Daily Papers

This study introduces a novel framework, G3Reg, for fast and robust global registration of LiDAR point clouds. In contrast to conventional complex keypoints and descriptors, we extract fundamental geometric primitives, including planes, clusters, and lines (PCL) from the raw point cloud to obtain low-level semantic segments. Each segment is represented as a unified Gaussian Ellipsoid Model (GEM), using a probability ellipsoid to ensure the ground truth centers are encompassed with a certain degree of probability. Utilizing these GEMs, we present a distrust-and-verify scheme based on a Pyramid Compatibility Graph for Global Registration (PAGOR). Specifically, we establish an upper bound, which can be traversed based on the confidence level for compatibility testing to construct the pyramid graph. Then, we solve multiple maximum cliques (MAC) for each level of the pyramid graph, thus generating the corresponding transformation candidates. In the verification phase, we adopt a precise and efficient metric for point cloud alignment quality, founded on geometric primitives, to identify the optimal candidate. The algorithm's performance is validated on three publicly available datasets and a self-collected multi-session dataset. Parameter settings remained unchanged during the experiment evaluations. The results exhibit superior robustness and real-time performance of the G3Reg framework compared to state-of-the-art methods. Furthermore, we demonstrate the potential for integrating individual GEM and PAGOR components into other registration frameworks to enhance their efficacy. Code: https://github.com/HKUST-Aerial-Robotics/G3Reg

As a fundamental problem in computer vision, 3D point cloud registration (PCR) aims to seek the optimal pose to align a point cloud pair. In this paper, we present a 3D registration method with maximal cliques (MAC). The key insight is to loosen the previous maximum clique constraint, and mine more local consensus information in a graph for accurate pose hypotheses generation: 1) A compatibility graph is constructed to render the affinity relationship between initial correspondences. 2) We search for maximal cliques in the graph, each of which represents a consensus set. We perform node-guided clique selection then, where each node corresponds to the maximal clique with the greatest graph weight. 3) Transformation hypotheses are computed for the selected cliques by the SVD algorithm and the best hypothesis is used to perform registration. Extensive experiments on U3M, 3DMatch, 3DLoMatch and KITTI demonstrate that MAC effectively increases registration accuracy, outperforms various state-of-the-art methods and boosts the performance of deep-learned methods. MAC combined with deep-learned methods achieves state-of-the-art registration recall of 95.7% / 78.9% on 3DMatch / 3DLoMatch.

City-scale 3D generation is of great importance for the development of embodied intelligence and world models. Existing methods, however, face significant challenges regarding quality, fidelity, and scalability in 3D world generation. Thus, we propose RAISECity, a Reality-Aligned Intelligent Synthesis Engine that creates detailed, City-scale 3D worlds. We introduce an agentic framework that leverages diverse multimodal foundation tools to acquire real-world knowledge, maintain robust intermediate representations, and construct complex 3D scenes. This agentic design, featuring dynamic data processing, iterative self-reflection and refinement, and the invocation of advanced multimodal tools, minimizes cumulative errors and enhances overall performance. Extensive quantitative experiments and qualitative analyses validate the superior performance of RAISECity in real-world alignment, shape precision, texture fidelity, and aesthetics level, achieving over a 90% win-rate against existing baselines for overall perceptual quality. This combination of 3D quality, reality alignment, scalability, and seamless compatibility with computer graphics pipelines makes RAISECity a promising foundation for applications in immersive media, embodied intelligence, and world models.

This paper studies the problem of recovering cameras from a set of fundamental matrices. A set of fundamental matrices is said to be compatible if a set of cameras exists for which they are the fundamental matrices. We focus on the complete graph, where fundamental matrices for each pair of cameras are given. Previous work has established necessary and sufficient conditions for compatibility as rank and eigenvalue conditions on the n-view fundamental matrix obtained by concatenating the individual fundamental matrices. In this work, we show that the eigenvalue condition is redundant. We provide explicit homogeneous polynomials that describe necessary and sufficient conditions for compatibility in terms of the fundamental matrices and their epipoles. In this direction, we find that quadruple-wise compatibility is enough to ensure global compatibility for any number of cameras. We demonstrate that for four cameras, compatibility is generically described by triple-wise conditions and one additional equation involving all fundamental matrices.

In compositional zero-shot learning, the goal is to recognize unseen compositions (e.g. old dog) of observed visual primitives states (e.g. old, cute) and objects (e.g. car, dog) in the training set. This is challenging because the same state can for example alter the visual appearance of a dog drastically differently from a car. As a solution, we propose a novel graph formulation called Compositional Graph Embedding (CGE) that learns image features, compositional classifiers, and latent representations of visual primitives in an end-to-end manner. The key to our approach is exploiting the dependency between states, objects, and their compositions within a graph structure to enforce the relevant knowledge transfer from seen to unseen compositions. By learning a joint compatibility that encodes semantics between concepts, our model allows for generalization to unseen compositions without relying on an external knowledge base like WordNet. We show that in the challenging generalized compositional zero-shot setting our CGE significantly outperforms the state of the art on MIT-States and UT-Zappos. We also propose a new benchmark for this task based on the recent GQA dataset. Code is available at: https://github.com/ExplainableML/czsl

Programming languages possess rich semantic information such as data flow that is represented by graphs and not available from the surface form of source code. Recent code language models have scaled to billions of parameters, but model source code solely as text tokens while ignoring any other structural information. Conversely, models that do encode structural information of code make modifications to the Transformer architecture, limiting their scale and compatibility with pretrained LLMs. In this work, we take the best of both worlds with GALLa - Graph Aligned Large Language Model. GALLa utilizes graph neural networks and cross-modal alignment technologies to inject the structural information of code into LLMs as an auxiliary task during finetuning. This framework is both model-agnostic and task-agnostic, as it can be applied to any code LLM for any code downstream task, and requires the structural graph data only at training time from a corpus unrelated to the finetuning data, while incurring no cost at inference time over the baseline LLM. Experiments on five code tasks with four different baseline LLMs ranging in size from 350M to 8B validate the effectiveness of GALLa, demonstrating consistent improvement over the baseline, even for powerful models such as LLaMA3.

3D surface reconstruction from images is essential for numerous applications. Recently, Neural Radiance Fields (NeRFs) have emerged as a promising framework for 3D modeling. However, NeRFs require accurate camera poses as input, and existing methods struggle to handle significantly noisy pose estimates (i.e., outliers), which are commonly encountered in real-world scenarios. To tackle this challenge, we present a novel approach that optimizes radiance fields with scene graphs to mitigate the influence of outlier poses. Our method incorporates an adaptive inlier-outlier confidence estimation scheme based on scene graphs, emphasizing images of high compatibility with the neighborhood and consistency in the rendering quality. We also introduce an effective intersection-over-union (IoU) loss to optimize the camera pose and surface geometry, together with a coarse-to-fine strategy to facilitate the training. Furthermore, we propose a new dataset containing typical outlier poses for a detailed evaluation. Experimental results on various datasets consistently demonstrate the effectiveness and superiority of our method over existing approaches, showcasing its robustness in handling outliers and producing high-quality 3D reconstructions. Our code and data are available at: https://github.com/Iris-cyy/SG-NeRF.

Recent years have witnessed the great success of graph pre-training for graph representation learning. With hundreds of graph pre-training tasks proposed, integrating knowledge acquired from multiple pre-training tasks has become a popular research topic. In this paper, we identify two important collaborative processes for this topic: (1) select: how to select an optimal task combination from a given task pool based on their compatibility, and (2) weigh: how to weigh the selected tasks based on their importance. While there currently has been a lot of work focused on weighing, comparatively little effort has been devoted to selecting. This paper proposes a novel instance-level framework for integrating multiple graph pre-training tasks, Weigh And Select (WAS), where the two collaborative processes, weighing and selecting, are combined by decoupled siamese networks. Specifically, it first adaptively learns an optimal combination of tasks for each instance from a given task pool, based on which a customized instance-level task weighing strategy is learned. Extensive experiments on 16 graph datasets across node-level and graph-level downstream tasks have demonstrated that by combining a few simple but classical tasks, WAS can achieve comparable performance to other leading counterparts. The code is available at https://github.com/TianyuFan0504/WAS.

A compelling portrayal of characters is essential to the success of narrative writing. For readers, appreciating a character's traits requires the ability to infer their evolving beliefs, desires, and intentions over the course of a complex storyline, a cognitive skill known as Theory-of-Mind (ToM). Performing ToM reasoning in prolonged narratives requires readers to integrate historical context with current narrative information, a task at which humans excel but Large Language Models (LLMs) often struggle. To systematically evaluate LLMs' ToM reasoning capability in long narratives, we construct LitCharToM, a benchmark of character-centric questions across four ToM dimensions from classic literature. Further, we introduce EvolvTrip, a perspective-aware temporal knowledge graph that tracks psychological development throughout narratives. Our experiments demonstrate that EvolvTrip consistently enhances performance of LLMs across varying scales, even in challenging extended-context scenarios. EvolvTrip proves to be particularly valuable for smaller models, partially bridging the performance gap with larger LLMs and showing great compatibility with lengthy narratives. Our findings highlight the importance of explicit representation of temporal character mental states in narrative comprehension and offer a foundation for more sophisticated character understanding. Our data and code are publicly available at https://github.com/Bernard-Yang/EvolvTrip.

External knowledge (a.k.a. side information) plays a critical role in zero-shot learning (ZSL) which aims to predict with unseen classes that have never appeared in training data. Several kinds of external knowledge, such as text and attribute, have been widely investigated, but they alone are limited with incomplete semantics. Some very recent studies thus propose to use Knowledge Graph (KG) due to its high expressivity and compatibility for representing kinds of knowledge. However, the ZSL community is still in short of standard benchmarks for studying and comparing different external knowledge settings and different KG-based ZSL methods. In this paper, we proposed six resources covering three tasks, i.e., zero-shot image classification (ZS-IMGC), zero-shot relation extraction (ZS-RE), and zero-shot KG completion (ZS-KGC). Each resource has a normal ZSL benchmark and a KG containing semantics ranging from text to attribute, from relational knowledge to logical expressions. We have clearly presented these resources including their construction, statistics, data formats and usage cases w.r.t. different ZSL methods. More importantly, we have conducted a comprehensive benchmarking study, with two general and state-of-the-art methods, two setting-specific methods and one interpretable method. We discussed and compared different ZSL paradigms w.r.t. different external knowledge settings, and found that our resources have great potential for developing more advanced ZSL methods and more solutions for applying KGs for augmenting machine learning. All the resources are available at https://github.com/China-UK-ZSL/Resources_for_KZSL.

Tool-Augmented Language Models (TALMs) leverage external APIs to answer user queries across various domains. However, existing benchmark datasets for TALM research often feature simplistic dialogues that do not reflect real-world scenarios, such as the need for models to ask clarifying questions or proactively call additional APIs when essential information is missing. To address these limitations, we construct and release ToolDial, a dataset comprising 11,111 multi-turn dialogues, with an average of 8.95 turns per dialogue, based on APIs from RapidAPI. ToolDial has two key characteristics. First, the dialogues incorporate 16 user and system actions (e.g., "Request", "Clarify", "Fail inform") to capture the rich dynamics of real-world interactions. Second, we simulate dialogues where the system requests necessary information from the user based on API documentation and seeks additional APIs if the user fails to provide the required information. To facilitate this process, we introduce a method for generating an API graph that represents input and output compatibility between APIs. Using ToolDial, we evaluate a suite of language models on their ability to predict correct actions and extract input parameter values for API calls from the dialogue history. Modern language models achieve accuracy scores below 70%, indicating substantial room for improvement. We release our dataset and code at https://github.com/holi-lab/ToolDial.

Creating immersive and playable 3D worlds from texts or images remains a fundamental challenge in computer vision and graphics. Existing world generation approaches typically fall into two categories: video-based methods that offer rich diversity but lack 3D consistency and rendering efficiency, and 3D-based methods that provide geometric consistency but struggle with limited training data and memory-inefficient representations. To address these limitations, we present HunyuanWorld 1.0, a novel framework that combines the best of both worlds for generating immersive, explorable, and interactive 3D scenes from text and image conditions. Our approach features three key advantages: 1) 360{\deg} immersive experiences via panoramic world proxies; 2) mesh export capabilities for seamless compatibility with existing computer graphics pipelines; 3) disentangled object representations for augmented interactivity. The core of our framework is a semantically layered 3D mesh representation that leverages panoramic images as 360{\deg} world proxies for semantic-aware world decomposition and reconstruction, enabling the generation of diverse 3D worlds. Extensive experiments demonstrate that our method achieves state-of-the-art performance in generating coherent, explorable, and interactive 3D worlds while enabling versatile applications in virtual reality, physical simulation, game development, and interactive content creation.

Previous works on Treatment Effect Estimation (TEE) are not in widespread use because they are predominantly theoretical, where strong parametric assumptions are made but untractable for practical application. Recent work uses multilayer perceptron (MLP) for modeling casual relationships, however, MLPs lag far behind recent advances in ML methodology, which limits their applicability and generalizability. To extend beyond the single domain formulation and towards more realistic learning scenarios, we explore model design spaces beyond MLPs, i.e., transformer backbones, which provide flexibility where attention layers govern interactions among treatments and covariates to exploit structural similarities of potential outcomes for confounding control. Through careful model design, Transformers as Treatment Effect Estimators (TransTEE) is proposed. We show empirically that TransTEE can: (1) serve as a general purpose treatment effect estimator that significantly outperforms competitive baselines in a variety of challenging TEE problems (e.g., discrete, continuous, structured, or dosage-associated treatments) and is applicable to both when covariates are tabular and when they consist of structural data (e.g., texts, graphs); (2) yield multiple advantages: compatibility with propensity score modeling, parameter efficiency, robustness to continuous treatment value distribution shifts, explainable in covariate adjustment, and real-world utility in auditing pre-trained language models

Subgraph matching is vital in knowledge graph (KG) question answering, molecule design, scene graph, code and circuit search, etc. Neural methods have shown promising results for subgraph matching. Our study of recent systems suggests refactoring them into a unified design space for graph matching networks. Existing methods occupy only a few isolated patches in this space, which remains largely uncharted. We undertake the first comprehensive exploration of this space, featuring such axes as attention-based vs. soft permutation-based interaction between query and corpus graphs, aligning nodes vs. edges, and the form of the final scoring network that integrates neural representations of the graphs. Our extensive experiments reveal that judicious and hitherto-unexplored combinations of choices in this space lead to large performance benefits. Beyond better performance, our study uncovers valuable insights and establishes general design principles for neural graph representation and interaction, which may be of wider interest.

