Muhan Zhang

Zehao Dong, Weidong Cao, Muhan Zhang et al. · tsinghua

The electronic design automation of analog circuits has been a longstanding challenge in the integrated circuit field due to the huge design space and complex design trade-offs among circuit specifications. In the past decades, intensive research efforts have mostly been paid to automate the transistor sizing with a given circuit topology. By recognizing the graph nature of circuits, this paper presents a Circuit Graph Neural Network (CktGNN) that simultaneously automates the circuit topology generation and device sizing based on the encoder-dependent optimization subroutines. Particularly, CktGNN encodes circuit graphs using a two-level GNN framework (of nested GNN) where circuits are represented as combinations of subgraphs in a known subgraph basis. In this way, it significantly improves design efficiency by reducing the number of subgraphs to perform message passing. Nonetheless, another critical roadblock to advancing learning-assisted circuit design automation is a lack of public benchmarks to perform canonical assessment and reproducible research. To tackle the challenge, we introduce Open Circuit Benchmark (OCB), an open-sourced dataset that contains $10$K distinct operational amplifiers with carefully-extracted circuit specifications. OCB is also equipped with communicative circuit generation and evaluation capabilities such that it can help to generalize CktGNN to design various analog circuits by producing corresponding datasets. Experiments on OCB show the extraordinary advantages of CktGNN through representation-based optimization frameworks over other recent powerful GNN baselines and human experts' manual designs. Our work paves the way toward a learning-based open-sourced design automation for analog circuits. Our source code is available at \url{https://github.com/zehao-dong/CktGNN}.

Ling Yang, Ye Tian, Minkai Xu et al.

GNN-to-MLP distillation aims to utilize knowledge distillation (KD) to learn computationally-efficient multi-layer perceptron (student MLP) on graph data by mimicking the output representations of teacher GNN. Existing methods mainly make the MLP to mimic the GNN predictions over a few class labels. However, the class space may not be expressive enough for covering numerous diverse local graph structures, thus limiting the performance of knowledge transfer from GNN to MLP. To address this issue, we propose to learn a new powerful graph representation space by directly labeling nodes' diverse local structures for GNN-to-MLP distillation. Specifically, we propose a variant of VQ-VAE to learn a structure-aware tokenizer on graph data that can encode each node's local substructure as a discrete code. The discrete codes constitute a codebook as a new graph representation space that is able to identify different local graph structures of nodes with the corresponding code indices. Then, based on the learned codebook, we propose a new distillation target, namely soft code assignments, to directly transfer the structural knowledge of each node from GNN to MLP. The resulting framework VQGraph achieves new state-of-the-art performance on GNN-to-MLP distillation in both transductive and inductive settings across seven graph datasets. We show that VQGraph with better performance infers faster than GNNs by 828x, and also achieves accuracy improvement over GNNs and stand-alone MLPs by 3.90% and 28.05% on average, respectively. Code: https://github.com/YangLing0818/VQGraph.

Haotong Yang, Zhouchen Lin, Muhan Zhang

Most knowledge graphs (KGs) are incomplete, which motivates one important research topic on automatically complementing knowledge graphs. However, evaluation of knowledge graph completion (KGC) models often ignores the incompleteness -- facts in the test set are ranked against all unknown triplets which may contain a large number of missing facts not included in the KG yet. Treating all unknown triplets as false is called the closed-world assumption. This closed-world assumption might negatively affect the fairness and consistency of the evaluation metrics. In this paper, we study KGC evaluation under a more realistic setting, namely the open-world assumption, where unknown triplets are considered to include many missing facts not included in the training or test sets. For the currently most used metrics such as mean reciprocal rank (MRR) and Hits@K, we point out that their behavior may be unexpected under the open-world assumption. Specifically, with not many missing facts, their numbers show a logarithmic trend with respect to the true strength of the model, and thus, the metric increase could be insignificant in terms of reflecting the true model improvement. Further, considering the variance, we show that the degradation in the reported numbers may result in incorrect comparisons between different models, where stronger models may have lower metric numbers. We validate the phenomenon both theoretically and experimentally. Finally, we suggest possible causes and solutions for this problem. Our code and data are available at https://github.com/GraphPKU/Open-World-KG .

Xiyuan Wang, Haotong Yang, Muhan Zhang

In this work, we propose a novel link prediction model and further boost it by studying graph incompleteness. First, we introduce MPNN-then-SF, an innovative architecture leveraging structural feature (SF) to guide MPNN's representation pooling, with its implementation, namely Neural Common Neighbor (NCN). NCN exhibits superior expressiveness and scalability compared with existing models, which can be classified into two categories: SF-then-MPNN, augmenting MPNN's input with SF, and SF-and-MPNN, decoupling SF and MPNN. Second, we investigate the impact of graph incompleteness -- the phenomenon that some links are unobserved in the input graph -- on SF, like the common neighbor. Through dataset visualization, we observe that incompleteness reduces common neighbors and induces distribution shifts, significantly affecting model performance. To address this issue, we propose to use a link prediction model to complete the common neighbor structure. Combining this method with NCN, we propose Neural Common Neighbor with Completion (NCNC). NCN and NCNC outperform recent strong baselines by large margins, and NCNC further surpasses state-of-the-art models in standard link prediction benchmarks. Our code is available at https://github.com/GraphPKU/NeuralCommonNeighbor.

Zehao Dong, Muhan Zhang, Fuhai Li et al.

Optimization of directed acyclic graph (DAG) structures has many applications, such as neural architecture search (NAS) and probabilistic graphical model learning. Encoding DAGs into real vectors is a dominant component in most neural-network-based DAG optimization frameworks. Currently, most DAG encoders use an asynchronous message passing scheme which sequentially processes nodes according to the dependency between nodes in a DAG. That is, a node must not be processed until all its predecessors are processed. As a result, they are inherently not parallelizable. In this work, we propose a Parallelizable Attention-based Computation structure Encoder (PACE) that processes nodes simultaneously and encodes DAGs in parallel. We demonstrate the superiority of PACE through encoder-dependent optimization subroutines that search the optimal DAG structure based on the learned DAG embeddings. Experiments show that PACE not only improves the effectiveness over previous sequential DAG encoders with a significantly boosted training and inference speed, but also generates smooth latent (DAG encoding) spaces that are beneficial to downstream optimization subroutines. Our source code is available at \url{https://github.com/zehao-dong/PACE}

