Daily Papers

Aspect-based sentiment analysis (ABSA) aims at automatically inferring the specific sentiment polarities toward certain aspects of products or services behind the social media texts or reviews, which has been a fundamental application to the real-world society. Since the early 2010s, ABSA has achieved extraordinarily high accuracy with various deep neural models. However, existing ABSA models with strong in-house performances may fail to generalize to some challenging cases where the contexts are variable, i.e., low robustness to real-world environments. In this study, we propose to enhance the ABSA robustness by systematically rethinking the bottlenecks from all possible angles, including model, data, and training. First, we strengthen the current best-robust syntax-aware models by further incorporating the rich external syntactic dependencies and the labels with aspect simultaneously with a universal-syntax graph convolutional network. In the corpus perspective, we propose to automatically induce high-quality synthetic training data with various types, allowing models to learn sufficient inductive bias for better robustness. Last, we based on the rich pseudo data perform adversarial training to enhance the resistance to the context perturbation and meanwhile employ contrastive learning to reinforce the representations of instances with contrastive sentiments. Extensive robustness evaluations are conducted. The results demonstrate that our enhanced syntax-aware model achieves better robustness performances than all the state-of-the-art baselines. By additionally incorporating our synthetic corpus, the robust testing results are pushed with around 10% accuracy, which are then further improved by installing the advanced training strategies. In-depth analyses are presented for revealing the factors influencing the ABSA robustness.

Semantic role labeling (SRL) is the task of identifying the predicate-argument structure of a sentence. It is typically regarded as an important step in the standard NLP pipeline. As the semantic representations are closely related to syntactic ones, we exploit syntactic information in our model. We propose a version of graph convolutional networks (GCNs), a recent class of neural networks operating on graphs, suited to model syntactic dependency graphs. GCNs over syntactic dependency trees are used as sentence encoders, producing latent feature representations of words in a sentence. We observe that GCN layers are complementary to LSTM ones: when we stack both GCN and LSTM layers, we obtain a substantial improvement over an already state-of-the-art LSTM SRL model, resulting in the best reported scores on the standard benchmark (CoNLL-2009) both for Chinese and English.

Transformer-based models dominate NLP tasks like sentiment analysis, machine translation, and claim verification. However, their massive computational demands and lack of interpretability pose challenges for real-world applications requiring efficiency and transparency. In this work, we explore Graph Neural Networks (GNNs) and Hyperbolic Graph Neural Networks (HGNNs) as lightweight yet effective alternatives for Environmental Claim Detection, reframing it as a graph classification problem. We construct dependency parsing graphs to explicitly model syntactic structures, using simple word embeddings (word2vec) for node features with dependency relations encoded as edge features. Our results demonstrate that these graph-based models achieve comparable or superior performance to state-of-the-art transformers while using 30x fewer parameters. This efficiency highlights the potential of structured, interpretable, and computationally efficient graph-based approaches.

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.

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.

Graphs are a fundamental data structure for representing relationships in real-world scenarios. With the success of Large Language Models (LLMs) across various natural language processing (NLP) tasks, there has been growing interest in integrating LLMs for graph learning. However, applying LLMs to graph-related tasks poses significant challenges, as these models are not inherently designed to capture the complex structural information present in graphs. Existing approaches address this challenge through two strategies: the chain of tasks approach, which uses Graph Neural Networks (GNNs) to encode the graph structure so that LLMs are relieved from understanding spatial positions; and Graph-to-Text Conversion, which translates graph structures into semantic text representations that LLMs can process. Despite their progress, these methods often struggle to fully preserve the topological information of graphs or require extensive computational resources, limiting their practical applicability. In this work, we introduce Node Tokenizer for Large Language Models (NT-LLM), a novel framework that efficiently encodes graph structures by selecting key nodes as anchors and representing each node based on its relative distance to these anchors. This position-anchored encoding effectively captures the graph topology, enabling enhanced reasoning capabilities in LLMs over graph data. Additionally, we implement a task-specific tuning procedure to further improve structural understanding within LLMs. Through extensive empirical evaluations, NT-LLM demonstrates significant performance improvements across a variety of graph-related tasks.