Link prediction, a fundamental task on graphs, has proven indispensable in various applications, e.g., friend recommendation, protein analysis, and drug interaction prediction. However, since datasets span a multitude of domains, they could have distinct underlying mechanisms of link formation. Evidence in existing literature underscores the absence of a universally best algorithm suitable for all datasets. In this paper, we endeavor to explore principles of link prediction across diverse datasets from a data-centric perspective. We recognize three fundamental factors critical to link prediction: local structural proximity, global structural proximity, and feature proximity. We then unearth relationships among those factors where (i) global structural proximity only shows effectiveness when local structural proximity is deficient. (ii) The incompatibility can be found between feature and structural proximity. Such incompatibility leads to GNNs for Link Prediction (GNN4LP) consistently underperforming on edges where the feature proximity factor dominates. Inspired by these new insights from a data perspective, we offer practical instruction for GNN4LP model design and guidelines for selecting appropriate benchmark datasets for more comprehensive evaluations.

Current scene graph datasets suffer from strong long-tail distributions of their predicate classes. Due to a very low number of some predicate classes in the test sets, no reliable metrics can be retrieved for the rarest classes. We construct a new panoptic scene graph dataset and a set of metrics that are designed as a benchmark for the predictive performance especially on rare predicate classes. To construct the new dataset, we propose a model-assisted annotation pipeline that efficiently finds rare predicate classes that are hidden in a large set of images like needles in a haystack. Contrary to prior scene graph datasets, Haystack contains explicit negative annotations, i.e. annotations that a given relation does not have a certain predicate class. Negative annotations are helpful especially in the field of scene graph generation and open up a whole new set of possibilities to improve current scene graph generation models. Haystack is 100% compatible with existing panoptic scene graph datasets and can easily be integrated with existing evaluation pipelines. Our dataset and code can be found here: https://lorjul.github.io/haystack/. It includes annotation files and simple to use scripts and utilities, to help with integrating our dataset in existing work.

Graph databases are gaining momentum thanks to the flexibility and expressiveness of their data models and query languages. A standardization activity driven by the ISO/IEC standardization body is also ongoing and has already conducted to the specification of the first versions of two standard graph query languages, namely SQL/PGQ and GQL, respectively in 2023 and 2024. Apart from the standards, there exists a panoply of concrete graph query languages provided by current graph database systems, each offering different query features. A common limitation of current graph query engines is the absence of an algebraic approach for evaluating path queries. To address this, we introduce an abstract algebra for evaluating path queries, allowing paths to be treated as first-class entities within the query processing pipeline. We demonstrate that our algebra can express a core fragment of path queries defined in GQL and SQL/PGQ, thereby serving as a formal framework for studying both standards and supporting their implementation in current graph database systems. We also show that evaluation trees for path algebra expressions can function as logical plans for evaluating path queries and enable the application of query optimization techniques. Our algebraic framework has the potential to act as a lingua franca for path query evaluation, enabling different implementations to be expressed and compared.

Learning compatible representations enables the interchangeable use of semantic features as models are updated over time. This is particularly relevant in search and retrieval systems where it is crucial to avoid reprocessing of the gallery images with the updated model. While recent research has shown promising empirical evidence, there is still a lack of comprehensive theoretical understanding about learning compatible representations. In this paper, we demonstrate that the stationary representations learned by the d-Simplex fixed classifier optimally approximate compatibility representation according to the two inequality constraints of its formal definition. This not only establishes a solid foundation for future works in this line of research but also presents implications that can be exploited in practical learning scenarios. An exemplary application is the now-standard practice of downloading and fine-tuning new pre-trained models. Specifically, we show the strengths and critical issues of stationary representations in the case in which a model undergoing sequential fine-tuning is asynchronously replaced by downloading a better-performing model pre-trained elsewhere. Such a representation enables seamless delivery of retrieval service (i.e., no reprocessing of gallery images) and offers improved performance without operational disruptions during model replacement. Code available at: https://github.com/miccunifi/iamcl2r.

Graph retrieval based on subgraph isomorphism has several real-world applications such as scene graph retrieval, molecular fingerprint detection and circuit design. Roy et al. [35] proposed IsoNet, a late interaction model for subgraph matching, which first computes the node and edge embeddings of each graph independently of paired graph and then computes a trainable alignment map. Here, we present IsoNet++, an early interaction graph neural network (GNN), based on several technical innovations. First, we compute embeddings of all nodes by passing messages within and across the two input graphs, guided by an injective alignment between their nodes. Second, we update this alignment in a lazy fashion over multiple rounds. Within each round, we run a layerwise GNN from scratch, based on the current state of the alignment. After the completion of one round of GNN, we use the last-layer embeddings to update the alignments, and proceed to the next round. Third, IsoNet++ incorporates a novel notion of node-pair partner interaction. Traditional early interaction computes attention between a node and its potential partners in the other graph, the attention then controlling messages passed across graphs. In contrast, we consider node pairs (not single nodes) as potential partners. Existence of an edge between the nodes in one graph and non-existence in the other provide vital signals for refining the alignment. Our experiments on several datasets show that the alignments get progressively refined with successive rounds, resulting in significantly better retrieval performance than existing methods. We demonstrate that all three innovations contribute to the enhanced accuracy. Our code and datasets are publicly available at https://github.com/structlearning/isonetpp.

Many real-world graphs frequently present challenges for graph learning due to the presence of both heterophily and heterogeneity. However, existing benchmarks for graph learning often focus on heterogeneous graphs with homophily or homogeneous graphs with heterophily, leaving a gap in understanding how methods perform on graphs that are both heterogeneous and heterophilic. To bridge this gap, we introduce H2GB, a novel graph benchmark that brings together the complexities of both the heterophily and heterogeneity properties of graphs. Our benchmark encompasses 9 diverse real-world datasets across 5 domains, 28 baseline model implementations, and 26 benchmark results. In addition, we present a modular graph transformer framework UnifiedGT and a new model variant, H2G-former, that excels at this challenging benchmark. By integrating masked label embeddings, cross-type heterogeneous attention, and type-specific FFNs, H2G-former effectively tackles graph heterophily and heterogeneity. Extensive experiments across 26 baselines on H2GB reveal inadequacies of current models on heterogeneous heterophilic graph learning, and demonstrate the superiority of our H2G-former over existing solutions. Both the benchmark and the framework are available on GitHub (https://github.com/junhongmit/H2GB) and PyPI (https://pypi.org/project/H2GB), and documentation can be found at https://junhongmit.github.io/H2GB/.

With the emergence of data marketplaces, the demand for methods to assess the value of data has increased significantly. While numerous techniques have been proposed for this purpose, none have specifically addressed graphs as the main data modality. Graphs are widely used across various fields, ranging from chemical molecules to social networks. In this study, we break down graphs into two main components: structural and featural, and we focus on evaluating data without relying on specific task-related metrics, making it applicable in practical scenarios where validation requirements may be lacking. We introduce a novel framework called blind message passing, which aligns the seller's and buyer's graphs using a shared node permutation based on graph matching. This allows us to utilize the graph Wasserstein distance to quantify the differences in the structural distribution of graph datasets, called the structural disparities. We then consider featural aspects of buyers' and sellers' graphs for data valuation and capture their statistical similarities and differences, referred to as relevance and diversity, respectively. Our approach ensures that buyers and sellers remain unaware of each other's datasets. Our experiments on real datasets demonstrate the effectiveness of our approach in capturing the relevance, diversity, and structural disparities of seller data for buyers, particularly in graph-based data valuation scenarios.

Existing graph matching methods typically assume that there are similar structures between graphs and they are matchable. However, these assumptions do not align with real-world applications. This work addresses a more realistic scenario where graphs exhibit diverse modes, requiring graph grouping before or along with matching, a task termed mixture graph matching and clustering. We introduce Minorize-Maximization Matching and Clustering (M3C), a learning-free algorithm that guarantees theoretical convergence through the Minorize-Maximization framework and offers enhanced flexibility via relaxed clustering. Building on M3C, we develop UM3C, an unsupervised model that incorporates novel edge-wise affinity learning and pseudo label selection. Extensive experimental results on public benchmarks demonstrate that our method outperforms state-of-the-art graph matching and mixture graph matching and clustering approaches in both accuracy and efficiency. Source code will be made publicly available.

Entity resolution is a widely studied problem with several proposals to match records across relations. Matching textual content is a widespread task in many applications, such as question answering and search. While recent methods achieve promising results for these two tasks, there is no clear solution for the more general problem of matching textual content and structured data. We introduce a framework that supports this new task in an unsupervised setting for any pair of corpora, being relational tables or text documents. Our method builds a fine-grained graph over the content of the corpora and derives word embeddings to represent the objects to match in a low dimensional space. The learned representation enables effective and efficient matching at different granularity, from relational tuples to text sentences and paragraphs. Our flexible framework can exploit pre-trained resources, but it does not depends on their existence and achieves better quality performance in matching content when the vocabulary is domain specific. We also introduce optimizations in the graph creation process with an "expand and compress" approach that first identifies new valid relationships across elements, to improve matching, and then prunes nodes and edges, to reduce the graph size. Experiments on real use cases and public datasets show that our framework produces embeddings that outperform word embeddings and fine-tuned language models both in results' quality and in execution times.

Representation learning on text-attributed graphs (TAGs) integrates structural connectivity with rich textual semantics, enabling applications in diverse domains. Current methods largely rely on contrastive learning to maximize cross-modal similarity, assuming tighter coupling between graph and text representations improves transfer performance. However, our empirical analysis reveals that both natural gap expansion and forced gap reduction result in performance degradation by disrupting pre-trained knowledge structures and impairing generalization. This arises from the geometric incompatibility between encoders, where graph encoders capture topological patterns, while text encoders capture semantic structures. Over-alignment compresses these distinct spaces into shared subspaces, causing structure collapse that diminishes both topological reasoning and semantic understanding. We propose LLM4GTA, a gap-aware alignment framework that preserves representation gaps as geometric necessities for maintaining modality-specific knowledge and improving transfer performance. LLM4GTA includes an adaptive gap preservation module to prevent over-alignment by monitoring similarity evolution and an intra-modal compensation mechanism that boosts discriminative power using auxiliary classifiers in graph space. Extensive experiments show significant improvements over existing methods in zero-shot and few-shot scenarios.

We consider the problem of graph matching, or learning vertex correspondence, between two correlated stochastic block models (SBMs). The graph matching problem arises in various fields, including computer vision, natural language processing and bioinformatics, and in particular, matching graphs with inherent community structure has significance related to de-anonymization of correlated social networks. Compared to the correlated Erdos-Renyi (ER) model, where various efficient algorithms have been developed, among which a few algorithms have been proven to achieve the exact matching with constant edge correlation, no low-order polynomial algorithm has been known to achieve exact matching for the correlated SBMs with constant correlation. In this work, we propose an efficient algorithm for matching graphs with community structure, based on the comparison between partition trees rooted from each vertex, by extending the idea of Mao et al. (2021) to graphs with communities. The partition tree divides the large neighborhoods of each vertex into disjoint subsets using their edge statistics to different communities. Our algorithm is the first low-order polynomial-time algorithm achieving exact matching between two correlated SBMs with high probability in dense graphs.

Language models have been effective in a wide range of applications, yet the most sophisticated models are often proprietary. For example, GPT-4 by OpenAI and various models by Anthropic are expensive and consume substantial energy. In contrast, the open-source community has produced competitive models, like Llama3. Furthermore, niche-specific smaller language models, such as those tailored for legal, medical or financial tasks, have outperformed their proprietary counterparts. This paper introduces a novel approach that employs functional tokens to integrate multiple open-source models, each optimized for particular tasks. Our newly developed Octopus v4 model leverages functional tokens to intelligently direct user queries to the most appropriate vertical model and reformat the query to achieve the best performance. Octopus v4, an evolution of the Octopus v1, v2, and v3 models, excels in selection and parameter understanding and reformatting. Additionally, we explore the use of graph as a versatile data structure that effectively coordinates multiple open-source models by harnessing the capabilities of the Octopus model and functional tokens. Use our open-sourced GitHub (https://www.nexa4ai.com/) to try Octopus v4 models (https://huggingface.co/NexaAIDev/Octopus-v4), and contrite to a larger graph of language models. By activating models less than 10B parameters, we achieved SOTA MMLU score of 74.8 among the same level models.

Assessing the degree of similarity of code fragments is crucial for ensuring software quality, but it remains challenging due to the need to capture the deeper semantic aspects of code. Traditional syntactic methods often fail to identify these connections. Recent advancements have addressed this challenge, though they frequently sacrifice interpretability. To improve this, we present an approach aiming to improve the transparency of the similarity assessment by using GraphCodeBERT, which enables the identification of semantic relationships between code fragments. This approach identifies similar code fragments and clarifies the reasons behind that identification, helping developers better understand and trust the results. The source code for our implementation is available at https://www.github.com/jorge-martinez-gil/graphcodebert-interpretability.

DisCoPy is a Python toolkit for computing with monoidal categories. It comes with two flexible data structures for string diagrams: the first one for planar monoidal categories based on lists of layers, the second one for symmetric monoidal categories based on cospans of hypergraphs. Algorithms for functor application then allow to translate string diagrams into code for numerical computation, be it differentiable, probabilistic or quantum. This report gives an overview of the library and the new developments released in its version 1.0. In particular, we showcase the implementation of diagram equality for a large fragment of the hierarchy of graphical languages for monoidal categories, as well as a new syntax for defining string diagrams as Python functions.

Since long, corporations are looking for knowledge sources which can provide structured description of data and can focus on meaning and shared understanding. Structures which can facilitate open world assumptions and can be flexible enough to incorporate and recognize more than one name for an entity. A source whose major purpose is to facilitate human communication and interoperability. Clearly, databases fail to provide these features and ontologies have emerged as an alternative choice, but corporations working on same domain tend to make different ontologies. The problem occurs when they want to share their data/knowledge. Thus we need tools to merge ontologies into one. This task is termed as ontology matching. This is an emerging area and still we have to go a long way in having an ideal matcher which can produce good results. In this paper we have shown a framework to matching ontologies using graphs.