Yanbo Wang, Muhan Zhang

Research on the theoretical expressiveness of Graph Neural Networks (GNNs) has developed rapidly, and many methods have been proposed to enhance the expressiveness. However, most methods do not have a uniform expressiveness measure except for a few that strictly follow the $k$-dimensional Weisfeiler-Lehman ($k$-WL) test hierarchy, leading to difficulties in quantitatively comparing their expressiveness. Previous research has attempted to use datasets for measurement, but facing problems with difficulty (any model surpassing 1-WL has nearly 100% accuracy), granularity (models tend to be either 100% correct or near random guess), and scale (only several essentially different graphs involved). To address these limitations, we study the realized expressive power that a practical model instance can achieve using a novel expressiveness dataset, BREC, which poses greater difficulty (with up to 4-WL-indistinguishable graphs), finer granularity (enabling comparison of models between 1-WL and 3-WL), a larger scale (consisting of 800 1-WL-indistinguishable graphs that are non-isomorphic to each other). We synthetically test 23 models with higher-than-1-WL expressiveness on BREC. Our experiment gives the first thorough measurement of the realized expressiveness of those state-of-the-art beyond-1-WL GNN models and reveals the gap between theoretical and realized expressiveness. Dataset and evaluation codes are released at: https://github.com/GraphPKU/BREC.

Fanxu Meng, Haotong Yang, Yiding Wang et al. · pku

The human brain is naturally equipped to comprehend and interpret visual information rapidly. When confronted with complex problems or concepts, we use flowcharts, sketches, and diagrams to aid our thought process. Leveraging this inherent ability can significantly enhance logical reasoning. However, current Large Language Models (LLMs) do not utilize such visual intuition to help their thinking. Even the most advanced version language models (e.g., GPT-4V and LLaVA) merely align images into textual space, which means their reasoning processes remain purely verbal. To mitigate such limitations, we present a Chain of Images (CoI) approach, which can convert complex language reasoning problems to simple pattern recognition by generating a series of images as intermediate representations. Furthermore, we have developed a CoI evaluation dataset encompassing 15 distinct domains where images can intuitively aid problem-solving. Based on this dataset, we aim to construct a benchmark to assess the capability of future multimodal large-scale models to leverage images for reasoning. In supporting our CoI reasoning, we introduce a symbolic multimodal large language model (SyMLLM) that generates images strictly based on language instructions and accepts both text and image as input. Experiments on Geometry, Chess and Common Sense tasks sourced from the CoI evaluation dataset show that CoI improves performance significantly over the pure-language Chain of Thoughts (CoT) baselines. The code is available at https://github.com/GraphPKU/CoI.

Jiaqi Li, Mengmeng Wang, Zilong Zheng et al.

Large language models (LLMs), despite their impressive performance in various language tasks, are typically limited to processing texts within context-window size. This limitation has spurred significant research efforts to enhance LLMs' long-context understanding with high-quality long-sequence benchmarks. However, prior datasets in this regard suffer from shortcomings, such as short context length compared to the context window of modern LLMs; outdated documents that have data leakage problems; and an emphasis on short dependency tasks rather than long dependency tasks. In this paper, we present LooGLE, a Long Context Generic Language Evaluation benchmark for LLMs' long context understanding. LooGLE features relatively new documents post-2022, with over 24,000 tokens per document and 6,000 newly generated questions spanning diverse domains. Human annotators meticulously crafted more than 1,100 high-quality question-answer pairs to meet the long dependency requirements. These pairs underwent thorough cross-validation, yielding the most precise assessment of LLMs' long dependency capabilities. The evaluation of eight state-of-the-art LLMs on LooGLE revealed key findings: (i) commercial models outperformed open-sourced models; (ii) LLMs excelled in short dependency tasks like short question-answering and cloze tasks but struggled with more intricate long dependency tasks; (iii) in-context learning and chaining thoughts offered only marginal improvements; (iv) retrieval-based techniques demonstrated substantial benefits for short question-answering, while strategies for extending context window length had limited impact on long context understanding. As such, LooGLE not only provides a systematic and comprehensive evaluation schema on long-context LLMs, but also sheds light on future development of enhanced models towards "true long-context understanding".

Lecheng Kong, Jiarui Feng, Hao Liu et al.

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.

Haorui Wang, Haoteng Yin, Muhan Zhang et al.

Graph neural networks (GNN) have shown great advantages in many graph-based learning tasks but often fail to predict accurately for a task-based on sets of nodes such as link/motif prediction and so on. Many works have recently proposed to address this problem by using random node features or node distance features. However, they suffer from either slow convergence, inaccurate prediction, or high complexity. In this work, we revisit GNNs that allow using positional features of nodes given by positional encoding (PE) techniques such as Laplacian Eigenmap, Deepwalk, etc. GNNs with PE often get criticized because they are not generalizable to unseen graphs (inductive) or stable. Here, we study these issues in a principled way and propose a provable solution, a class of GNN layers termed PEG with rigorous mathematical analysis. PEG uses separate channels to update the original node features and positional features. PEG imposes permutation equivariance w.r.t. the original node features and imposes $O(p)$ (orthogonal group) equivariance w.r.t. the positional features simultaneously, where $p$ is the dimension of used positional features. Extensive link prediction experiments over 8 real-world networks demonstrate the advantages of PEG in generalization and scalability.

Yinan Huang, William Lu, Joshua Robinson et al.

Designing effective positional encodings for graphs is key to building powerful graph transformers and enhancing message-passing graph neural networks. Although widespread, using Laplacian eigenvectors as positional encodings faces two fundamental challenges: (1) \emph{Non-uniqueness}: there are many different eigendecompositions of the same Laplacian, and (2) \emph{Instability}: small perturbations to the Laplacian could result in completely different eigenspaces, leading to unpredictable changes in positional encoding. Despite many attempts to address non-uniqueness, most methods overlook stability, leading to poor generalization on unseen graph structures. We identify the cause of instability to be a ``hard partition'' of eigenspaces. Hence, we introduce Stable and Expressive Positional Encodings (SPE), an architecture for processing eigenvectors that uses eigenvalues to ``softly partition'' eigenspaces. SPE is the first architecture that is (1) provably stable, and (2) universally expressive for basis invariant functions whilst respecting all symmetries of eigenvectors. Besides guaranteed stability, we prove that SPE is at least as expressive as existing methods, and highly capable of counting graph structures. Finally, we evaluate the effectiveness of our method on molecular property prediction, and out-of-distribution generalization tasks, finding improved generalization compared to existing positional encoding methods. Our code is available at \url{https://github.com/Graph-COM/SPE}.

Xiaojuan Tang, Song-Chun Zhu, Yitao Liang et al.