Syntax-incorporated machine translation models have been proven successful in improving the model's reasoning and meaning preservation ability. In this paper, we propose a simple yet effective graph-structured encoder, the Recurrent Graph Syntax Encoder, dubbed RGSE, which enhances the ability to capture useful syntactic information. The RGSE is done over a standard encoder (recurrent or self-attention encoder), regarding recurrent network units as graph nodes and injects syntactic dependencies as edges, such that RGSE models syntactic dependencies and sequential information (i.e., word order) simultaneously. Our approach achieves considerable improvements over several syntax-aware NMT models in EnglishRightarrowGerman and EnglishRightarrowCzech translation tasks. And RGSE-equipped big model obtains competitive result compared with the state-of-the-art model in WMT14 En-De task. Extensive analysis further verifies that RGSE could benefit long sentence modeling, and produces better translations.

Foundation models like ChatGPT and GPT-4 have revolutionized artificial intelligence, exhibiting remarkable abilities to generalize across a wide array of tasks and applications beyond their initial training objectives. However, graph learning has predominantly focused on single-graph models, tailored to specific tasks or datasets, lacking the ability to transfer learned knowledge to different domains. This limitation stems from the inherent complexity and diversity of graph structures, along with the different feature and label spaces specific to graph data. In this paper, we recognize text as an effective unifying medium and employ Text-Attributed Graphs (TAGs) to leverage this potential. We present our UniGraph framework, designed to learn a foundation model for TAGs, which is capable of generalizing to unseen graphs and tasks across diverse domains. Unlike single-graph models that use pre-computed node features of varying dimensions as input, our approach leverages textual features for unifying node representations, even for graphs such as molecular graphs that do not naturally have textual features. We propose a novel cascaded architecture of Language Models (LMs) and Graph Neural Networks (GNNs) as backbone networks. Additionally, we propose the first pre-training algorithm specifically designed for large-scale self-supervised learning on TAGs, based on Masked Graph Modeling. We introduce graph instruction tuning using Large Language Models (LLMs) to enable zero-shot prediction ability. Our comprehensive experiments across various graph learning tasks and domains demonstrate the model's effectiveness in self-supervised representation learning on unseen graphs, few-shot in-context transfer, and zero-shot transfer, even surpassing or matching the performance of GNNs that have undergone supervised training on target datasets.

Despite that going deep has proven successful in many neural architectures, the existing graph transformers are relatively shallow. In this work, we explore whether more layers are beneficial to graph transformers, and find that current graph transformers suffer from the bottleneck of improving performance by increasing depth. Our further analysis reveals the reason is that deep graph transformers are limited by the vanishing capacity of global attention, restricting the graph transformer from focusing on the critical substructure and obtaining expressive features. To this end, we propose a novel graph transformer model named DeepGraph that explicitly employs substructure tokens in the encoded representation, and applies local attention on related nodes to obtain substructure based attention encoding. Our model enhances the ability of the global attention to focus on substructures and promotes the expressiveness of the representations, addressing the limitation of self-attention as the graph transformer deepens. Experiments show that our method unblocks the depth limitation of graph transformers and results in state-of-the-art performance across various graph benchmarks with deeper models.

Foundation models in language and vision have the ability to run inference on any textual and visual inputs thanks to the transferable representations such as a vocabulary of tokens in language. Knowledge graphs (KGs) have different entity and relation vocabularies that generally do not overlap. The key challenge of designing foundation models on KGs is to learn such transferable representations that enable inference on any graph with arbitrary entity and relation vocabularies. In this work, we make a step towards such foundation models and present ULTRA, an approach for learning universal and transferable graph representations. ULTRA builds relational representations as a function conditioned on their interactions. Such a conditioning strategy allows a pre-trained ULTRA model to inductively generalize to any unseen KG with any relation vocabulary and to be fine-tuned on any graph. Conducting link prediction experiments on 57 different KGs, we find that the zero-shot inductive inference performance of a single pre-trained ULTRA model on unseen graphs of various sizes is often on par or better than strong baselines trained on specific graphs. Fine-tuning further boosts the performance.