Subgraph matching is a fundamental building block for graph-based applications and is challenging due to its high-order combinatorial nature. Existing studies usually tackle it by combinatorial optimization or learning-based methods. However, they suffer from exponential computational costs or searching the matching without theoretical guarantees. In this paper, we develop D2Match by leveraging the efficiency of Deep learning and Degeneracy for subgraph matching. More specifically, we first prove that subgraph matching can degenerate to subtree matching, and subsequently is equivalent to finding a perfect matching on a bipartite graph. We can then yield an implementation of linear time complexity by the built-in tree-structured aggregation mechanism on graph neural networks. Moreover, circle structures and node attributes can be easily incorporated in D2Match to boost the matching performance. Finally, we conduct extensive experiments to show the superior performance of our D2Match and confirm that our D2Match indeed exploits the subtrees and differs from existing GNNs-based subgraph matching methods that depend on memorizing the data distribution divergence

Hypergraphs offer a powerful framework for modeling higher-order interactions that traditional pairwise graphs cannot fully capture. However, practical constraints often lead to their simplification into projected graphs, resulting in substantial information loss and ambiguity in representing higher-order relationships. In this work, we propose MARIOH, a supervised approach for reconstructing the original hypergraph from its projected graph by leveraging edge multiplicity. To overcome the difficulties posed by the large search space, MARIOH integrates several key ideas: (a) identifying provable size-2 hyperedges, which reduces the candidate search space, (b) predicting the likelihood of candidates being hyperedges by utilizing both structural and multiplicity-related features, and (c) not only targeting promising hyperedge candidates but also examining less confident ones to explore alternative possibilities. Together, these ideas enable MARIOH to efficiently and effectively explore the search space. In our experiments using 10 real-world datasets, MARIOH achieves up to 74.51% higher reconstruction accuracy compared to state-of-the-art methods.

Compatible features enable the direct comparison of old and new learned features allowing to use them interchangeably over time. In visual search systems, this eliminates the need to extract new features from the gallery-set when the representation model is upgraded with novel data. This has a big value in real applications as re-indexing the gallery-set can be computationally expensive when the gallery-set is large, or even infeasible due to privacy or other concerns of the application. In this paper, we propose CoReS, a new training procedure to learn representations that are compatible with those previously learned, grounding on the stationarity of the features as provided by fixed classifiers based on polytopes. With this solution, classes are maximally separated in the representation space and maintain their spatial configuration stationary as new classes are added, so that there is no need to learn any mappings between representations nor to impose pairwise training with the previously learned model. We demonstrate that our training procedure largely outperforms the current state of the art and is particularly effective in the case of multiple upgrades of the training-set, which is the typical case in real applications.

Graph Neural Networks (GNNs) have demonstrated superior performance on various graph learning tasks, including recommendation, where they leverage user-item collaborative filtering signals in graphs. However, theoretical formulations of their capability are scarce, despite their empirical effectiveness in state-of-the-art recommender models. Recently, research has explored the expressiveness of GNNs in general, demonstrating that message passing GNNs are at most as powerful as the Weisfeiler-Lehman test, and that GNNs combined with random node initialization are universal. Nevertheless, the concept of "expressiveness" for GNNs remains vaguely defined. Most existing works adopt the graph isomorphism test as the metric of expressiveness, but this graph-level task may not effectively assess a model's ability in recommendation, where the objective is to distinguish nodes of different closeness. In this paper, we provide a comprehensive theoretical analysis of the expressiveness of GNNs in recommendation, considering three levels of expressiveness metrics: graph isomorphism (graph-level), node automorphism (node-level), and topological closeness (link-level). We propose the topological closeness metric to evaluate GNNs' ability to capture the structural distance between nodes, which aligns closely with the objective of recommendation. To validate the effectiveness of this new metric in evaluating recommendation performance, we introduce a learning-less GNN algorithm that is optimal on the new metric and can be optimal on the node-level metric with suitable modification. We conduct extensive experiments comparing the proposed algorithm against various types of state-of-the-art GNN models to explore the explainability of the new metric in the recommendation task. For reproducibility, implementation codes are available at https://github.com/HKUDS/GTE.

With the web getting bigger and assimilating knowledge about different concepts and domains, it is becoming very difficult for simple database driven applications to capture the data for a domain. Thus developers have come out with ontology based systems which can store large amount of information and can apply reasoning and produce timely information. Thus facilitating effective knowledge management. Though this approach has made our lives easier, but at the same time has given rise to another problem. Two different ontologies assimilating same knowledge tend to use different terms for the same concepts. This creates confusion among knowledge engineers and workers, as they do not know which is a better term then the other. Thus we need to merge ontologies working on same domain so that the engineers can develop a better application over it. This paper shows the development of one such matcher which merges the concepts available in two ontologies at two levels; 1) at string level and 2) at semantic level; thus producing better merged ontologies. We have used a graph matching technique which works at the core of the system. We have also evaluated the system and have tested its performance with its predecessor which works only on string matching. Thus current approach produces better results.

Putting together an ideal outfit is a process that involves creativity and style intuition. This makes it a particularly difficult task to automate. Existing styling products generally involve human specialists and a highly curated set of fashion items. In this paper, we will describe how we bootstrapped the Complete The Look (CTL) system at Pinterest. This is a technology that aims to learn the subjective task of "style compatibility" in order to recommend complementary items that complete an outfit. In particular, we want to show recommendations from other categories that are compatible with an item of interest. For example, what are some heels that go well with this cocktail dress? We will introduce our outfit dataset of over 1 million outfits and 4 million objects, a subset of which we will make available to the research community, and describe the pipeline used to obtain and refresh this dataset. Furthermore, we will describe how we evaluate this subjective task and compare model performance across multiple training methods. Lastly, we will share our lessons going from experimentation to working prototype, and how to mitigate failure modes in the production environment. Our work represents one of the first examples of an industrial-scale solution for compatibility-based fashion recommendation.

We study graph data augmentation by mixup, which has been used successfully on images. A key operation of mixup is to compute a convex combination of a pair of inputs. This operation is straightforward for grid-like data, such as images, but challenging for graph data. The key difficulty lies in the fact that different graphs typically have different numbers of nodes, and thus there lacks a node-level correspondence between graphs. In this work, we propose S-Mixup, a simple yet effective mixup method for graph classification by soft alignments. Specifically, given a pair of graphs, we explicitly obtain node-level correspondence via computing a soft assignment matrix to match the nodes between two graphs. Based on the soft assignments, we transform the adjacency and node feature matrices of one graph, so that the transformed graph is aligned with the other graph. In this way, any pair of graphs can be mixed directly to generate an augmented graph. We conduct systematic experiments to show that S-Mixup can improve the performance and generalization of graph neural networks (GNNs) on various graph classification tasks. In addition, we show that S-Mixup can increase the robustness of GNNs against noisy labels.

Graph foundation models represent a transformative paradigm for learning transferable representations across diverse graph domains. Recent methods leverage large language models to unify graph and text modalities into a shared representation space using contrastive learning. However, systematic evaluations reveal significant performance degradation at structural boundaries where distinct topological patterns converge, with accuracy losses exceeding 20 percentage points. This issue arises from a key limitation: current methods assume all graph structures can be encoded within a single Euclidean space. In reality, tree structures require hyperbolic geometry to preserve hierarchical branching, while cyclic patterns depend on spherical geometry for closure properties. At structural boundaries, nodes experience conflicting geometric constraints that uniform encoding spaces cannot resolve. This raises a crucial challenge: Can alignment frameworks be designed to respect the intrinsic geometric diversity of graph structures? We introduce GraphShaper, a geometry-aware framework that enhances graph encoding through multi-geometric specialization. Our approach employs expert networks tailored to different geometric spaces, dynamically computing fusion weights to adaptively integrate geometric properties based on local structural characteristics. This adaptive fusion preserves structural integrity before alignment with text embeddings. Extensive experiments demonstrate that GraphShaper achieves 9.47\% accuracy improvements on citation networks and 7.63\% on social networks in zero-shot settings.

Large Language Models (LLMs) excel in stand-alone code tasks like HumanEval and MBPP, but struggle with handling entire code repositories. This challenge has prompted research on enhancing LLM-codebase interaction at a repository scale. Current solutions rely on similarity-based retrieval or manual tools and APIs, each with notable drawbacks. Similarity-based retrieval often has low recall in complex tasks, while manual tools and APIs are typically task-specific and require expert knowledge, reducing their generalizability across diverse code tasks and real-world applications. To mitigate these limitations, we introduce \framework, a system that integrates LLM agents with graph database interfaces extracted from code repositories. By leveraging the structural properties of graph databases and the flexibility of the graph query language, \framework enables the LLM agent to construct and execute queries, allowing for precise, code structure-aware context retrieval and code navigation. We assess \framework using three benchmarks: CrossCodeEval, SWE-bench, and EvoCodeBench. Additionally, we develop five real-world coding applications. With a unified graph database schema, \framework demonstrates competitive performance and potential in both academic and real-world environments, showcasing its versatility and efficacy in software engineering. Our application demo: https://github.com/modelscope/modelscope-agent/tree/master/apps/codexgraph_agent.

We study the implications of the modeling choice to use a graph, instead of a hypergraph, to represent real-world interconnected systems whose constituent relationships are of higher order by nature. Such a modeling choice typically involves an underlying projection process that maps the original hypergraph onto a graph, and is common in graph-based analysis. While hypergraph projection can potentially lead to loss of higher-order relations, there exists very limited studies on the consequences of doing so, as well as its remediation. This work fills this gap by doing two things: (1) we develop analysis based on graph and set theory, showing two ubiquitous patterns of hyperedges that are root to structural information loss in all hypergraph projections; we also quantify the combinatorial impossibility of recovering the lost higher-order structures if no extra help is provided; (2) we still seek to recover the lost higher-order structures in hypergraph projection, and in light of (1)'s findings we propose to relax the problem into a learning-based setting. Under this setting, we develop a learning-based hypergraph reconstruction method based on an important statistic of hyperedge distributions that we find. Our reconstruction method is evaluated on 8 real-world datasets under different settings, and exhibits consistently good performance. We also demonstrate benefits of the reconstructed hypergraphs via use cases of protein rankings and link predictions.

This tutorial serves as a comprehensive guide for understanding graph databases, focusing on the fundamentals of graph theory while showcasing practical applications across various fields. It starts by introducing foundational concepts and delves into the structure of graphs through nodes and edges, covering different types such as undirected, directed, weighted, and unweighted graphs. Key graph properties, terminologies, and essential algorithms for network analysis are outlined, including Dijkstras shortest path algorithm and methods for calculating node centrality and graph connectivity. The tutorial highlights the advantages of graph databases over traditional relational databases, particularly in efficiently managing complex, interconnected data. It examines leading graph database systems such as Neo4j, Amazon Neptune, and ArangoDB, emphasizing their unique features for handling large datasets. Practical instructions on graph operations using NetworkX and Neo4j are provided, covering node and edge creation, attribute assignment, and advanced queries with Cypher. Additionally, the tutorial explores common graph visualization techniques using tools like Plotly and Neo4j Bloom, which enhance the interpretation and usability of graph data. It also delves into community detection algorithms, including the Louvain method, which facilitates clustering in large networks. Finally, the paper concludes with recommendations for researchers interested in exploring the vast potential of graph technologies.

A subgraph is constructed by using a subset of vertices and edges of a given graph. There exist many graph properties that are hereditary for subgraphs. Hence, researchers from different communities have paid a great deal of attention in studying numerous subgraph problems, on top of the ordinary graph problems. Many algorithms are proposed in studying subgraph problems, where one common approach is by extracting the patterns and structures of a given graph. Due to the complex structures of certain types of graphs and to improve overall performances of the existing frameworks, machine learning techniques have recently been employed in dealing with various subgraph problems. In this article, we present a comprehensive review on five well known subgraph problems that have been tackled by using machine learning methods. They are subgraph isomorphism (both counting and matching), maximum common subgraph, community detection and community search problems. We provide an outline of each proposed method, and examine its designs and performances. We also explore non-learning-based algorithms for each problem and a brief discussion is given. We then suggest some promising research directions in this area, hoping that relevant subgraph problems can be tackled by using a similar strategy. Since there is a huge growth in employing machine learning techniques in recent years, we believe that this survey will serve as a good reference point to relevant research communities.

This paper presents a novel approach for source code similarity detection that integrates an additional output feature into the classification process with the goal of improving model performance. Our approach is based on the GraphCodeBERT model, extended with a custom output feature layer and a concatenation mechanism for improved feature representation. The model was trained and evaluated, achieving promising results in terms of precision, recall, and f-measure. The implementation details, including model architecture and training strategies are discussed. The source code that illustrates our approach can be downloaded from https://www.github.com/jorge-martinez-gil/graphcodebert-feature-integration.

Learning an effective outfit-level representation is critical for predicting the compatibility of items in an outfit, and retrieving complementary items for a partial outfit. We present a framework, OutfitTransformer, that uses the proposed task-specific tokens and leverages the self-attention mechanism to learn effective outfit-level representations encoding the compatibility relationships between all items in the entire outfit for addressing both compatibility prediction and complementary item retrieval tasks. For compatibility prediction, we design an outfit token to capture a global outfit representation and train the framework using a classification loss. For complementary item retrieval, we design a target item token that additionally takes the target item specification (in the form of a category or text description) into consideration. We train our framework using a proposed set-wise outfit ranking loss to generate a target item embedding given an outfit, and a target item specification as inputs. The generated target item embedding is then used to retrieve compatible items that match the rest of the outfit. Additionally, we adopt a pre-training approach and a curriculum learning strategy to improve retrieval performance. Since our framework learns at an outfit-level, it allows us to learn a single embedding capturing higher-order relations among multiple items in the outfit more effectively than pairwise methods. Experiments demonstrate that our approach outperforms state-of-the-art methods on compatibility prediction, fill-in-the-blank, and complementary item retrieval tasks. We further validate the quality of our retrieval results with a user study.

With the increasing prevalence of graph-structured data, multi-view graph clustering has been widely used in various downstream applications. Existing approaches primarily rely on a unified message passing mechanism, which significantly enhances clustering performance. Nevertheless, this mechanism limits its applicability to heterophilous situations, as it is fundamentally predicated on the assumption of homophily, i.e., the connected nodes often belong to the same class. In reality, this assumption does not always hold; a moderately or even mildly homophilous graph is more common than a fully homophilous one due to inevitable heterophilous information in the graph. To address this issue, in this paper, we propose a novel SiMilarity-enhanced Homophily for Multi-view Heterophilous Graph Clustering (SMHGC) approach. By analyzing the relationship between similarity and graph homophily, we propose to enhance the homophily by introducing three similarity terms, i.e., neighbor pattern similarity, node feature similarity, and multi-view global similarity, in a label-free manner. Then, a consensus-based inter- and intra-view fusion paradigm is proposed to fuse the improved homophilous graph from different views and utilize them for clustering. The state-of-the-art experimental results on both multi-view heterophilous and homophilous datasets collectively demonstrate the strong capacity of similarity for unsupervised multi-view heterophilous graph learning. Additionally, the consistent performance across semi-synthetic datasets with varying levels of homophily serves as further evidence of SMHGC's resilience to heterophily.