Knowledge graph (KG) reasoning is an important problem for knowledge graphs. In this paper, we propose a novel and principled framework called \textbf{RulE} (stands for {Rul}e {E}mbedding) to effectively leverage logical rules to enhance KG reasoning. Unlike knowledge graph embedding (KGE) methods, RulE learns rule embeddings from existing triplets and first-order {rules} by jointly representing \textbf{entities}, \textbf{relations} and \textbf{logical rules} in a unified embedding space. Based on the learned rule embeddings, a confidence score can be calculated for each rule, reflecting its consistency with the observed triplets. This allows us to perform logical rule inference in a soft way, thus alleviating the brittleness of logic. On the other hand, RulE injects prior logical rule information into the embedding space, enriching and regularizing the entity/relation embeddings. This makes KGE alone perform better too. RulE is conceptually simple and empirically effective. We conduct extensive experiments to verify each component of RulE. Results on multiple benchmarks reveal that our model outperforms the majority of existing embedding-based and rule-based approaches.

Zuoyu Yan, Junru Zhou, Liangcai Gao et al. · pku

We investigate the enhancement of graph neural networks' (GNNs) representation power through their ability in substructure counting. Recent advances have seen the adoption of subgraph GNNs, which partition an input graph into numerous subgraphs, subsequently applying GNNs to each to augment the graph's overall representation. Despite their ability to identify various substructures, subgraph GNNs are hindered by significant computational and memory costs. In this paper, we tackle a critical question: Is it possible for GNNs to count substructures both \textbf{efficiently} and \textbf{provably}? Our approach begins with a theoretical demonstration that the distance to rooted nodes in subgraphs is key to boosting the counting power of subgraph GNNs. To avoid the need for repetitively applying GNN across all subgraphs, we introduce precomputed structural embeddings that encapsulate this crucial distance information. Experiments validate that our proposed model retains the counting power of subgraph GNNs while achieving significantly faster performance.

Cai Zhou, Xiyuan Wang, Muhan Zhang · mit

Node-level random walk has been widely used to improve Graph Neural Networks. However, there is limited attention to random walk on edge and, more generally, on $k$-simplices. This paper systematically analyzes how random walk on different orders of simplicial complexes (SC) facilitates GNNs in their theoretical expressivity. First, on $0$-simplices or node level, we establish a connection between existing positional encoding (PE) and structure encoding (SE) methods through the bridge of random walk. Second, on $1$-simplices or edge level, we bridge edge-level random walk and Hodge $1$-Laplacians and design corresponding edge PE respectively. In the spatial domain, we directly make use of edge level random walk to construct EdgeRWSE. Based on the spectral analysis of Hodge $1$-Laplcians, we propose Hodge1Lap, a permutation equivariant and expressive edge-level positional encoding. Third, we generalize our theory to random walk on higher-order simplices and propose the general principle to design PE on simplices based on random walk and Hodge Laplacians. Inter-level random walk is also introduced to unify a wide range of simplicial networks. Extensive experiments verify the effectiveness of our random walk-based methods.

Xiyuan Wang, Muhan Zhang

Spectral Graph Neural Network is a kind of Graph Neural Network (GNN) based on graph signal filters. Some models able to learn arbitrary spectral filters have emerged recently. However, few works analyze the expressive power of spectral GNNs. This paper studies spectral GNNs' expressive power theoretically. We first prove that even spectral GNNs without nonlinearity can produce arbitrary graph signals and give two conditions for reaching universality. They are: 1) no multiple eigenvalues of graph Laplacian, and 2) no missing frequency components in node features. We also establish a connection between the expressive power of spectral GNNs and Graph Isomorphism (GI) testing, the latter of which is often used to characterize spatial GNNs' expressive power. Moreover, we study the difference in empirical performance among different spectral GNNs with the same expressive power from an optimization perspective, and motivate the use of an orthogonal basis whose weight function corresponds to the graph signal density in the spectrum. Inspired by the analysis, we propose JacobiConv, which uses Jacobi basis due to its orthogonality and flexibility to adapt to a wide range of weight functions. JacobiConv deserts nonlinearity while outperforming all baselines on both synthetic and real-world datasets.

Yinan Huang, Xingang Peng, Jianzhu Ma et al.

Deep learning has achieved tremendous success in designing novel chemical compounds with desirable pharmaceutical properties. In this work, we focus on a new type of drug design problem -- generating a small "linker" to physically attach two independent molecules with their distinct functions. The main computational challenges include: 1) the generation of linkers is conditional on the two given molecules, in contrast to generating full molecules from scratch in previous works; 2) linkers heavily depend on the anchor atoms of the two molecules to be connected, which are not known beforehand; 3) 3D structures and orientations of the molecules need to be considered to avoid atom clashes, for which equivariance to E(3) group are necessary. To address these problems, we propose a conditional generative model, named 3DLinker, which is able to predict anchor atoms and jointly generate linker graphs and their 3D structures based on an E(3) equivariant graph variational autoencoder. So far as we know, there are no previous models that could achieve this task. We compare our model with multiple conditional generative models modified from other molecular design tasks and find that our model has a significantly higher rate in recovering molecular graphs, and more importantly, accurately predicting the 3D coordinates of all the atoms.

Yinan Huang, Xingang Peng, Jianzhu Ma et al.

Message Passing Neural Networks (MPNNs) are a widely used class of Graph Neural Networks (GNNs). The limited representational power of MPNNs inspires the study of provably powerful GNN architectures. However, knowing one model is more powerful than another gives little insight about what functions they can or cannot express. It is still unclear whether these models are able to approximate specific functions such as counting certain graph substructures, which is essential for applications in biology, chemistry and social network analysis. Motivated by this, we propose to study the counting power of Subgraph MPNNs, a recent and popular class of powerful GNN models that extract rooted subgraphs for each node, assign the root node a unique identifier and encode the root node's representation within its rooted subgraph. Specifically, we prove that Subgraph MPNNs fail to count more-than-4-cycles at node level, implying that node representations cannot correctly encode the surrounding substructures like ring systems with more than four atoms. To overcome this limitation, we propose I$^2$-GNNs to extend Subgraph MPNNs by assigning different identifiers for the root node and its neighbors in each subgraph. I$^2$-GNNs' discriminative power is shown to be strictly stronger than Subgraph MPNNs and partially stronger than the 3-WL test. More importantly, I$^2$-GNNs are proven capable of counting all 3, 4, 5 and 6-cycles, covering common substructures like benzene rings in organic chemistry, while still keeping linear complexity. To the best of our knowledge, it is the first linear-time GNN model that can count 6-cycles with theoretical guarantees. We validate its counting power in cycle counting tasks and demonstrate its competitive performance in molecular prediction benchmarks.

Jinyu Yang, Cheng Yang, Junze Chen et al.

