\%, and on the USA Math Olympiad (AIME), it solves 46.7\% of problems using only 21k mixed-code-math datasets. In multimodal tasks like GeoQA and MathVista-GEO, RedStar-Geo achieves competitive results with minimal Long-CoT data, outperforming other slow-thinking systems like QvQ-Preview. Compared to QwQ, RedStar strikes the perfect balance between reasoning and generalizability. Our work highlights that, with careful tuning, scaling Long-CoT can unlock extraordinary reasoning capabilities-even with limited dataset and set a new standard for slow-thinking models across diverse challenges. Our data and models are released at https://huggingface.co/RedStar-Reasoning.

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