Backward compatibility of model predictions is a desired property when updating a machine learning driven application. It allows to seamlessly improve the underlying model without introducing regression bugs. In classification tasks these bugs occur in the form of negative flips. This means an instance that was correctly classified by the old model is now classified incorrectly by the updated model. This has direct negative impact on the user experience of such systems e.g. a frequently used voice assistant query is suddenly misclassified. A common reason to update the model is when new training data becomes available and needs to be incorporated. Simply retraining the model with the updated data introduces the unwanted negative flips. We study the problem of regression during data updates and propose Backward Compatible Weight Interpolation (BCWI). This method interpolates between the weights of the old and new model and we show in extensive experiments that it reduces negative flips without sacrificing the improved accuracy of the new model. BCWI is straight forward to implement and does not increase inference cost. We also explore the use of importance weighting during interpolation and averaging the weights of multiple new models in order to further reduce negative flips.

A Harris Graph is a tough, Eulerian, non-Hamiltonian graph. Several approaches to creating new Harris graphs from existing ones are explored, including creating families of Harris graphs and combining Harris graphs. Pictures of all Harris Graphs through order 9 and the number of Harris graphs through order 12 are included. We also prove a result about barnacle-free Harris graphs.

We propose MESA and DMESA as novel feature matching methods, which utilize Segment Anything Model (SAM) to effectively mitigate matching redundancy. The key insight of our methods is to establish implicit-semantic area matching prior to point matching, based on advanced image understanding of SAM. Then, informative area matches with consistent internal semantic are able to undergo dense feature comparison, facilitating precise inside-area point matching. Specifically, MESA adopts a sparse matching framework and first obtains candidate areas from SAM results through a novel Area Graph (AG). Then, area matching among the candidates is formulated as graph energy minimization and solved by graphical models derived from AG. To address the efficiency issue of MESA, we further propose DMESA as its dense counterpart, applying a dense matching framework. After candidate areas are identified by AG, DMESA establishes area matches through generating dense matching distributions. The distributions are produced from off-the-shelf patch matching utilizing the Gaussian Mixture Model and refined via the Expectation Maximization. With less repetitive computation, DMESA showcases a speed improvement of nearly five times compared to MESA, while maintaining competitive accuracy. Our methods are extensively evaluated on five datasets encompassing indoor and outdoor scenes. The results illustrate consistent performance improvements from our methods for five distinct point matching baselines across all datasets. Furthermore, our methods exhibit promise generalization and improved robustness against image resolution variations. The code is publicly available at https://github.com/Easonyesheng/A2PM-MESA.

The need to analyze graphs is ubiquitous across various fields, from social networks to biological research and recommendation systems. Therefore, enabling the ability of large language models (LLMs) to process graphs is an important step toward more advanced general intelligence. However, current LLM benchmarks on graph analysis require models to directly reason over the prompts describing graph topology, and are thus limited to small graphs with only a few dozens of nodes. In contrast, human experts typically write programs based on popular libraries for task solving, and can thus handle graphs with different scales. To this end, a question naturally arises: can LLMs analyze graphs like professionals? In this paper, we introduce ProGraph, a manually crafted benchmark containing 3 categories of graph tasks. The benchmark expects solutions based on programming instead of directly reasoning over raw inputs. Our findings reveal that the performance of current LLMs is unsatisfactory, with the best model achieving only 36% accuracy. To bridge this gap, we propose LLM4Graph datasets, which include crawled documents and auto-generated codes based on 6 widely used graph libraries. By augmenting closed-source LLMs with document retrieval and fine-tuning open-source ones on the codes, we show 11-32% absolute improvements in their accuracies. Our results underscore that the capabilities of LLMs in handling structured data are still under-explored, and show the effectiveness of LLM4Graph in enhancing LLMs' proficiency of graph analysis. The benchmark, datasets and enhanced open-source models are available at https://github.com/BUPT-GAMMA/ProGraph.

Semi-transitive graphs, defined in hps98 as examples where ``uniform percolation" holds whenever p>p_c, are a large class of graphs more general than quasi-transitive graphs. Let G be a semi-transitive graph with one end which can be properly embedded into the plane with uniformly bounded face degree for finite faces and minimal vertex degree at least 7. We show that p_u^{site}(G) +p_c^{site}(G_*)=1, where G_* denotes the matching graph of G. This fulfils and extends an observation of Sykes and Essam in 1964 (SE64) to semi-transitive graphs.

We introduce ReMatching, a novel shape correspondence solution based on the functional maps framework. Our method, by exploiting a new and appropriate re-meshing paradigm, can target shape-matching tasks even on meshes counting millions of vertices, where the original functional maps does not apply or requires a massive computational cost. The core of our procedure is a time-efficient remeshing algorithm which constructs a low-resolution geometry while acting conservatively on the original topology and metric. These properties allow translating the functional maps optimization problem on the resulting low-resolution representation, thus enabling efficient computation of correspondences with functional map approaches. Finally, we propose an efficient technique for extending the estimated correspondence to the original meshes. We show that our method is more efficient and effective through quantitative and qualitative comparisons, outperforming state-of-the-art pipelines in quality and computational cost.

Recently, there has been a surge of interest in employing neural networks for graph generation, a fundamental statistical learning problem with critical applications like molecule design and community analysis. However, most approaches encounter significant limitations when generating large-scale graphs. This is due to their requirement to output the full adjacency matrices whose size grows quadratically with the number of nodes. In response to this challenge, we introduce a new, simple, and scalable graph representation named gap encoded edge list (GEEL) that has a small representation size that aligns with the number of edges. In addition, GEEL significantly reduces the vocabulary size by incorporating the gap encoding and bandwidth restriction schemes. GEEL can be autoregressively generated with the incorporation of node positional encoding, and we further extend GEEL to deal with attributed graphs by designing a new grammar. Our findings reveal that the adoption of this compact representation not only enhances scalability but also bolsters performance by simplifying the graph generation process. We conduct a comprehensive evaluation across ten non-attributed and two molecular graph generation tasks, demonstrating the effectiveness of GEEL.

The Berge-Fulkerson conjecture states that every bridgeless cubic graph can be covered with six perfect matchings such that each edge is covered exactly twice. An equivalent reformulation is that it's possible to find a 6-cycle 4-cover. In this paper we discuss the oriented version (o6c4c) of the latter statement, pose it as a conjecture and prove it for the family of Isaacs flower snarks. Similarly to the case of oriented cycle double cover, we can always construct an orientable surface (possibly with boundary) from an o6c4c solution. If the o6c4c solution itself splits into two (not necessarily oriented) cycle double covers, then it's also possible to build another pair of orientable surfaces (also possibly with boundaries). Finally we show how to build a ribbon graph, and for some special o6c4c cases we show that this ribbon graph corresponds to an oriented 6-cycle double cover. Github: https://github.com/gexahedron/cycle-double-covers

Knowledge graphs have been proven extremely useful in powering diverse applications in semantic search and natural language understanding. In this paper, we present GraphGen4Code, a toolkit to build code knowledge graphs that can similarly power various applications such as program search, code understanding, bug detection, and code automation. GraphGen4Code uses generic techniques to capture code semantics with the key nodes in the graph representing classes, functions, and methods. Edges indicate function usage (e.g., how data flows through function calls, as derived from program analysis of real code), and documentation about functions (e.g., code documentation, usage documentation, or forum discussions such as StackOverflow). Our toolkit uses named graphs in RDF to model graphs per program, or can output graphs as JSON. We show the scalability of the toolkit by applying it to 1.3 million Python files drawn from GitHub, 2,300 Python modules, and 47 million forum posts. This results in an integrated code graph with over 2 billion triples. We make the toolkit to build such graphs as well as the sample extraction of the 2 billion triples graph publicly available to the community for use.

Deep graph generative modeling has proven capable of learning the distribution of complex, multi-scale structures characterizing real-world graphs. However, one of the main limitations of existing methods is their large output space, which limits generation scalability and hinders accurate modeling of the underlying distribution. To overcome these limitations, we propose a novel approach that significantly reduces the output space of existing graph generative models. Specifically, starting from the observation that many real-world graphs have low graph bandwidth, we restrict graph bandwidth during training and generation. Our strategy improves both generation scalability and quality without increasing architectural complexity or reducing expressiveness. Our approach is compatible with existing graph generative methods, and we describe its application to both autoregressive and one-shot models. We extensively validate our strategy on synthetic and real datasets, including molecular graphs. Our experiments show that, in addition to improving generation efficiency, our approach consistently improves generation quality and reconstruction accuracy. The implementation is made available.

In this paper, we propose a method to partially mimic natural intelligence for the problem of lifelong learning representations that are compatible. We take the perspective of a learning agent that is interested in recognizing object instances in an open dynamic universe in a way in which any update to its internal feature representation does not render the features in the gallery unusable for visual search. We refer to this learning problem as Compatible Lifelong Learning Representations (CL2R) as it considers compatible representation learning within the lifelong learning paradigm. We identify stationarity as the property that the feature representation is required to hold to achieve compatibility and propose a novel training procedure that encourages local and global stationarity on the learned representation. Due to stationarity, the statistical properties of the learned features do not change over time, making them interoperable with previously learned features. Extensive experiments on standard benchmark datasets show that our CL2R training procedure outperforms alternative baselines and state-of-the-art methods. We also provide novel metrics to specifically evaluate compatible representation learning under catastrophic forgetting in various sequential learning tasks. Code at https://github.com/NiccoBiondi/CompatibleLifelongRepresentation.

Graphs are able to model interconnected entities in many online services, supporting a wide range of applications on the Web. This raises an important question: How can we train a graph foundational model on multiple source domains and adapt to an unseen target domain? A major obstacle is that graphs from different domains often exhibit divergent characteristics. Some studies leverage large language models to align multiple domains based on textual descriptions associated with the graphs, limiting their applicability to text-attributed graphs. For text-free graphs, a few recent works attempt to align different feature distributions across domains, while generally neglecting structural differences. In this work, we propose a novel Structure Alignment framework for text-free Multi-domain Graph Pre-Training and cross-domain adaptation (SAMGPT). It is designed to learn multi-domain knowledge from graphs originating in multiple source domains, which can then be adapted to address applications in an unseen target domain. Specifically, we introduce a set of structure tokens to harmonize structure-based aggregation across source domains during the pre-training phase. Next, for cross-domain adaptation, we design dual prompts, namely, holistic prompts and specific prompts, which adapt unified multi-domain structural knowledge and fine-grained, domain-specific information, respectively, to a target domain. Finally, we conduct comprehensive experiments on seven public datasets to evaluate and analyze the effectiveness of SAMGPT.

Feature-based image matching has extensive applications in computer vision. Keypoints detected in images can be naturally represented as graph structures, and Graph Neural Networks (GNNs) have been shown to outperform traditional deep learning techniques. Consequently, the paradigm of image matching via GNNs has gained significant prominence in recent academic research. In this paper, we first introduce an innovative adaptive graph construction method that utilizes a filtering mechanism based on distance and dynamic threshold similarity. This method dynamically adjusts the criteria for incorporating new vertices based on the characteristics of existing vertices, allowing for the construction of more precise and robust graph structures while avoiding redundancy. We further combine the vertex processing capabilities of GNNs with the global awareness capabilities of Transformers to enhance the model's representation of spatial and feature information within graph structures. This hybrid model provides a deeper understanding of the interrelationships between vertices and their contributions to the matching process. Additionally, we employ the Sinkhorn algorithm to iteratively solve for optimal matching results. Finally, we validate our system using extensive image datasets and conduct comprehensive comparative experiments. Experimental results demonstrate that our system achieves an average improvement of 3.8x-40.3x in overall matching performance. Additionally, the number of vertices and edges significantly impacts training efficiency and memory usage; therefore, we employ multi-GPU technology to accelerate the training process. Our code is available at https://github.com/songxf1024/GIMS.

Large Language Models (LLMs) have demonstrated their potential in hardware design tasks, such as Hardware Description Language (HDL) generation and debugging. Yet, their performance in real-world, repository-level HDL projects with thousands or even tens of thousands of code lines is hindered. To this end, we propose HDLxGraph, a novel framework that integrates Graph Retrieval Augmented Generation (Graph RAG) with LLMs, introducing HDL-specific graph representations by incorporating Abstract Syntax Trees (ASTs) and Data Flow Graphs (DFGs) to capture both code graph view and hardware graph view. HDLxGraph utilizes a dual-retrieval mechanism that not only mitigates the limited recall issues inherent in similarity-based semantic retrieval by incorporating structural information, but also enhances its extensibility to various real-world tasks by a task-specific retrieval finetuning. Additionally, to address the lack of comprehensive HDL search benchmarks, we introduce HDLSearch, a multi-granularity evaluation dataset derived from real-world repository-level projects. Experimental results demonstrate that HDLxGraph significantly improves average search accuracy, debugging efficiency and completion quality by 12.04%, 12.22% and 5.04% compared to similarity-based RAG, respectively. The code of HDLxGraph and collected HDLSearch benchmark are available at https://github.com/Nick-Zheng-Q/HDLxGraph.

Large language models (LLMs) have demonstrated remarkable success across a wide range of tasks; however, they still encounter challenges in reasoning tasks that require understanding and inferring relationships between distinct pieces of information within text sequences. This challenge is particularly pronounced in tasks involving multi-step processes, such as logical reasoning and multi-hop question answering, where understanding implicit relationships between entities and leveraging multi-hop connections in the given context are crucial. Graphs, as fundamental data structures, explicitly represent pairwise relationships between entities, thereby offering the potential to enhance LLMs' reasoning capabilities. External graphs have proven effective in supporting LLMs across multiple tasks. However, in many reasoning tasks, no pre-existing graph structure is provided. Can we structure implicit knowledge derived from context into graphs to assist LLMs in reasoning? In this paper, we propose Reasoning with Graphs (RwG) by first constructing explicit graphs from the context and then leveraging these graphs to enhance LLM reasoning performance on reasoning tasks. Extensive experiments demonstrate the effectiveness of the proposed method in improving both logical reasoning and multi-hop question answering tasks.

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified communities and connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. The graph has an inherently scale-free nature, is highly connected, and can be used for graph reasoning by taking advantage of transitive and isomorphic properties that reveal unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. We compute deep node embeddings for combinatorial node similarity ranking for use in a path sampling strategy links dissimilar concepts that have previously not been related. One comparison revealed structural parallels between biological materials and Beethoven's 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed a hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky's 'Composition VII' painting. The resulting material integrates an innovative set of concepts that include a balance of chaos/order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.

This paper introduces layout-aware graph modeling for multimodal RAG. Different from traditional RAG methods that mostly deal with flat text chunks, the proposed method takes into account the relationship of multimodalities by using a graph structure. To do that, a graph modeling structure is defined based on document layout parsing. The structure of an input document is retained with the connection of text chunks, tables, and figures. This representation allows the method to handle complex questions that require information from multimodalities. To confirm the efficiency of the graph modeling, a flexible RAG pipeline is developed using robust components. Experimental results on four benchmark test sets confirm the contribution of the layout-aware modeling for performance improvement of the RAG pipeline.