Relational databases (RDBs) remain the cornerstone of modern data systems and support diverse predictive tasks. Recent relational deep learning (RDL) methods enable end-to-end prediction by converting RDBs into graphs, where rows are represented as nodes and inter-table interactions are represented as edges, and then applying graph-based models for representation learning. Despite the strong capability of RDL, effective self-supervised pre-training for RDBs remains non-trivial. RDB tasks often require multi-faceted information across different perspectives and granularities. For example, user churn classification may rely more on interaction patterns, whereas consumption value prediction requires both user-item behaviors and intrinsic user attributes for fine-grained regression. Such heterogeneous needs challenge RDB representation learning, as pre-training objectives should cover comprehensive information for downstream adaptation. However, existing SSL methods typically derive supervision from a single facet, such as node-level intrinsic attributes or subgraph-level relational structures, providing limited adaptability. To this end, we propose RelPrism, a multi-faceted self-supervised learning framework for RDBs. RelPrism constructs intrinsic, relational, and hybrid attributes from distinct perspectives, and applies multi-granularity clustering to each perspective to form corresponding pseudo-task pools. Pre-training over these pools exposes representations to broader perspectives and granularity levels, yielding a stronger basis for downstream adaptation. Experiments on 14 tasks across 5 real-world datasets show that RelPrism improves ROC-AUC by 4.15% for classification and reduces MAE by 10.75% for regression over state-of-the-art baselines. Our code is available at https://anonymous.4open.science/r/RelPrism.

Yang Hu, Xiyuan Wang, Zhouchen Lin et al.

Link prediction is one important application of graph neural networks (GNNs). Most existing GNNs for link prediction are based on one-dimensional Weisfeiler-Lehman (1-WL) test. 1-WL-GNNs first compute node representations by iteratively passing neighboring node features to the center, and then obtain link representations by aggregating the pairwise node representations. As pointed out by previous works, this two-step procedure results in low discriminating power, as 1-WL-GNNs by nature learn node-level representations instead of link-level. In this paper, we study a completely different approach which can directly obtain node pair (link) representations based on \textit{two-dimensional Weisfeiler-Lehman (2-WL) tests}. 2-WL tests directly use links (2-tuples) as message passing units instead of nodes, and thus can directly obtain link representations. We theoretically analyze the expressive power of 2-WL tests to discriminate non-isomorphic links, and prove their superior link discriminating power than 1-WL. Based on different 2-WL variants, we propose a series of novel 2-WL-GNN models for link prediction. Experiments on a wide range of real-world datasets demonstrate their competitive performance to state-of-the-art baselines and superiority over plain 1-WL-GNNs.

Jiarui Feng, Yixin Chen, Fuhai Li et al.

The most popular design paradigm for Graph Neural Networks (GNNs) is 1-hop message passing -- aggregating information from 1-hop neighbors repeatedly. However, the expressive power of 1-hop message passing is bounded by the Weisfeiler-Lehman (1-WL) test. Recently, researchers extended 1-hop message passing to K-hop message passing by aggregating information from K-hop neighbors of nodes simultaneously. However, there is no work on analyzing the expressive power of K-hop message passing. In this work, we theoretically characterize the expressive power of K-hop message passing. Specifically, we first formally differentiate two different kernels of K-hop message passing which are often misused in previous works. We then characterize the expressive power of K-hop message passing by showing that it is more powerful than 1-WL and can distinguish almost all regular graphs. Despite the higher expressive power, we show that K-hop message passing still cannot distinguish some simple regular graphs and its expressive power is bounded by 3-WL. To further enhance its expressive power, we introduce a KP-GNN framework, which improves K-hop message passing by leveraging the peripheral subgraph information in each hop. We show that KP-GNN can distinguish many distance regular graphs which could not be distinguished by previous distance encoding or 3-WL methods. Experimental results verify the expressive power and effectiveness of KP-GNN. KP-GNN achieves competitive results across all benchmark datasets.

Xiyuan Wang, Muhan Zhang

We introduce PyTorch Geometric High Order (PyGHO), a library for High Order Graph Neural Networks (HOGNNs) that extends PyTorch Geometric (PyG). Unlike ordinary Message Passing Neural Networks (MPNNs) that exchange messages between nodes, HOGNNs, encompassing subgraph GNNs and k-WL GNNs, encode node tuples, a method previously lacking a standardized framework and often requiring complex coding. PyGHO's main objective is to provide an unified and user-friendly interface for various HOGNNs. It accomplishes this through streamlined data structures for node tuples, comprehensive data processing utilities, and a flexible suite of operators for high-order GNN methodologies. In this work, we present a detailed in-depth of PyGHO and compare HOGNNs implemented with PyGHO with their official implementation on real-world tasks. PyGHO achieves up to $50\%$ acceleration and reduces the code needed for implementation by an order of magnitude. Our library is available at \url{https://github.com/GraphPKU/PygHO}.

Cai Zhou, Zijie Chen, Zian Li et al.

Many generative tasks in chemistry and science involve distributions invariant to group symmetries (e.g., permutation and rotation). A common strategy enforces invariance and equivariance through architectural constraints such as equivariant denoisers and invariant priors. In this paper, we challenge this tradition through the alternative canonicalization perspective: first map each sample to an orbit representative with a canonical pose or order, train an unconstrained (non-equivariant) diffusion or flow model on the canonical slice, and finally recover the invariant distribution by sampling a random symmetry transform at generation time. Building on a formal quotient-space perspective, our work provides a comprehensive theory of canonical diffusion by proving: (i) the correctness, universality and superior expressivity of canonical generative models over invariant targets; (ii) canonicalization accelerates training by removing diffusion score complexity induced by group mixtures and reducing conditional variance in flow matching. We then show that aligned priors and optimal transport act complementarily with canonicalization and further improves training efficiency. We instantiate the framework for molecular graph generation under $S_n \times SE(3)$ symmetries. By leveraging geometric spectra-based canonicalization and mild positional encodings, canonical diffusion significantly outperforms equivariant baselines in 3D molecule generation tasks, with similar or even less computation. Moreover, with a novel architecture Canon, CanonFlow achieves state-of-the-art performance on the challenging GEOM-DRUG dataset, and the advantage remains large in few-step generation.

Haoteng Yin, Muhan Zhang, Jianguo Wang et al.