While machine learning on graphs has demonstrated promise in drug design and molecular property prediction, significant benchmarking challenges hinder its further progress and relevance. Current benchmarking practices often lack focus on transformative, real-world applications, favoring narrow domains like two-dimensional molecular graphs over broader, impactful areas such as combinatorial optimization, relational databases, or chip design. Additionally, many benchmark datasets poorly represent the underlying data, leading to inadequate abstractions and misaligned use cases. Fragmented evaluations and an excessive focus on accuracy further exacerbate these issues, incentivizing overfitting rather than fostering generalizable insights. These limitations have prevented the development of truly useful graph foundation models. This position paper calls for a paradigm shift toward more meaningful benchmarks, rigorous evaluation protocols, and stronger collaboration with domain experts to drive impactful and reliable advances in graph learning research, unlocking the potential of graph learning.

The expressivity of Graph Neural Networks (GNNs) has been studied broadly in recent years to reveal the design principles for more powerful GNNs. Graph canonization is known as a typical approach to distinguish non-isomorphic graphs, yet rarely adopted when developing expressive GNNs. This paper proposes to maximize the expressivity of GNNs by graph canonization, then the power of such GNNs is studies from the perspective of model stability. A stable GNN will map similar graphs to close graph representations in the vectorial space, and the stability of GNNs is critical to generalize their performance to unseen graphs. We theoretically reveal the trade-off of expressivity and stability in graph-canonization-enhanced GNNs. Then we introduce a notion of universal graph canonization as the general solution to address the trade-off and characterize a widely applicable sufficient condition to solve the universal graph canonization. A comprehensive set of experiments demonstrates the effectiveness of the proposed method. In many popular graph benchmark datasets, graph canonization successfully enhances GNNs and provides highly competitive performance, indicating the capability and great potential of proposed method in general graph representation learning. In graph datasets where the sufficient condition holds, GNNs enhanced by universal graph canonization consistently outperform GNN baselines and successfully improve the SOTA performance up to 31%, providing the optimal solution to numerous challenging real-world graph analytical tasks like gene network representation learning in bioinformatics.

Large Language Models (LLMs) are frequently updated due to data or architecture changes to improve their performance. When updating models, developers often focus on increasing overall performance metrics with less emphasis on being compatible with previous model versions. However, users often build a mental model of the functionality and capabilities of a particular machine learning model they are interacting with. They have to adapt their mental model with every update -- a draining task that can lead to user dissatisfaction. In practice, fine-tuned downstream task adapters rely on pretrained LLM base models. When these base models are updated, these user-facing downstream task models experience instance regression or negative flips -- previously correct instances are now predicted incorrectly. This happens even when the downstream task training procedures remain identical. Our work aims to provide seamless model updates to a user in two ways. First, we provide evaluation metrics for a notion of compatibility to prior model versions, specifically for generative tasks but also applicable for discriminative tasks. We observe regression and inconsistencies between different model versions on a diverse set of tasks and model updates. Second, we propose a training strategy to minimize the number of inconsistencies in model updates, involving training of a compatibility model that can enhance task fine-tuned language models. We reduce negative flips -- instances where a prior model version was correct, but a new model incorrect -- by up to 40% from Llama 1 to Llama 2.

Graphs are a powerful tool for representing and analyzing complex relationships in real-world applications such as social networks, recommender systems, and computational finance. Reasoning on graphs is essential for drawing inferences about the relationships between entities in a complex system, and to identify hidden patterns and trends. Despite the remarkable progress in automated reasoning with natural text, reasoning on graphs with large language models (LLMs) remains an understudied problem. In this work, we perform the first comprehensive study of encoding graph-structured data as text for consumption by LLMs. We show that LLM performance on graph reasoning tasks varies on three fundamental levels: (1) the graph encoding method, (2) the nature of the graph task itself, and (3) interestingly, the very structure of the graph considered. These novel results provide valuable insight on strategies for encoding graphs as text. Using these insights we illustrate how the correct choice of encoders can boost performance on graph reasoning tasks inside LLMs by 4.8% to 61.8%, depending on the task.

Large language models (LLMs), such as ChatGPT and LLaMA, are creating significant advancements in natural language processing, due to their strong text encoding/decoding ability and newly found emergent capability (e.g., reasoning). While LLMs are mainly designed to process pure texts, there are many real-world scenarios where text data are associated with rich structure information in the form of graphs (e.g., academic networks, and e-commerce networks) or scenarios where graph data are paired with rich textual information (e.g., molecules with descriptions). Besides, although LLMs have shown their pure text-based reasoning ability, it is underexplored whether such ability can be generalized to graph scenarios (i.e., graph-based reasoning). In this paper, we provide a systematic review of scenarios and techniques related to large language models on graphs. We first summarize potential scenarios of adopting LLMs on graphs into three categories, namely pure graphs, text-rich graphs, and text-paired graphs. We then discuss detailed techniques for utilizing LLMs on graphs, including LLM as Predictor, LLM as Encoder, and LLM as Aligner, and compare the advantages and disadvantages of different schools of models. Furthermore, we mention the real-world applications of such methods and summarize open-source codes and benchmark datasets. Finally, we conclude with potential future research directions in this fast-growing field. The related source can be found at https://github.com/PeterGriffinJin/Awesome-Language-Model-on-Graphs.

Existing commonsense knowledge bases often organize tuples in an isolated manner, which is deficient for commonsense conversational models to plan the next steps. To fill the gap, we curate a large-scale multi-turn human-written conversation corpus, and create the first Chinese commonsense conversation knowledge graph which incorporates both social commonsense knowledge and dialog flow information. To show the potential of our graph, we develop a graph-conversation matching approach, and benchmark two graph-grounded conversational tasks.

We present a unified representation for actionable spatial perception: 3D Dynamic Scene Graphs. Scene graphs are directed graphs where nodes represent entities in the scene (e.g. objects, walls, rooms), and edges represent relations (e.g. inclusion, adjacency) among nodes. Dynamic scene graphs (DSGs) extend this notion to represent dynamic scenes with moving agents (e.g. humans, robots), and to include actionable information that supports planning and decision-making (e.g. spatio-temporal relations, topology at different levels of abstraction). Our second contribution is to provide the first fully automatic Spatial PerceptIon eNgine(SPIN) to build a DSG from visual-inertial data. We integrate state-of-the-art techniques for object and human detection and pose estimation, and we describe how to robustly infer object, robot, and human nodes in crowded scenes. To the best of our knowledge, this is the first paper that reconciles visual-inertial SLAM and dense human mesh tracking. Moreover, we provide algorithms to obtain hierarchical representations of indoor environments (e.g. places, structures, rooms) and their relations. Our third contribution is to demonstrate the proposed spatial perception engine in a photo-realistic Unity-based simulator, where we assess its robustness and expressiveness. Finally, we discuss the implications of our proposal on modern robotics applications. 3D Dynamic Scene Graphs can have a profound impact on planning and decision-making, human-robot interaction, long-term autonomy, and scene prediction. A video abstract is available at https://youtu.be/SWbofjhyPzI

Text-attributed graphs are widely used across domains, offering rich opportunities for zero-shot learning via graph-text alignment. However, existing methods struggle with tasks requiring fine-grained pattern recognition, particularly on heterophilic graphs. Through empirical and theoretical analysis, we identify an over-abstraction problem: current approaches operate at excessively large hyperbolic radii, compressing multi-scale structural information into uniform high-level abstractions. This abstraction-induced information loss obscures critical local patterns essential for accurate predictions. By analyzing embeddings in hyperbolic space, we demonstrate that optimal graph learning requires faithful preservation of fine-grained structural details, better retained by representations positioned closer to the origin. To address this, we propose H4G, a framework that systematically reduces embedding radii using learnable block-diagonal scaling matrices and M\"obius matrix multiplication. This approach restores access to fine-grained patterns while maintaining global receptive ability with minimal computational overhead. Experiments show H4G achieves state-of-the-art zero-shot performance with 12.8\% improvement on heterophilic graphs and 8.4\% on homophilic graphs, confirming that radius reduction enables faithful multi-scale representation for advancing zero-shot graph learning.

Various human-designed prompt engineering techniques have been proposed to improve problem solvers based on Large Language Models (LLMs), yielding many disparate code bases. We unify these approaches by describing LLM-based agents as computational graphs. The nodes implement functions to process multimodal data or query LLMs, and the edges describe the information flow between operations. Graphs can be recursively combined into larger composite graphs representing hierarchies of inter-agent collaboration (where edges connect operations of different agents). Our novel automatic graph optimizers (1) refine node-level LLM prompts (node optimization) and (2) improve agent orchestration by changing graph connectivity (edge optimization). Experiments demonstrate that our framework can be used to efficiently develop, integrate, and automatically improve various LLM agents. The code can be found at https://github.com/metauto-ai/gptswarm.

We introduce EvoGit, a decentralized multi-agent framework for collaborative software development driven by autonomous code evolution. EvoGit deploys a population of independent coding agents, each proposing edits to a shared codebase without centralized coordination, explicit message passing, or shared memory. Instead, all coordination emerges through a Git-based phylogenetic graph that tracks the full version lineage and enables agents to asynchronously read from and write to the evolving code repository. This graph-based structure supports fine-grained branching, implicit concurrency, and scalable agent interaction while preserving a consistent historical record. Human involvement is minimal but strategic: users define high-level goals, periodically review the graph, and provide lightweight feedback to promote promising directions or prune unproductive ones. Experiments demonstrate EvoGit's ability to autonomously produce functional and modular software artifacts across two real-world tasks: (1) building a web application from scratch using modern frameworks, and (2) constructing a meta-level system that evolves its own language-model-guided solver for the bin-packing optimization problem. Our results underscore EvoGit's potential to establish a new paradigm for decentralized, automated, and continual software development. EvoGit is open-sourced at https://github.com/BillHuang2001/evogit.

We introduce the task of predicting functional 3D scene graphs for real-world indoor environments from posed RGB-D images. Unlike traditional 3D scene graphs that focus on spatial relationships of objects, functional 3D scene graphs capture objects, interactive elements, and their functional relationships. Due to the lack of training data, we leverage foundation models, including visual language models (VLMs) and large language models (LLMs), to encode functional knowledge. We evaluate our approach on an extended SceneFun3D dataset and a newly collected dataset, FunGraph3D, both annotated with functional 3D scene graphs. Our method significantly outperforms adapted baselines, including Open3DSG and ConceptGraph, demonstrating its effectiveness in modeling complex scene functionalities. We also demonstrate downstream applications such as 3D question answering and robotic manipulation using functional 3D scene graphs. See our project page at https://openfungraph.github.io

Given a graph G and the desired size k in bits, how can we summarize G within k bits, while minimizing the information loss? Large-scale graphs have become omnipresent, posing considerable computational challenges. Analyzing such large graphs can be fast and easy if they are compressed sufficiently to fit in main memory or even cache. Graph summarization, which yields a coarse-grained summary graph with merged nodes, stands out with several advantages among graph compression techniques. Thus, a number of algorithms have been developed for obtaining a concise summary graph with little information loss or equivalently small reconstruction error. However, the existing methods focus solely on reducing the number of nodes, and they often yield dense summary graphs, failing to achieve better compression rates. Moreover, due to their limited scalability, they can be applied only to moderate-size graphs. In this work, we propose SSumM, a scalable and effective graph-summarization algorithm that yields a sparse summary graph. SSumM not only merges nodes together but also sparsifies the summary graph, and the two strategies are carefully balanced based on the minimum description length principle. Compared with state-of-the-art competitors, SSumM is (a) Concise: yields up to 11.2X smaller summary graphs with similar reconstruction error, (b) Accurate: achieves up to 4.2X smaller reconstruction error with similarly concise outputs, and (c) Scalable: summarizes 26X larger graphs while exhibiting linear scalability. We validate these advantages through extensive experiments on 10 real-world graphs.

Recently, subgraph GNNs have emerged as an important direction for developing expressive graph neural networks (GNNs). While numerous architectures have been proposed, so far there is still a limited understanding of how various design paradigms differ in terms of expressive power, nor is it clear what design principle achieves maximal expressiveness with minimal architectural complexity. To address these fundamental questions, this paper conducts a systematic study of general node-based subgraph GNNs through the lens of Subgraph Weisfeiler-Lehman Tests (SWL). Our central result is to build a complete hierarchy of SWL with strictly growing expressivity. Concretely, we prove that any node-based subgraph GNN falls into one of the six SWL equivalence classes, among which SSWL achieves the maximal expressive power. We also study how these equivalence classes differ in terms of their practical expressiveness such as encoding graph distance and biconnectivity. Furthermore, we give a tight expressivity upper bound of all SWL algorithms by establishing a close relation with localized versions of WL and Folklore WL (FWL) tests. Our results provide insights into the power of existing subgraph GNNs, guide the design of new architectures, and point out their limitations by revealing an inherent gap with the 2-FWL test. Finally, experiments demonstrate that SSWL-inspired subgraph GNNs can significantly outperform prior architectures on multiple benchmarks despite great simplicity.

There is a surge of interest in image scene graph generation (object, attribute and relationship detection) due to the need of building fine-grained image understanding models that go beyond object detection. Due to the lack of a good benchmark, the reported results of different scene graph generation models are not directly comparable, impeding the research progress. We have developed a much-needed scene graph generation benchmark based on the maskrcnn-benchmark and several popular models. This paper presents main features of our benchmark and a comprehensive ablation study of scene graph generation models using the Visual Genome and OpenImages Visual relationship detection datasets. Our codebase is made publicly available at https://github.com/microsoft/scene_graph_benchmark.

Associating unstructured data with structured information is crucial for real-world tasks that require relevance search. However, existing graph learning benchmarks often overlook the rich semantic information associate with each node. To bridge such gap, we introduce the Multimodal Graph Benchmark (MM-GRAPH), the first comprehensive multi-modal graph benchmark that incorporates both textual and visual information. MM-GRAPH surpasses previous efforts, which have primarily focused on text-attributed graphs with various connectivity patterns. MM-GRAPH consists of five graph learning datasets of various scales that are appropriate for different learning tasks. Their multimodal node features, enabling a more comprehensive evaluation of graph learning algorithms in real-world scenarios. To facilitate research on multimodal graph learning, we further provide an extensive study on the performance of various graph neural networks in the presence of features from various modalities. MM-GRAPH aims to foster research on multimodal graph learning and drive the development of more advanced and robust graph learning algorithms. By providing a diverse set of datasets and benchmarks, MM-GRAPH enables researchers to evaluate and compare their models in realistic settings, ultimately leading to improved performance on real-world applications that rely on multimodal graph data.