Subgraph-based graph representation learning (SGRL) has recently emerged as a powerful tool in many prediction tasks on graphs due to its advantages in model expressiveness and generalization ability. Most previous SGRL models face computational challenges associated with the high cost of subgraph extraction for each training or test query. Recently, SUREL was proposed to accelerate SGRL, which samples random walks offline and joins these walks online as a proxy of subgraph for representation learning. Thanks to the reusability of sampled walks across different queries, SUREL achieves state-of-the-art performance in terms of scalability and prediction accuracy. However, SUREL still suffers from high computational overhead caused by node duplication in sampled walks. In this work, we propose a novel framework SUREL+ that upgrades SUREL by using node sets instead of walks to represent subgraphs. This set-based representation eliminates repeated nodes by definition but can also be irregular in size. To address this issue, we design a customized sparse data structure to efficiently store and access node sets and provide a specialized operator to join them in parallel batches. SUREL+ is modularized to support multiple types of set samplers, structural features, and neural encoders to complement the structural information loss after the reduction from walks to sets. Extensive experiments have been performed to validate SUREL+ in the prediction tasks of links, relation types, and higher-order patterns. SUREL+ achieves 3-11$\times$ speedups of SUREL while maintaining comparable or even better prediction performance; compared to other SGRL baselines, SUREL+ achieves $\sim$20$\times$ speedups and significantly improves the prediction accuracy.

Yu Huang, Min Zhou, Menglin Yang et al.

Recent advancements in graph learning have revolutionized the way to understand and analyze data with complex structures. Notably, Graph Neural Networks (GNNs), i.e. neural network architectures designed for learning graph representations, have become a popular paradigm. With these models being usually characterized by intuition-driven design or highly intricate components, placing them within the theoretical analysis framework to distill the core concepts, helps understand the key principles that drive the functionality better and guide further development. Given this surge in interest, this article provides a comprehensive summary of the theoretical foundations and breakthroughs concerning the approximation and learning behaviors intrinsic to prevalent graph learning models. Encompassing discussions on fundamental aspects such as expressiveness power, generalization, optimization, and unique phenomena such as over-smoothing and over-squashing, this piece delves into the theoretical foundations and frontier driving the evolution of graph learning. In addition, this article also presents several challenges and further initiates discussions on possible solutions.

Jiarui Feng, Lecheng Kong, Hao Liu et al.

Message passing neural networks (MPNNs) have emerged as the most popular framework of graph neural networks (GNNs) in recent years. However, their expressive power is limited by the 1-dimensional Weisfeiler-Lehman (1-WL) test. Some works are inspired by $k$-WL/FWL (Folklore WL) and design the corresponding neural versions. Despite the high expressive power, there are serious limitations in this line of research. In particular, (1) $k$-WL/FWL requires at least $O(n^k)$ space complexity, which is impractical for large graphs even when $k=3$; (2) The design space of $k$-WL/FWL is rigid, with the only adjustable hyper-parameter being $k$. To tackle the first limitation, we propose an extension, $(k,t)$-FWL. We theoretically prove that even if we fix the space complexity to $O(n^k)$ (for any $k\geq 2$) in $(k,t)$-FWL, we can construct an expressiveness hierarchy up to solving the graph isomorphism problem. To tackle the second problem, we propose $k$-FWL+, which considers any equivariant set as neighbors instead of all nodes, thereby greatly expanding the design space of $k$-FWL. Combining these two modifications results in a flexible and powerful framework $(k,t)$-FWL+. We demonstrate $(k,t)$-FWL+ can implement most existing models with matching expressiveness. We then introduce an instance of $(k,t)$-FWL+ called Neighborhood$^2$-FWL (N$^2$-FWL), which is practically and theoretically sound. We prove that N$^2$-FWL is no less powerful than 3-WL, and can encode many substructures while only requiring $O(n^2)$ space. Finally, we design its neural version named N$^2$-GNN and evaluate its performance on various tasks. N$^2$-GNN achieves record-breaking results on ZINC-Subset (0.059), outperforming previous SOTA results by 10.6%. Moreover, N$^2$-GNN achieves new SOTA results on the BREC dataset (71.8%) among all existing high-expressive GNN methods.

Hao Liu, Jiarui Feng, Lecheng Kong et al.

Designing a single model to address multiple tasks has been a long-standing objective in artificial intelligence. Recently, large language models have demonstrated exceptional capability in solving different tasks within the language domain. However, a unified model for various graph tasks remains underexplored, primarily due to the challenges unique to the graph learning domain. First, graph data from different areas carry distinct attributes and follow different distributions. Such discrepancy makes it hard to represent graphs in a single representation space. Second, tasks on graphs diversify into node, link, and graph tasks, requiring distinct embedding strategies. Finally, an appropriate graph prompting paradigm for in-context learning is unclear. We propose \textbf{One for All (OFA)}, the first general framework that can use a single graph model to address the above challenges. Specifically, OFA proposes text-attributed graphs to unify different graph data by describing nodes and edges with natural language and uses language models to encode the diverse and possibly cross-domain text attributes to feature vectors in the same embedding space. Furthermore, OFA introduces the concept of nodes-of-interest to standardize different tasks with a single task representation. For in-context learning on graphs, OFA introduces a novel graph prompting paradigm that appends prompting substructures to the input graph, which enables it to address varied tasks without fine-tuning. We train the OFA model using graph data from multiple domains (including citation networks, molecular graphs, knowledge graphs, etc.) simultaneously and evaluate its ability in supervised, few-shot, and zero-shot learning scenarios. OFA performs well across different tasks, making it the first general-purpose across-domains classification model on graphs.

Lecheng Kong, Yixin Chen, Muhan Zhang

Graph Neural Networks (GNNs) have recently been applied to graph learning tasks and achieved state-of-the-art (SOTA) results. However, many competitive methods run GNNs multiple times with subgraph extraction and customized labeling to capture information that is hard for normal GNNs to learn. Such operations are time-consuming and do not scale to large graphs. In this paper, we propose an efficient GNN framework called Geodesic GNN (GDGNN) that requires only one GNN run and injects conditional relationships between nodes into the model without labeling. This strategy effectively reduces the runtime of subgraph methods. Specifically, we view the shortest paths between two nodes as the spatial graph context of the neighborhood around them. The GNN embeddings of nodes on the shortest paths are used to generate geodesic representations. Conditioned on the geodesic representations, GDGNN can generate node, link, and graph representations that carry much richer structural information than plain GNNs. We theoretically prove that GDGNN is more powerful than plain GNNs. We present experimental results to show that GDGNN achieves highly competitive performance with SOTA GNN models on various graph learning tasks while taking significantly less time.

Zian Li, Xiyuan Wang, Yinan Huang et al.