Node classification is a classical graph machine learning task on which Graph Neural Networks (GNNs) have recently achieved strong results. However, it is often believed that standard GNNs only work well for homophilous graphs, i.e., graphs where edges tend to connect nodes of the same class. Graphs without this property are called heterophilous, and it is typically assumed that specialized methods are required to achieve strong performance on such graphs. In this work, we challenge this assumption. First, we show that the standard datasets used for evaluating heterophily-specific models have serious drawbacks, making results obtained by using them unreliable. The most significant of these drawbacks is the presence of a large number of duplicate nodes in the datasets Squirrel and Chameleon, which leads to train-test data leakage. We show that removing duplicate nodes strongly affects GNN performance on these datasets. Then, we propose a set of heterophilous graphs of varying properties that we believe can serve as a better benchmark for evaluating the performance of GNNs under heterophily. We show that standard GNNs achieve strong results on these heterophilous graphs, almost always outperforming specialized models. Our datasets and the code for reproducing our experiments are available at https://github.com/yandex-research/heterophilous-graphs

Line segments are powerful features complementary to points. They offer structural cues, robust to drastic viewpoint and illumination changes, and can be present even in texture-less areas. However, describing and matching them is more challenging compared to points due to partial occlusions, lack of texture, or repetitiveness. This paper introduces a new matching paradigm, where points, lines, and their descriptors are unified into a single wireframe structure. We propose GlueStick, a deep matching Graph Neural Network (GNN) that takes two wireframes from different images and leverages the connectivity information between nodes to better glue them together. In addition to the increased efficiency brought by the joint matching, we also demonstrate a large boost of performance when leveraging the complementary nature of these two features in a single architecture. We show that our matching strategy outperforms the state-of-the-art approaches independently matching line segments and points for a wide variety of datasets and tasks. The code is available at https://github.com/cvg/GlueStick.

Large language models (LLMs) have achieved impressive success across several fields, but their proficiency in understanding and resolving complex graph problems is less explored. To bridge this gap, we introduce GraphInstruct, a novel and comprehensive instruction-tuning dataset designed to equip language models with the ability to tackle a broad spectrum of graph problems using explicit reasoning paths. Utilizing GraphInstruct, we build GraphWiz, an open-source language model capable of resolving various graph problem types while generating clear reasoning processes. To enhance the model's capability and reliability, we incorporate the Direct Preference Optimization (DPO) framework into the graph problem-solving context. The enhanced model, GraphWiz-DPO, achieves an average accuracy of 65% across nine tasks with different complexity levels, surpassing GPT-4 which has an average accuracy of 43.8%. Moreover, our research delves into the delicate balance between training data volume and model performance, highlighting the potential for overfitting with increased data. We also explore the transferability of the model's reasoning ability across different graph tasks, indicating the model's adaptability and practical application potential. Our investigation offers a new blueprint and valuable insights for developing LLMs specialized in graph reasoning and problem-solving.

Many recent language model (LM) interpretability studies have adopted the circuits framework, which aims to find the minimal computational subgraph, or circuit, that explains LM behavior on a given task. Most studies determine which edges belong in a LM's circuit by performing causal interventions on each edge independently, but this scales poorly with model size. Edge attribution patching (EAP), gradient-based approximation to interventions, has emerged as a scalable but imperfect solution to this problem. In this paper, we introduce a new method - EAP with integrated gradients (EAP-IG) - that aims to better maintain a core property of circuits: faithfulness. A circuit is faithful if all model edges outside the circuit can be ablated without changing the model's performance on the task; faithfulness is what justifies studying circuits, rather than the full model. Our experiments demonstrate that circuits found using EAP are less faithful than those found using EAP-IG, even though both have high node overlap with circuits found previously using causal interventions. We conclude more generally that when using circuits to compare the mechanisms models use to solve tasks, faithfulness, not overlap, is what should be measured.

We investigate novel random graph embeddings that can be computed in expected polynomial time and that are able to distinguish all non-isomorphic graphs in expectation. Previous graph embeddings have limited expressiveness and either cannot distinguish all graphs or cannot be computed efficiently for every graph. To be able to approximate arbitrary functions on graphs, we are interested in efficient alternatives that become arbitrarily expressive with increasing resources. Our approach is based on Lov\'asz' characterisation of graph isomorphism through an infinite dimensional vector of homomorphism counts. Our empirical evaluation shows competitive results on several benchmark graph learning tasks.

The exponential growth of scientific literature requires effective management and extraction of valuable insights. While existing scientific search engines excel at delivering search results based on relational databases, they often neglect the analysis of collaborations between scientific entities and the evolution of ideas, as well as the in-depth analysis of content within scientific publications. The representation of heterogeneous graphs and the effective measurement, analysis, and mining of such graphs pose significant challenges. To address these challenges, we present AceMap, an academic system designed for knowledge discovery through academic graph. We present advanced database construction techniques to build the comprehensive AceMap database with large-scale academic entities that contain rich visual, textual, and numerical information. AceMap also employs innovative visualization, quantification, and analysis methods to explore associations and logical relationships among academic entities. AceMap introduces large-scale academic network visualization techniques centered on nebular graphs, providing a comprehensive view of academic networks from multiple perspectives. In addition, AceMap proposes a unified metric based on structural entropy to quantitatively measure the knowledge content of different academic entities. Moreover, AceMap provides advanced analysis capabilities, including tracing the evolution of academic ideas through citation relationships and concept co-occurrence, and generating concise summaries informed by this evolutionary process. In addition, AceMap uses machine reading methods to generate potential new ideas at the intersection of different fields. Exploring the integration of large language models and knowledge graphs is a promising direction for future research in idea evolution. Please visit https://www.acemap.info for further exploration.

Graph measures that express closeness or distance between nodes can be employed for graph nodes clustering using metric clustering algorithms. There are numerous measures applicable to this task, and which one performs better is an open question. We study the performance of 25 graph measures on generated graphs with different parameters. While usually measure comparisons are limited to general measure ranking on a particular dataset, we aim to explore the performance of various measures depending on graph features. Using an LFR graph generator, we create a dataset of 11780 graphs covering the whole LFR parameter space. For each graph, we assess the quality of clustering with k-means algorithm for each considered measure. Based on this, we determine the best measure for each area of the parameter space. We find that the parameter space consists of distinct zones where one particular measure is the best. We analyze the geometry of the resulting zones and describe it with simple criteria. Given particular graph parameters, this allows us to recommend a particular measure to use for clustering.

This paper presents BPMN Assistant, a tool that leverages Large Language Models (LLMs) for natural language-based creation and editing of BPMN diagrams. A specialized JSON-based representation is introduced as a structured alternative to the direct handling of XML to enhance the accuracy of process modifications. Process generation quality is evaluated using Graph Edit Distance (GED) and Relative Graph Edit Distance (RGED), while editing performance is evaluated with a binary success metric. Results show that JSON and XML achieve similar similarity scores in generation, but JSON offers greater reliability, faster processing, and significantly higher editing success rates. We discuss key trade-offs, limitations, and future improvements. The implementation is available at https://github.com/jtlicardo/bpmn-assistant.

It has been shown that a message passing neural networks (MPNNs), a popular family of neural networks for graph-structured data, are at most as expressive as the first-order Weisfeiler-Leman (1-WL) graph isomorphism test, which has motivated the development of more expressive architectures. In this work, we analyze if the limited expressiveness is actually a limiting factor for MPNNs and other WL-based models in standard graph datasets. Interestingly, we find that the expressiveness of WL is sufficient to identify almost all graphs in most datasets. Moreover, we find that the classification accuracy upper bounds are often close to 100\%. Furthermore, we find that simple WL-based neural networks and several MPNNs can be fitted to several datasets. In sum, we conclude that the performance of WL/MPNNs is not limited by their expressiveness in practice.

In this work, we seek new insights into the underlying challenges of the Scene Graph Generation (SGG) task. Quantitative and qualitative analysis of the Visual Genome dataset implies -- 1) Ambiguity: even if inter-object relationship contains the same object (or predicate), they may not be visually or semantically similar, 2) Asymmetry: despite the nature of the relationship that embodied the direction, it was not well addressed in previous studies, and 3) Higher-order contexts: leveraging the identities of certain graph elements can help to generate accurate scene graphs. Motivated by the analysis, we design a novel SGG framework, Local-to-Global Interaction Networks (LOGIN). Locally, interactions extract the essence between three instances of subject, object, and background, while baking direction awareness into the network by explicitly constraining the input order of subject and object. Globally, interactions encode the contexts between every graph component (i.e., nodes and edges). Finally, Attract & Repel loss is utilized to fine-tune the distribution of predicate embeddings. By design, our framework enables predicting the scene graph in a bottom-up manner, leveraging the possible complementariness. To quantify how much LOGIN is aware of relational direction, a new diagnostic task called Bidirectional Relationship Classification (BRC) is also proposed. Experimental results demonstrate that LOGIN can successfully distinguish relational direction than existing methods (in BRC task), while showing state-of-the-art results on the Visual Genome benchmark (in SGG task).

Graphs are ubiquitous structures found in numerous real-world applications, such as drug discovery, recommender systems, and social network analysis. To model graph-structured data, graph neural networks (GNNs) have become a popular tool. However, existing GNN architectures encounter challenges in cross-graph learning where multiple graphs have different feature spaces. To address this, recent approaches introduce text-attributed graphs (TAGs), where each node is associated with a textual description, which can be projected into a unified feature space using textual encoders. While promising, this method relies heavily on the availability of text-attributed graph data, which is difficult to obtain in practice. To bridge this gap, we propose a novel method named Topology-Aware Node description Synthesis (TANS), leveraging large language models (LLMs) to convert existing graphs into text-attributed graphs. The key idea is to integrate topological information into LLMs to explain how graph topology influences node semantics. We evaluate our TANS on text-rich, text-limited, and text-free graphs, demonstrating its applicability. Notably, on text-free graphs, our method significantly outperforms existing approaches that manually design node features, showcasing the potential of LLMs for preprocessing graph-structured data in the absence of textual information. The code and data are available at https://github.com/Zehong-Wang/TANS.

The growing importance of understanding and addressing algorithmic bias in artificial intelligence (AI) has led to a surge in research on AI fairness, which often assumes that the underlying data is independent and identically distributed (IID). However, real-world data frequently exists in non-IID graph structures that capture connections among individual units. To effectively mitigate bias in AI systems, it is essential to bridge the gap between traditional fairness literature, designed for IID data, and the prevalence of non-IID graph data. This survey reviews recent advancements in fairness amidst non-IID graph data, including the newly introduced fair graph generation and the commonly studied fair graph classification. In addition, available datasets and evaluation metrics for future research are identified, the limitations of existing work are highlighted, and promising future directions are proposed.

Existing foundation models, such as CLIP, aim to learn a unified embedding space for multimodal data, enabling a wide range of downstream web-based applications like search, recommendation, and content classification. However, these models often overlook the inherent graph structures in multimodal datasets, where entities and their relationships are crucial. Multimodal graphs (MMGs) represent such graphs where each node is associated with features from different modalities, while the edges capture the relationships between these entities. On the other hand, existing graph foundation models primarily focus on text-attributed graphs (TAGs) and are not designed to handle the complexities of MMGs. To address these limitations, we propose UniGraph2, a novel cross-domain graph foundation model that enables general representation learning on MMGs, providing a unified embedding space. UniGraph2 employs modality-specific encoders alongside a graph neural network (GNN) to learn a unified low-dimensional embedding space that captures both the multimodal information and the underlying graph structure. We propose a new cross-domain multi-graph pre-training algorithm at scale to ensure effective transfer learning across diverse graph domains and modalities. Additionally, we adopt a Mixture of Experts (MoE) component to align features from different domains and modalities, ensuring coherent and robust embeddings that unify the information across modalities. Extensive experiments on a variety of multimodal graph tasks demonstrate that UniGraph2 significantly outperforms state-of-the-art models in tasks such as representation learning, transfer learning, and multimodal generative tasks, offering a scalable and flexible solution for learning on MMGs.

Graph neural networks (GNNs) based methods have achieved impressive performance on node clustering task. However, they are designed on the homophilic assumption of graph and clustering on heterophilic graph is overlooked. Due to the lack of labels, it is impossible to first identify a graph as homophilic or heterophilic before a suitable GNN model can be found. Hence, clustering on real-world graph with various levels of homophily poses a new challenge to the graph research community. To fill this gap, we propose a novel graph clustering method, which contains three key components: graph reconstruction, a mixed filter, and dual graph clustering network. To be graph-agnostic, we empirically construct two graphs which are high homophily and heterophily from each data. The mixed filter based on the new graphs extracts both low-frequency and high-frequency information. To reduce the adverse coupling between node attribute and topological structure, we separately map them into two subspaces in dual graph clustering network. Extensive experiments on 11 benchmark graphs demonstrate our promising performance. In particular, our method dominates others on heterophilic graphs.

Textual scene graph parsing has become increasingly important in various vision-language applications, including image caption evaluation and image retrieval. However, existing scene graph parsers that convert image captions into scene graphs often suffer from two types of errors. First, the generated scene graphs fail to capture the true semantics of the captions or the corresponding images, resulting in a lack of faithfulness. Second, the generated scene graphs have high inconsistency, with the same semantics represented by different annotations. To address these challenges, we propose a novel dataset, which involves re-annotating the captions in Visual Genome (VG) using a new intermediate representation called FACTUAL-MR. FACTUAL-MR can be directly converted into faithful and consistent scene graph annotations. Our experimental results clearly demonstrate that the parser trained on our dataset outperforms existing approaches in terms of faithfulness and consistency. This improvement leads to a significant performance boost in both image caption evaluation and zero-shot image retrieval tasks. Furthermore, we introduce a novel metric for measuring scene graph similarity, which, when combined with the improved scene graph parser, achieves state-of-the-art (SOTA) results on multiple benchmark datasets for the aforementioned tasks. The code and dataset are available at https://github.com/zhuang-li/FACTUAL .

Large language models (LLMs) are increasingly adopted for a variety of tasks with implicit graphical structures, such as planning in robotics, multi-hop question answering or knowledge probing, structured commonsense reasoning, and more. While LLMs have advanced the state-of-the-art on these tasks with structure implications, whether LLMs could explicitly process textual descriptions of graphs and structures, map them to grounded conceptual spaces, and perform structured operations remains underexplored. To this end, we propose NLGraph (Natural Language Graph), a comprehensive benchmark of graph-based problem solving designed in natural language. NLGraph contains 29,370 problems, covering eight graph reasoning tasks with varying complexity from simple tasks such as connectivity and shortest path up to complex problems such as maximum flow and simulating graph neural networks. We evaluate LLMs (GPT-3/4) with various prompting approaches on the NLGraph benchmark and find that 1) language models do demonstrate preliminary graph reasoning abilities, 2) the benefit of advanced prompting and in-context learning diminishes on more complex graph problems, while 3) LLMs are also (un)surprisingly brittle in the face of spurious correlations in graph and problem settings. We then propose Build-a-Graph Prompting and Algorithmic Prompting, two instruction-based approaches to enhance LLMs in solving natural language graph problems. Build-a-Graph and Algorithmic prompting improve the performance of LLMs on NLGraph by 3.07% to 16.85% across multiple tasks and settings, while how to solve the most complicated graph reasoning tasks in our setup with language models remains an open research question. The NLGraph benchmark and evaluation code are available at https://github.com/Arthur-Heng/NLGraph.