Graph Neural Networks (GNNs) are often used for tasks involving the 3D geometry of a given graph, such as molecular dynamics simulation. While incorporating Euclidean distance into Message Passing Neural Networks (referred to as Vanilla DisGNN) is a straightforward way to learn the geometry, it has been demonstrated that Vanilla DisGNN is geometrically incomplete. In this work, we first construct families of novel and symmetric geometric graphs that Vanilla DisGNN cannot distinguish even when considering all-pair distances, which greatly expands the existing counterexample families. Our counterexamples show the inherent limitation of Vanilla DisGNN to capture symmetric geometric structures. We then propose $k$-DisGNNs, which can effectively exploit the rich geometry contained in the distance matrix. We demonstrate the high expressive power of $k$-DisGNNs from three perspectives: 1. They can learn high-order geometric information that cannot be captured by Vanilla DisGNN. 2. They can unify some existing well-designed geometric models. 3. They are universal function approximators from geometric graphs to scalars (when $k\geq 2$) and vectors (when $k\geq 3$). Most importantly, we establish a connection between geometric deep learning (GDL) and traditional graph representation learning (GRL), showing that those highly expressive GNN models originally designed for GRL can also be applied to GDL with impressive performance, and that existing complicated, equivariant models are not the only solution. Experiments verify our theory. Our $k$-DisGNNs achieve many new state-of-the-art results on MD17.

Yewei Liu, Xiyuan Wang, Yansheng Mao et al.

We propose SHINE (Scalable Hyper In-context NEtwork), a scalable hypernetwork that can map diverse meaningful contexts into high-quality LoRA adapters for large language models (LLM). By reusing the frozen LLM's own parameters in an in-context hypernetwork design and introducing architectural innovations, SHINE overcomes key limitations of prior hypernetworks and achieves strong expressive power with a relatively small number of parameters. We introduce a pretraining and instruction fine-tuning pipeline, and train our hypernetwork to generate high quality LoRA adapters from diverse meaningful contexts in a single forward pass. It updates LLM parameters without any fine-tuning, and immediately enables complex question answering tasks related to the context without directly accessing the context, effectively transforming in-context knowledge to in-parameter knowledge in one pass. Our work achieves outstanding results on various tasks, greatly saves time, computation and memory costs compared to SFT-based LLM adaptation, and shows great potential for scaling. Our code is available at https://github.com/Yewei-Liu/SHINE

Hao Liu, Jiarui Feng, Lecheng Kong et al.

Graph Neural Networks (GNNs) have become popular in Graph Representation Learning (GRL). One fundamental application is few-shot node classification. Most existing methods follow the meta learning paradigm, showing the ability of fast generalization to few-shot tasks. However, recent works indicate that graph contrastive learning combined with fine-tuning can significantly outperform meta learning methods. Despite the empirical success, there is limited understanding of the reasons behind it. In our study, we first identify two crucial advantages of contrastive learning compared to meta learning, including (1) the comprehensive utilization of graph nodes and (2) the power of graph augmentations. To integrate the strength of both contrastive learning and meta learning on the few-shot node classification tasks, we introduce a new paradigm: Contrastive Few-Shot Node Classification (COLA). Specifically, COLA employs graph augmentations to identify semantically similar nodes, which enables the construction of meta-tasks without the need for label information. Therefore, COLA can utilize all nodes to construct meta-tasks, further reducing the risk of overfitting. Through extensive experiments, we validate the essentiality of each component in our design and demonstrate that COLA achieves new state-of-the-art on all tasks.

Xiyuan Wang, Pan Li, Muhan Zhang

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.

Muhan Zhang

In the realm of deep learning, the self-attention mechanism has substantiated its pivotal role across a myriad of tasks, encompassing natural language processing and computer vision. Despite achieving success across diverse applications, the traditional self-attention mechanism primarily leverages linear transformations for the computation of query, key, and value (QKV), which may not invariably be the optimal choice under specific circumstances. This paper probes into a novel methodology for QKV computation-implementing a specially-designed neural network structure for the calculation. Utilizing a modified Marian model, we conducted experiments on the IWSLT 2017 German-English translation task dataset and juxtaposed our method with the conventional approach. The experimental results unveil a significant enhancement in BLEU scores with our method. Furthermore, our approach also manifested superiority when training the Roberta model with the Wikitext-103 dataset, reflecting a notable reduction in model perplexity compared to its original counterpart. These experimental outcomes not only validate the efficacy of our method but also reveal the immense potential in optimizing the self-attention mechanism through neural network-based QKV computation, paving the way for future research and practical applications. The source code and implementation details for our proposed method can be accessed at https://github.com/ocislyjrti/NeuralAttention.

Yanbo Wang, Jiaxuan You, Chuan Shi et al.

Relational Databases (RDBs) are the backbone of modern business, yet they lack foundation models comparable to those in text or vision. A key obstacle is that high-quality RDBs are private, scarce and structurally heterogeneous, making internet-scale pre-training infeasible. To overcome this data scarcity, We introduce $\textbf{RDB-PFN}$, the first relational foundation model trained purely via $\textbf{synthetic data}$. Inspired by Prior-Data Fitted Networks (PFNs) where synthetic data generated from Structural Causal Models (SCMs) enables reasoning on single tables, we design a $\textbf{Relational Prior Generator}$ to create an infinite stream of diverse RDBs from scratch. Pre-training on $\textbf{over 2 million}$ synthetic single-table and relational tasks, RDB-PFN learns to adapt to any new database instantly via genuine $\textbf{in-context learning}$. Experiments verify RDB-PFN achieves strong few-shot performance on 19 real-world relational prediction tasks, outperforming graph-based and single-table foundation-model baselines (given the same DFS-linearized inputs), while using a lightweight architecture and fast inference. The code is available at https://github.com/MuLabPKU/RDBPFN

Xiyuan Wang, Muhan Zhang

Modeling molecular potential energy surface is of pivotal importance in science. Graph Neural Networks have shown great success in this field. However, their message passing schemes need special designs to capture geometric information and fulfill symmetry requirement like rotation equivariance, leading to complicated architectures. To avoid these designs, we introduce a novel local frame method to molecule representation learning and analyze its expressivity. Projected onto a frame, equivariant features like 3D coordinates are converted to invariant features, so that we can capture geometric information with these projections and decouple the symmetry requirement from GNN design. Theoretically, we prove that given non-degenerate frames, even ordinary GNNs can encode molecules injectively and reach maximum expressivity with coordinate projection and frame-frame projection. In experiments, our model uses a simple ordinary GNN architecture yet achieves state-of-the-art accuracy. The simpler architecture also leads to higher scalability. Our model only takes about 30% inference time and 10% GPU memory compared to the most efficient baselines.

Junru Zhou, Jiarui Feng, Xiyuan Wang et al.

The ability of graph neural networks (GNNs) to count certain graph substructures, especially cycles, is important for the success of GNNs on a wide range of tasks. It has been recently used as a popular metric for evaluating the expressive power of GNNs. Many of the proposed GNN models with provable cycle counting power are based on subgraph GNNs, i.e., extracting a bag of subgraphs from the input graph, generating representations for each subgraph, and using them to augment the representation of the input graph. However, those methods require heavy preprocessing, and suffer from high time and memory costs. In this paper, we overcome the aforementioned limitations of subgraph GNNs by proposing a novel class of GNNs -- $d$-Distance-Restricted FWL(2) GNNs, or $d$-DRFWL(2) GNNs. $d$-DRFWL(2) GNNs use node pairs whose mutual distances are at most $d$ as the units for message passing to balance the expressive power and complexity. By performing message passing among distance-restricted node pairs in the original graph, $d$-DRFWL(2) GNNs avoid the expensive subgraph extraction operations in subgraph GNNs, making both the time and space complexity lower. We theoretically show that the discriminative power of $d$-DRFWL(2) GNNs strictly increases as $d$ increases. More importantly, $d$-DRFWL(2) GNNs have provably strong cycle counting power even with $d=2$: they can count all 3, 4, 5, 6-cycles. Since 6-cycles (e.g., benzene rings) are ubiquitous in organic molecules, being able to detect and count them is crucial for achieving robust and generalizable performance on molecular tasks. Experiments on both synthetic datasets and molecular datasets verify our theory. To the best of our knowledge, our model is the most efficient GNN model to date (both theoretically and empirically) that can count up to 6-cycles.

Yi Hu, Cai Zhou, Muhan Zhang

The scaling of large language models (LLMs) emphasizes increasing depth, yet performance gains diminish with added layers. Prior work introduces the concept of "effective depth", arguing that deeper models fail to fully utilize their layers for meaningful computation. Building on this, we systematically study how effective depth varies with model scale, training type, and task difficulty. First, we analyze the model behavior of Qwen-2.5 family (1.5B-32B) and find that while the number of effective layers grows with model size, the effective depth ratio remains stable. Besides, comparisons between base and corresponding long-CoT models show no increase in effective depth, suggesting that improved reasoning stems from longer context rather than deeper per-token computation. Furthermore, evaluations across tasks of varying difficulty indicate that models do not dynamically use more layers for harder problems. Our results suggest that current LLMs underuse available depth across scales, training paradigms and tasks of varying difficulties, pointing out research opportunities on increasing the layer utilization rate of LLMs, model pruning, and early exiting. Our code is released at https://github.com/AheadOFpotato/what_affects_effective_depth.

Yufei Xu, Fanxu Meng, Fan Jiang et al.

Token-level sparse attention mechanisms, exemplified by DeepSeek Sparse Attention (DSA), achieve fine-grained key selection by scoring every historical token for each query using a lightweight indexer, and then computing attention only over the selected subset. While the downstream sparse attention scales efficiently, the indexer still scans the entire prefix for every query, introducing an O($L^2$) per-layer bottleneck that becomes prohibitive as context length grows. We propose HISA (Hierarchical Indexed Sparse Attention), a drop-in replacement for the indexer that transforms the search process from a flat token scan into a two-stage hierarchical procedure. First, a block-level coarse filter scores pooled block representatives to prune irrelevant regions. Then, a token-level refinement applies the original indexer only within the remaining candidate blocks. HISA preserves the exact token-level top-k sparsity pattern required by the downstream Sparse MLA operator and requires no additional training. On kernel-level benchmarks, HISA achieves a 2$\times$ speedup at 32K context length and 4$\times$ at 128K. On Needle-in-a-Haystack and LongBench, we directly replace the indexer in DeepSeek-V3.2 with HISA, without any fine-tuning. HISA closely matches the original DSA in quality while significantly outperforming block-sparse baselines. Moreover, the token selection sets produced by HISA and the original DSA exhibit a mean IoU greater than 99%, indicating that the efficiency gains come with virtually no impact on selection fidelity.

Fanxu Meng, Zhaohui Wang, Muhan Zhang

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.

Hao Wang, Wanyu Lin, Hao He et al.

Recent years have seen advances on principles and guidance relating to accountable and ethical use of artificial intelligence (AI) spring up around the globe. Specifically, Data Privacy, Accountability, Interpretability, Robustness, and Reasoning have been broadly recognized as fundamental principles of using machine learning (ML) technologies on decision-critical and/or privacy-sensitive applications. On the other hand, in tremendous real-world applications, data itself can be well represented as various structured formalisms, such as graph-structured data (e.g., networks), grid-structured data (e.g., images), sequential data (e.g., text), etc. By exploiting the inherently structured knowledge, one can design plausible approaches to identify and use more relevant variables to make reliable decisions, thereby facilitating real-world deployments.

Hao Liu, Muhan Zhang, Zehao Dong et al.

Rich Electronic Health Records (EHR), have created opportunities to improve clinical processes using machine learning methods. Prediction of the same patient events at different time horizons can have very different applications and interpretations; however, limited number of events in each potential time window hurts the effectiveness of conventional machine learning algorithms. We propose a novel time associated meta learning (TAML) method to make effective predictions at multiple future time points. We view time-associated disease prediction as classification tasks at multiple time points. Such closely-related classification tasks are an excellent candidate for model-based meta learning. To address the sparsity problem after task splitting, TAML employs a temporal information sharing strategy to augment the number of positive samples and include the prediction of related phenotypes or events in the meta-training phase. We demonstrate the effectiveness of TAML on multiple clinical datasets, where it consistently outperforms a range of strong baselines. We also develop a MetaEHR package for implementing both time-associated and time-independent few-shot prediction on EHR data.

Lecheng Kong, Jiarui Feng, Hao Liu et al.

While Graph Neural Networks (GNNs) recently became powerful tools in graph learning tasks, considerable efforts have been spent on improving GNNs' structural encoding ability. A particular line of work proposed subgraph GNNs that use subgraph information to improve GNNs' expressivity and achieved great success. However, such effectivity sacrifices the efficiency of GNNs by enumerating all possible subgraphs. In this paper, we analyze the necessity of complete subgraph enumeration and show that a model can achieve a comparable level of expressivity by considering a small subset of the subgraphs. We then formulate the identification of the optimal subset as a combinatorial optimization problem and propose Magnetic Graph Neural Network (MAG-GNN), a reinforcement learning (RL) boosted GNN, to solve the problem. Starting with a candidate subgraph set, MAG-GNN employs an RL agent to iteratively update the subgraphs to locate the most expressive set for prediction. This reduces the exponential complexity of subgraph enumeration to the constant complexity of a subgraph search algorithm while keeping good expressivity. We conduct extensive experiments on many datasets, showing that MAG-GNN achieves competitive performance to state-of-the-art methods and even outperforms many subgraph GNNs. We also demonstrate that MAG-GNN effectively reduces the running time of subgraph GNNs.