Artificial General Intelligence (AGI) has revolutionized numerous fields, yet its integration with graph data, a cornerstone in our interconnected world, remains nascent. This paper presents a pioneering survey on the emerging domain of graph prompts in AGI, addressing key challenges and opportunities in harnessing graph data for AGI applications. Despite substantial advancements in AGI across natural language processing and computer vision, the application to graph data is relatively underexplored. This survey critically evaluates the current landscape of AGI in handling graph data, highlighting the distinct challenges in cross-modality, cross-domain, and cross-task applications specific to graphs. Our work is the first to propose a unified framework for understanding graph prompt learning, offering clarity on prompt tokens, token structures, and insertion patterns in the graph domain. We delve into the intrinsic properties of graph prompts, exploring their flexibility, expressiveness, and interplay with existing graph models. A comprehensive taxonomy categorizes over 100 works in this field, aligning them with pre-training tasks across node-level, edge-level, and graph-level objectives. Additionally, we present, ProG, a Python library, and an accompanying website, to support and advance research in graph prompting. The survey culminates in a discussion of current challenges and future directions, offering a roadmap for research in graph prompting within AGI. Through this comprehensive analysis, we aim to catalyze further exploration and practical applications of AGI in graph data, underlining its potential to reshape AGI fields and beyond. ProG and the website can be accessed by https://github.com/WxxShirley/Awesome-Graph-Prompt, and https://github.com/sheldonresearch/ProG, respectively.

Neural networks that process the parameters of other neural networks find applications in domains as diverse as classifying implicit neural representations, generating neural network weights, and predicting generalization errors. However, existing approaches either overlook the inherent permutation symmetry in the neural network or rely on intricate weight-sharing patterns to achieve equivariance, while ignoring the impact of the network architecture itself. In this work, we propose to represent neural networks as computational graphs of parameters, which allows us to harness powerful graph neural networks and transformers that preserve permutation symmetry. Consequently, our approach enables a single model to encode neural computational graphs with diverse architectures. We showcase the effectiveness of our method on a wide range of tasks, including classification and editing of implicit neural representations, predicting generalization performance, and learning to optimize, while consistently outperforming state-of-the-art methods. The source code is open-sourced at https://github.com/mkofinas/neural-graphs.

Graph Neural Networks (GNNs) are neural models that leverage the dependency structure in graphical data via message passing among the graph nodes. GNNs have emerged as pivotal architectures in analyzing graph-structured data, and their expansive application in sensitive domains requires a comprehensive understanding of their decision-making processes -- necessitating a framework for GNN explainability. An explanation function for GNNs takes a pre-trained GNN along with a graph as input, to produce a `sufficient statistic' subgraph with respect to the graph label. A main challenge in studying GNN explainability is to provide fidelity measures that evaluate the performance of these explanation functions. This paper studies this foundational challenge, spotlighting the inherent limitations of prevailing fidelity metrics, including Fid_+, Fid_-, and Fid_Delta. Specifically, a formal, information-theoretic definition of explainability is introduced and it is shown that existing metrics often fail to align with this definition across various statistical scenarios. The reason is due to potential distribution shifts when subgraphs are removed in computing these fidelity measures. Subsequently, a robust class of fidelity measures are introduced, and it is shown analytically that they are resilient to distribution shift issues and are applicable in a wide range of scenarios. Extensive empirical analysis on both synthetic and real datasets are provided to illustrate that the proposed metrics are more coherent with gold standard metrics. The source code is available at https://trustai4s-lab.github.io/fidelity.

We introduce the task of text-to-diagram generation, which focuses on creating structured visual representations directly from textual descriptions. Existing approaches in text-to-image and text-to-code generation lack the logical organization and flexibility needed to produce accurate, editable diagrams, often resulting in outputs that are either unstructured or difficult to modify. To address this gap, we introduce DiagramGenBenchmark, a comprehensive evaluation framework encompassing eight distinct diagram categories, including flowcharts, model architecture diagrams, and mind maps. Additionally, we present DiagramAgent, an innovative framework with four core modules-Plan Agent, Code Agent, Check Agent, and Diagram-to-Code Agent-designed to facilitate both the generation and refinement of complex diagrams. Our extensive experiments, which combine objective metrics with human evaluations, demonstrate that DiagramAgent significantly outperforms existing baseline models in terms of accuracy, structural coherence, and modifiability. This work not only establishes a foundational benchmark for the text-to-diagram generation task but also introduces a powerful toolset to advance research and applications in this emerging area.

Understanding the origins of militarized conflict is a complex, yet important undertaking. Existing research seeks to build this understanding by considering bi-lateral relationships between entity pairs (dyadic causes) and multi-lateral relationships among multiple entities (systemic causes). The aim of this work is to compare these two causes in terms of how they correlate with conflict between two entities. We do this by devising a set of textual and graph-based features which represent each of the causes. The features are extracted from Wikipedia and modeled as a large graph. Nodes in this graph represent entities connected by labeled edges representing ally or enemy-relationships. This allows casting the problem as an edge classification task, which we term dyad classification. We propose and evaluate classifiers to determine if a particular pair of entities are allies or enemies. Our results suggest that our systemic features might be slightly better correlates of conflict. Further, we find that Wikipedia articles of allies are semantically more similar than enemies.

In recent years, Graph Neural Networks (GNNs) have made significant advances in processing structured data. However, most of them primarily adopted a model-centric approach, which simplifies graphs by converting them into undirected formats and emphasizes model designs. This approach is inherently limited in real-world applications due to the unavoidable information loss in simple undirected graphs and the model optimization challenges that arise when exceeding the upper bounds of this sub-optimal data representational capacity. As a result, there has been a shift toward data-centric methods that prioritize improving graph quality and representation. Specifically, various types of graphs can be derived from naturally structured data, including heterogeneous graphs, hypergraphs, and directed graphs. Among these, directed graphs offer distinct advantages in topological systems by modeling causal relationships, and directed GNNs have been extensively studied in recent years. However, a comprehensive survey of this emerging topic is still lacking. Therefore, we aim to provide a comprehensive review of directed graph learning, with a particular focus on a data-centric perspective. Specifically, we first introduce a novel taxonomy for existing studies. Subsequently, we re-examine these methods from the data-centric perspective, with an emphasis on understanding and improving data representation. It demonstrates that a deep understanding of directed graphs and their quality plays a crucial role in model performance. Additionally, we explore the diverse applications of directed GNNs across 10+ domains, highlighting their broad applicability. Finally, we identify key opportunities and challenges within the field, offering insights that can guide future research and development in directed graph learning.

We introduce X-Adapter, a universal upgrader to enable the pretrained plug-and-play modules (e.g., ControlNet, LoRA) to work directly with the upgraded text-to-image diffusion model (e.g., SDXL) without further retraining. We achieve this goal by training an additional network to control the frozen upgraded model with the new text-image data pairs. In detail, X-Adapter keeps a frozen copy of the old model to preserve the connectors of different plugins. Additionally, X-Adapter adds trainable mapping layers that bridge the decoders from models of different versions for feature remapping. The remapped features will be used as guidance for the upgraded model. To enhance the guidance ability of X-Adapter, we employ a null-text training strategy for the upgraded model. After training, we also introduce a two-stage denoising strategy to align the initial latents of X-Adapter and the upgraded model. Thanks to our strategies, X-Adapter demonstrates universal compatibility with various plugins and also enables plugins of different versions to work together, thereby expanding the functionalities of diffusion community. To verify the effectiveness of the proposed method, we conduct extensive experiments and the results show that X-Adapter may facilitate wider application in the upgraded foundational diffusion model.

Graph representation learning is a fundamental research theme and can be generalized to benefit multiple downstream tasks from the node and link levels to the higher graph level. In practice, it is desirable to develop task-agnostic general graph representation learning methods that are typically trained in an unsupervised manner. Related research reveals that the power of graph representation learning methods depends on whether they can differentiate distinct graph structures as different embeddings and map isomorphic graphs to consistent embeddings (i.e., the isomorphic consistency of graph models). However, for task-agnostic general graph representation learning, existing unsupervised graph models, represented by the variational graph auto-encoders (VGAEs), can only keep the isomorphic consistency within the subgraphs of 1-hop neighborhoods and thus usually manifest inferior performance on the more difficult higher-level tasks. To overcome the limitations of existing unsupervised methods, in this paper, we propose the Isomorphic-Consistent VGAE (IsoC-VGAE) for multi-level task-agnostic graph representation learning. We first devise a decoding scheme to provide a theoretical guarantee of keeping the isomorphic consistency under the settings of unsupervised learning. We then propose the Inverse Graph Neural Network (Inv-GNN) decoder as its intuitive realization, which trains the model via reconstructing the GNN node embeddings with multi-hop neighborhood information, so as to maintain the high-order isomorphic consistency within the VGAE framework. We conduct extensive experiments on the representative graph learning tasks at different levels, including node classification, link prediction and graph classification, and the results verify that our proposed model generally outperforms both the state-of-the-art unsupervised methods and representative supervised methods.

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 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.

Large Language Models (LLMs) have achieved impressive performance in text understanding and have become an essential tool for building smart assistants. Originally focusing on text, they have been enhanced with multimodal capabilities in recent works that successfully built visual instruction following assistants. As far as the graph modality goes, however, no such assistants have yet been developed. Graph structures are complex in that they represent relation between different features and are permutation invariant. Moreover, representing them in purely textual form does not always lead to good LLM performance even for finetuned models. As a result, there is a need to develop a new method to integrate graphs in LLMs for general graph understanding. This work explores the integration of the graph modality in LLM for general graph instruction following tasks. It aims at producing a deep learning model that enhances an underlying LLM with graph embeddings and trains it to understand them and to produce, given an instruction, an answer grounded in the graph representation. The approach performs significantly better than a graph to text approach and remains consistent even for larger graphs.

The democratization of machine learning systems has made the process of fine-tuning accessible to practitioners, leading to a wide range of open-source models fine-tuned on specialized tasks and datasets. Recent work has proposed to merge such models to combine their functionalities. However, prior approaches are usually restricted to models that are fine-tuned from the same base model. Furthermore, the final merged model is typically required to be of the same size as the original models. In this work, we propose a new two-step algorithm to merge models -- termed PLeaS -- which relaxes these constraints. First, leveraging the Permutation symmetries inherent in the two models, PLeaS partially matches nodes in each layer by maximizing alignment. Next, PLeaS computes the weights of the merged model as a layer-wise Least Squares solution to minimize the approximation error between the features of the merged model and the permuted features of the original models. PLeaS allows a practitioner to merge two models sharing the same architecture into a single performant model of a desired size, even when the two original models are fine-tuned from different base models. We also demonstrate how our method can be extended to address a challenging scenario where no data is available from the fine-tuning domains. We demonstrate our method to merge ResNet and ViT models trained with shared and different label spaces, and show improvement over the state-of-the-art merging methods of up to 15 percentage points for the same target compute while merging models trained on DomainNet and fine-grained classification tasks. Our code is open-sourced at https://github.com/SewoongLab/PLeaS-Merging .

Open Source Software (OSS) is forming the spines of technology infrastructures, attracting millions of talents to contribute. Notably, it is challenging and critical to consider both the developers' interests and the semantic features of the project code to recommend appropriate development tasks to OSS developers. In this paper, we formulate the novel problem of code recommendation, whose purpose is to predict the future contribution behaviors of developers given their interaction history, the semantic features of source code, and the hierarchical file structures of projects. Considering the complex interactions among multiple parties within the system, we propose CODER, a novel graph-based code recommendation framework for open source software developers. CODER jointly models microscopic user-code interactions and macroscopic user-project interactions via a heterogeneous graph and further bridges the two levels of information through aggregation on file-structure graphs that reflect the project hierarchy. Moreover, due to the lack of reliable benchmarks, we construct three large-scale datasets to facilitate future research in this direction. Extensive experiments show that our CODER framework achieves superior performance under various experimental settings, including intra-project, cross-project, and cold-start recommendation. We will release all the datasets, code, and utilities for data retrieval upon the acceptance of this work.

As part of its scholarly data efforts, the Internet Archive (IA) releases a first version of a citation graph dataset, named refcat, derived from scholarly publications and additional data sources. It is composed of data gathered by the fatcat cataloging project (the catalog that underpins IA Scholar), related web-scale crawls targeting primary and secondary scholarly outputs, as well as metadata from the Open Library project and Wikipedia. This first version of the graph consists of over 1.3B citations. We release this dataset under a CC0 Public Domain Dedication, accessible through Internet Archive. The source code used for the derivation process, including exact and fuzzy citation matching, is released under an MIT license. The goal of this report is to describe briefly the current contents and the derivation of the dataset.

Semi-Supervised image classification is one of the most fundamental problem in computer vision, which significantly reduces the need for human labor. In this paper, we introduce a new semi-supervised learning algorithm - SimMatchV2, which formulates various consistency regularizations between labeled and unlabeled data from the graph perspective. In SimMatchV2, we regard the augmented view of a sample as a node, which consists of a label and its corresponding representation. Different nodes are connected with the edges, which are measured by the similarity of the node representations. Inspired by the message passing and node classification in graph theory, we propose four types of consistencies, namely 1) node-node consistency, 2) node-edge consistency, 3) edge-edge consistency, and 4) edge-node consistency. We also uncover that a simple feature normalization can reduce the gaps of the feature norm between different augmented views, significantly improving the performance of SimMatchV2. Our SimMatchV2 has been validated on multiple semi-supervised learning benchmarks. Notably, with ResNet-50 as our backbone and 300 epochs of training, SimMatchV2 achieves 71.9\% and 76.2\% Top-1 Accuracy with 1\% and 10\% labeled examples on ImageNet, which significantly outperforms the previous methods and achieves state-of-the-art performance. Code and pre-trained models are available at https://github.com/mingkai-zheng/SimMatchV2{https://github.com/mingkai-zheng/SimMatchV2}.