Pingzhi Tang, Ruijie Zhou, Fanxu Meng et al.

Current quantization methods for LLMs predominantly rely on block-wise structures to maintain efficiency, often at the cost of representational flexibility. In this work, we demonstrate that element-wise quantization can be made as efficient as block-wise scaling while providing strictly superior expressive power by modeling the scaling manifold as continuous low-rank matrices ($S = BA$). We propose Low-Rank Decomposed Scaling (LoRDS), a unified framework that rethinks quantization granularity through this low-rank decomposition. By "breaking the blocks" of spatial constraints, LoRDS establishes a seamless efficiency lifecycle: it provides high-fidelity PTQ initialization refined via iterative optimization, enables joint QAT of weights and scaling factors, and facilitates high-rank multiplicative PEFT adaptation. Unlike additive PEFT approaches such as QLoRA, LoRDS enables high-rank weight updates within a low-rank budget while incurring no additional inference overhead. Supported by highly optimized Triton kernels, LoRDS consistently outperforms state-of-the-art baselines across various model families in both quantization and downstream fine-tuning tasks. Notably, on Llama3-8B, our method achieves up to a 27.0% accuracy improvement at 3 bits over NormalFloat quantization and delivers a 1.5x inference speedup on NVIDIA RTX 4090 while enhancing PEFT performance by 9.6% on downstream tasks over 4bit QLoRA, offering a robust and integrated solution for unified compression and adaptation of LLMs.

Haotian Xu, Xing Wu, Weinong Wang et al.

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.

Haotong Yang, Yi Hu, Shijia Kang et al.

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.

Pingzhi Tang, Yiding Wang, Muhan Zhang · pku

Large Language Models (LLMs) face the "knowledge cutoff" challenge, where their frozen parametric memory prevents direct internalization of new information. While Supervised Fine-Tuning (SFT) is commonly used to update model knowledge, it often updates factual content without reliably improving the model's ability to use the newly incorporated information for question answering or decision-making. Reinforcement Learning (RL) is essential for acquiring reasoning skills; however, its high computational cost makes it impractical for efficient online adaptation. We empirically observe that the parameter updates induced by SFT and RL are nearly orthogonal. Based on this observation, we propose Parametric Skill Transfer (PaST), a framework that supports modular skill transfer for efficient and effective knowledge adaptation. By extracting a domain-agnostic Skill Vector from a source domain, we can linearly inject knowledge manipulation skills into a target model after it has undergone lightweight SFT on new data. Experiments on knowledge-incorporation QA (SQuAD, LooGLE) and agentic tool-use benchmarks (ToolBench) demonstrate the effectiveness of our method. On SQuAD, PaST outperforms the state-of-the-art self-editing SFT baseline by up to 9.9 points. PaST further scales to long-context QA on LooGLE with an 8.0-point absolute accuracy gain, and improves zero-shot ToolBench success rates by +10.3 points on average with consistent gains across tool categories, indicating strong scalability and cross-domain transferability of the Skill Vector.

Yuanshuo Zhang, Yuchen Hou, Bohan Tang et al.

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.

Minjie Wang, Quan Gan, David Wipf et al.

Although RDBs store vast amounts of rich, informative data spread across interconnected tables, the progress of predictive machine learning models as applied to such tasks arguably falls well behind advances in other domains such as computer vision or natural language processing. This deficit stems, at least in part, from the lack of established/public RDB benchmarks as needed for training and evaluation purposes. As a result, related model development thus far often defaults to tabular approaches trained on ubiquitous single-table benchmarks, or on the relational side, graph-based alternatives such as GNNs applied to a completely different set of graph datasets devoid of tabular characteristics. To more precisely target RDBs lying at the nexus of these two complementary regimes, we explore a broad class of baseline models predicated on: (i) converting multi-table datasets into graphs using various strategies equipped with efficient subsampling, while preserving tabular characteristics; and (ii) trainable models with well-matched inductive biases that output predictions based on these input subgraphs. Then, to address the dearth of suitable public benchmarks and reduce siloed comparisons, we assemble a diverse collection of (i) large-scale RDB datasets and (ii) coincident predictive tasks. From a delivery standpoint, we operationalize the above four dimensions (4D) of exploration within a unified, scalable open-source toolbox called 4DBInfer. We conclude by presenting evaluations using 4DBInfer, the results of which highlight the importance of considering each such dimension in the design of RDB predictive models, as well as the limitations of more naive approaches such as simply joining adjacent tables. Our source code is released at https://github.com/awslabs/multi-table-benchmark .

Haotong Yang, Fanxu Meng, Zhouchen Lin et al.

The pre-trained large language models (LLMs) have shown their extraordinary capacity to solve reasoning tasks, even on tasks that require a complex process involving multiple sub-steps. However, given the vast possible generation space of all the tasks, how the pretrained model learns the reasoning ability remains an open question. We firstly propose that an intrinsic structural constraint on the generated sequence of language-based reasoning -- we called it template-content structure (T-C structure) -- is the key to explain why LLMs can solve a large number of complex reasoning problems with limited training data by showing this structure can reduce the possible space from exponential level to linear level. Furthermore, by generalizing this structure to the hierarchical case, we demonstrate that models can achieve task composition, further reducing the space needed to learn from linear to logarithmic, thereby effectively learning on complex reasoning involving multiple steps. We provide both examples and formal theory of our T-C structure. We also experimentally validate the existence of the T-C structure in some current LLMs and its effectiveness for reasoning.

Yanbo Wang, Xiyuan Wang, Quan Gan et al.

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.

Jiarui Feng, Donghong Cai, Yixin Chen et al.

Large Language Models (LLMs) have demonstrated remarkable capabilities in modeling sequential textual data and generalizing across diverse tasks. However, adapting LLMs to effectively handle structural data, such as knowledge graphs or web data, remains a challenging problem. Some approaches adopt complex strategies to convert graphs into text sequences, resulting in significant token overhead and rendering them impractical for large-scale graphs. Others introduce additional modules to encode graphs into fixed-size token representations for LLMs. However, these methods typically require large-scale post-training on graph-text corpus and complex alignment procedures, yet often yield sub-optimal results due to poor modality alignment. Inspired by in-parameter knowledge injection for test-time adaptation of LLMs, we propose GRIP, a novel framework that equips LLMs with the ability to internalize complex relational information from graphs through carefully designed fine-tuning tasks. This knowledge is efficiently stored within lightweight LoRA parameters, enabling the fine-tuned LLM to perform a wide range of graph-related tasks without requiring access to the original graph at inference time. Extensive experiments across multiple benchmarks validate the effectiveness and efficiency of our approach.