Multi-modal recommender system focuses on utilizing rich modal information ( i.e., images and textual descriptions) of items to improve recommendation performance. The current methods have achieved remarkable success with the powerful structure modeling capability of graph neural networks. However, these methods are often hindered by sparse data in real-world scenarios. Although contrastive learning and homography ( i.e., homogeneous graphs) are employed to address the data sparsity challenge, existing methods still suffer two main limitations: 1) Simple multi-modal feature contrasts fail to produce effective representations, causing noisy modal-shared features and loss of valuable information in modal-unique features; 2) The lack of exploration of the homograph relations between user interests and item co-occurrence results in incomplete mining of user-item interplay. To address the above limitations, we propose a novel framework for REfining multi-modAl contRastive learning and hoMography relations (REARM). Specifically, we complement multi-modal contrastive learning by employing meta-network and orthogonal constraint strategies, which filter out noise in modal-shared features and retain recommendation-relevant information in modal-unique features. To mine homogeneous relationships effectively, we integrate a newly constructed user interest graph and an item co-occurrence graph with the existing user co-occurrence and item semantic graphs for graph learning. The extensive experiments on three real-world datasets demonstrate the superiority of REARM to various state-of-the-art baselines. Our visualization further shows an improvement made by REARM in distinguishing between modal-shared and modal-unique features. Code is available https://github.com/MrShouxingMa/REARM{here}.

Advancements in generative models have sparked significant interest in generating images while adhering to specific structural guidelines. Scene graph to image generation is one such task of generating images which are consistent with the given scene graph. However, the complexity of visual scenes poses a challenge in accurately aligning objects based on specified relations within the scene graph. Existing methods approach this task by first predicting a scene layout and generating images from these layouts using adversarial training. In this work, we introduce a novel approach to generate images from scene graphs which eliminates the need of predicting intermediate layouts. We leverage pre-trained text-to-image diffusion models and CLIP guidance to translate graph knowledge into images. Towards this, we first pre-train our graph encoder to align graph features with CLIP features of corresponding images using a GAN based training. Further, we fuse the graph features with CLIP embedding of object labels present in the given scene graph to create a graph consistent CLIP guided conditioning signal. In the conditioning input, object embeddings provide coarse structure of the image and graph features provide structural alignment based on relationships among objects. Finally, we fine tune a pre-trained diffusion model with the graph consistent conditioning signal with reconstruction and CLIP alignment loss. Elaborate experiments reveal that our method outperforms existing methods on standard benchmarks of COCO-stuff and Visual Genome dataset.

Structured representations like graphs and parse trees play a crucial role in many Natural Language Processing systems. In recent years, the advancements in multi-turn user interfaces necessitate the need for controlling and updating these structured representations given new sources of information. Although there have been many efforts focusing on improving the performance of the parsers that map text to graphs or parse trees, very few have explored the problem of directly manipulating these representations. In this paper, we explore the novel problem of graph modification, where the systems need to learn how to update an existing scene graph given a new user's command. Our novel models based on graph-based sparse transformer and cross attention information fusion outperform previous systems adapted from the machine translation and graph generation literature. We further contribute our large graph modification datasets to the research community to encourage future research for this new problem.

Existing methods for evaluating graph generative models primarily rely on Maximum Mean Discrepancy (MMD) metrics based on graph descriptors. While these metrics can rank generative models, they do not provide an absolute measure of performance. Their values are also highly sensitive to extrinsic parameters, namely kernel and descriptor parametrization, making them incomparable across different graph descriptors. We introduce PolyGraph Discrepancy (PGD), a new evaluation framework that addresses these limitations. It approximates the Jensen-Shannon distance of graph distributions by fitting binary classifiers to distinguish between real and generated graphs, featurized by these descriptors. The data log-likelihood of these classifiers approximates a variational lower bound on the JS distance between the two distributions. Resulting metrics are constrained to the unit interval [0,1] and are comparable across different graph descriptors. We further derive a theoretically grounded summary metric that combines these individual metrics to provide a maximally tight lower bound on the distance for the given descriptors. Thorough experiments demonstrate that PGD provides a more robust and insightful evaluation compared to MMD metrics. The PolyGraph framework for benchmarking graph generative models is made publicly available at https://github.com/BorgwardtLab/polygraph-benchmark.

Graph Neural Networks (GNNs) have shown great potential in the field of graph representation learning. Standard GNNs define a local message-passing mechanism which propagates information over the whole graph domain by stacking multiple layers. This paradigm suffers from two major limitations, over-squashing and poor long-range dependencies, that can be solved using global attention but significantly increases the computational cost to quadratic complexity. In this work, we propose an alternative approach to overcome these structural limitations by leveraging the ViT/MLP-Mixer architectures introduced in computer vision. We introduce a new class of GNNs, called Graph ViT/MLP-Mixer, that holds three key properties. First, they capture long-range dependency and mitigate the issue of over-squashing as demonstrated on Long Range Graph Benchmark and TreeNeighbourMatch datasets. Second, they offer better speed and memory efficiency with a complexity linear to the number of nodes and edges, surpassing the related Graph Transformer and expressive GNN models. Third, they show high expressivity in terms of graph isomorphism as they can distinguish at least 3-WL non-isomorphic graphs. We test our architecture on 4 simulated datasets and 7 real-world benchmarks, and show highly competitive results on all of them. The source code is available for reproducibility at: https://github.com/XiaoxinHe/Graph-ViT-MLPMixer.

With the increasing number of new neural architecture designs and substantial existing neural architectures, it becomes difficult for the researchers to situate their contributions compared with existing neural architectures or establish the connections between their designs and other relevant ones. To discover similar neural architectures in an efficient and automatic manner, we define a new problem Neural Architecture Retrieval which retrieves a set of existing neural architectures which have similar designs to the query neural architecture. Existing graph pre-training strategies cannot address the computational graph in neural architectures due to the graph size and motifs. To fulfill this potential, we propose to divide the graph into motifs which are used to rebuild the macro graph to tackle these issues, and introduce multi-level contrastive learning to achieve accurate graph representation learning. Extensive evaluations on both human-designed and synthesized neural architectures demonstrate the superiority of our algorithm. Such a dataset which contains 12k real-world network architectures, as well as their embedding, is built for neural architecture retrieval.

Seminal research in the field of graph neural networks (GNNs) has revealed a direct correspondence between the expressive capabilities of GNNs and the k-dimensional Weisfeiler-Leman (kWL) test, a widely-recognized method for verifying graph isomorphism. This connection has reignited interest in comprehending the specific graph properties effectively distinguishable by the kWL test. A central focus of research in this field revolves around determining the least dimensionality k, for which kWL can discern graphs with different number of occurrences of a pattern graph P. We refer to such a least k as the WL-dimension of this pattern counting problem. This inquiry traditionally delves into two distinct counting problems related to patterns: subgraph counting and induced subgraph counting. Intriguingly, despite their initial appearance as separate challenges with seemingly divergent approaches, both of these problems are interconnected components of a more comprehensive problem: "graph motif parameters". In this paper, we provide a precise characterization of the WL-dimension of labeled graph motif parameters. As specific instances of this result, we obtain characterizations of the WL-dimension of the subgraph counting and induced subgraph counting problem for every labeled pattern P. We additionally demonstrate that in cases where the kWL test distinguishes between graphs with varying occurrences of a pattern P, the exact number of occurrences of P can be computed uniformly using only local information of the last layer of a corresponding GNN. We finally delve into the challenge of recognizing the WL-dimension of various graph parameters. We give a polynomial time algorithm for determining the WL-dimension of the subgraph counting problem for given pattern P, answering an open question from previous work.

Machine learning on graphs has been extensively studied in both academic and industry. However, as the literature on graph learning booms with a vast number of emerging methods and techniques, it becomes increasingly difficult to manually design the optimal machine learning algorithm for different graph-related tasks. To solve this critical challenge, automated machine learning (AutoML) on graphs which combines the strength of graph machine learning and AutoML together, is gaining attention from the research community. Therefore, we comprehensively survey AutoML on graphs in this paper, primarily focusing on hyper-parameter optimization (HPO) and neural architecture search (NAS) for graph machine learning. We further overview libraries related to automated graph machine learning and in-depth discuss AutoGL, the first dedicated open-source library for AutoML on graphs. In the end, we share our insights on future research directions for automated graph machine learning. This paper is the first systematic and comprehensive review of automated machine learning on graphs to the best of our knowledge.

Graph representations of programs are commonly a central element of machine learning for code research. We introduce an open source Python library python_graphs that applies static analysis to construct graph representations of Python programs suitable for training machine learning models. Our library admits the construction of control-flow graphs, data-flow graphs, and composite ``program graphs'' that combine control-flow, data-flow, syntactic, and lexical information about a program. We present the capabilities and limitations of the library, perform a case study applying the library to millions of competitive programming submissions, and showcase the library's utility for machine learning research.

We propose a generalization of transformer neural network architecture for arbitrary graphs. The original transformer was designed for Natural Language Processing (NLP), which operates on fully connected graphs representing all connections between the words in a sequence. Such architecture does not leverage the graph connectivity inductive bias, and can perform poorly when the graph topology is important and has not been encoded into the node features. We introduce a graph transformer with four new properties compared to the standard model. First, the attention mechanism is a function of the neighborhood connectivity for each node in the graph. Second, the positional encoding is represented by the Laplacian eigenvectors, which naturally generalize the sinusoidal positional encodings often used in NLP. Third, the layer normalization is replaced by a batch normalization layer, which provides faster training and better generalization performance. Finally, the architecture is extended to edge feature representation, which can be critical to tasks s.a. chemistry (bond type) or link prediction (entity relationship in knowledge graphs). Numerical experiments on a graph benchmark demonstrate the performance of the proposed graph transformer architecture. This work closes the gap between the original transformer, which was designed for the limited case of line graphs, and graph neural networks, that can work with arbitrary graphs. As our architecture is simple and generic, we believe it can be used as a black box for future applications that wish to consider transformer and graphs.

Interdisciplinary scientific breakthroughs mostly emerge unexpectedly, and forecasting the formation of novel research fields remains a major challenge. We introduce FOS (Future Of Science), a comprehensive time-aware graph-based benchmark that reconstructs annual co-occurrence graphs of 65,027 research sub-fields (spanning 19 general domains) over the period 1827-2024. In these graphs, edges denote the co-occurrence of two fields in a single publication and are timestamped with the corresponding publication year. Nodes are enriched with semantic embeddings, and edges are characterized by temporal and topological descriptors. We formulate the prediction of new field-pair linkages as a temporal link-prediction task, emphasizing the "first-time" connections that signify pioneering interdisciplinary directions. Through extensive experiments, we evaluate a suite of state-of-the-art temporal graph architectures under multiple negative-sampling regimes and show that (i) embedding long-form textual descriptions of fields significantly boosts prediction accuracy, and (ii) distinct model classes excel under different evaluation settings. Case analyses show that top-ranked link predictions on FOS align with field pairings that emerge in subsequent years of academic publications. We publicly release FOS, along with its temporal data splits and evaluation code, to establish a reproducible benchmark for advancing research in predicting scientific frontiers.

Flowcharts are indispensable tools in software design and business-process analysis, yet current vision-language models (VLMs) frequently misinterpret the directional arrows and graph topology that set these diagrams apart from natural images. We introduce a seven-stage pipeline grouped into three broader processes: (1) arrow-aware detection of nodes and arrow endpoints; (2) optical character recognition (OCR) to extract node text; and (3) construction of a structured prompt that guides the VLMs. Tested on a 90-question benchmark distilled from 30 annotated flowcharts, the method raises overall accuracy from 80 % to 89 % (+9 percentage points) without any task-specific fine-tuning. The gain is most pronounced for next-step queries (25/30 -> 30/30; 100 %, +17 pp); branch-result questions improve more modestly, and before-step questions remain difficult. A parallel evaluation with an LLM-as-a-Judge protocol shows the same trends, reinforcing the advantage of explicit arrow encoding. Limitations include dependence on detector and OCR precision, the small evaluation set, and residual errors at nodes with multiple incoming edges. Future work will enlarge the benchmark with synthetic and handwritten flowcharts and assess the approach on Business Process Model and Notation (BPMN) and Unified Modeling Language (UML).

Text-to-image (T2I) generation has seen significant growth over the past few years. Despite this, there has been little work on generating diagrams with T2I models. A diagram is a symbolic/schematic representation that explains information using structurally rich and spatially complex visualizations (e.g., a dense combination of related objects, text labels, directional arrows, connection lines, etc.). Existing state-of-the-art T2I models often fail at diagram generation because they lack fine-grained object layout control when many objects are densely connected via complex relations such as arrows/lines and also often fail to render comprehensible text labels. To address this gap, we present DiagrammerGPT, a novel two-stage text-to-diagram generation framework that leverages the layout guidance capabilities of LLMs (e.g., GPT-4) to generate more accurate open-domain, open-platform diagrams. In the first stage, we use LLMs to generate and iteratively refine 'diagram plans' (in a planner-auditor feedback loop) which describe all the entities (objects and text labels), their relationships (arrows or lines), and their bounding box layouts. In the second stage, we use a diagram generator, DiagramGLIGEN, and a text label rendering module to generate diagrams following the diagram plans. To benchmark the text-to-diagram generation task, we introduce AI2D-Caption, a densely annotated diagram dataset built on top of the AI2D dataset. We show quantitatively and qualitatively that our DiagrammerGPT framework produces more accurate diagrams, outperforming existing T2I models. We also provide comprehensive analysis including open-domain diagram generation, vector graphic diagram generation in different platforms, human-in-the-loop diagram plan editing, and multimodal planner/auditor LLMs (e.g., GPT-4Vision). We hope our work can inspire further research on diagram generation via T2I models and LLMs.

Heterogeneous graph learning aims to capture complex relationships and diverse relational semantics among entities in a heterogeneous graph to obtain meaningful representations for nodes and edges. Recent advancements in heterogeneous graph neural networks (HGNNs) have achieved state-of-the-art performance by considering relation heterogeneity and using specialized message functions and aggregation rules. However, existing frameworks for heterogeneous graph learning have limitations in generalizing across diverse heterogeneous graph datasets. Most of these frameworks follow the "pre-train" and "fine-tune" paradigm on the same dataset, which restricts their capacity to adapt to new and unseen data. This raises the question: "Can we generalize heterogeneous graph models to be well-adapted to diverse downstream learning tasks with distribution shifts in both node token sets and relation type heterogeneity?'' To tackle those challenges, we propose HiGPT, a general large graph model with Heterogeneous graph instruction-tuning paradigm. Our framework enables learning from arbitrary heterogeneous graphs without the need for any fine-tuning process from downstream datasets. To handle distribution shifts in heterogeneity, we introduce an in-context heterogeneous graph tokenizer that captures semantic relationships in different heterogeneous graphs, facilitating model adaptation. We incorporate a large corpus of heterogeneity-aware graph instructions into our HiGPT, enabling the model to effectively comprehend complex relation heterogeneity and distinguish between various types of graph tokens. Furthermore, we introduce the Mixture-of-Thought (MoT) instruction augmentation paradigm to mitigate data scarcity by generating diverse and informative instructions. Through comprehensive evaluations, our proposed framework demonstrates exceptional performance in terms of generalization performance.