Syntactic structures used to play a vital role in natural language processing (NLP), but since the deep learning revolution, NLP has been gradually dominated by neural models that do not consider syntactic structures in their design. One vastly successful class of neural models is transformers. When used as an encoder, a transformer produces contextual representation of words in the input sentence. In this work, we propose a new model of contextual word representation, not from a neural perspective, but from a purely syntactic and probabilistic perspective. Specifically, we design a conditional random field that models discrete latent representations of all words in a sentence as well as dependency arcs between them; and we use mean field variational inference for approximate inference. Strikingly, we find that the computation graph of our model resembles transformers, with correspondences between dependencies and self-attention and between distributions over latent representations and contextual embeddings of words. Experiments show that our model performs competitively to transformers on small to medium sized datasets. We hope that our work could help bridge the gap between traditional syntactic and probabilistic approaches and cutting-edge neural approaches to NLP, and inspire more linguistically-principled neural approaches in the future.

Large Language Models (LLMs) have gained the ability to assimilate human knowledge and facilitate natural language interactions with both humans and other LLMs. However, despite their impressive achievements, LLMs have not made significant advancements in the realm of graph machine learning. This limitation arises because graphs encapsulate distinct relational data, making it challenging to transform them into natural language that LLMs understand. In this paper, we bridge this gap with a novel framework, GraphText, that translates graphs into natural language. GraphText derives a graph-syntax tree for each graph that encapsulates both the node attributes and inter-node relationships. Traversal of the tree yields a graph text sequence, which is then processed by an LLM to treat graph tasks as text generation tasks. Notably, GraphText offers multiple advantages. It introduces training-free graph reasoning: even without training on graph data, GraphText with ChatGPT can achieve on par with, or even surpassing, the performance of supervised-trained graph neural networks through in-context learning (ICL). Furthermore, GraphText paves the way for interactive graph reasoning, allowing both humans and LLMs to communicate with the model seamlessly using natural language. These capabilities underscore the vast, yet-to-be-explored potential of LLMs in the domain of graph machine learning.

Graph learning has become indispensable for interpreting and harnessing relational data in diverse fields, ranging from recommendation systems to social network analysis. In this context, a variety of GNNs have emerged as promising methodologies for encoding the structural information of graphs. By effectively capturing the graph's underlying structure, these GNNs have shown great potential in enhancing performance in graph learning tasks, such as link prediction and node classification. However, despite their successes, a significant challenge persists: these advanced methods often face difficulties in generalizing to unseen graph data that significantly differs from the training instances. In this work, our aim is to advance the graph learning paradigm by developing a general graph foundation model. This model is designed to understand the complex topological patterns present in diverse graph data, enabling it to excel in zero-shot graph learning tasks across different downstream datasets. To achieve this goal, we address several key technical challenges in our OpenGraph model. Firstly, we propose a unified graph tokenizer to adapt our graph model to generalize well on unseen graph data, even when the underlying graph properties differ significantly from those encountered during training. Secondly, we develop a scalable graph transformer as the foundational encoder, which effectively captures node-wise dependencies within the global topological context. Thirdly, we introduce a data augmentation mechanism enhanced by a LLM to alleviate the limitations of data scarcity in real-world scenarios. Extensive experiments validate the effectiveness of our framework. By adapting our OpenGraph to new graph characteristics and comprehending the nuances of diverse graphs, our approach achieves remarkable zero-shot graph learning performance across various settings and domains.

Graph-structured data plays a vital role in numerous domains, such as social networks, citation networks, commonsense reasoning graphs and knowledge graphs. While graph neural networks have been employed for graph processing, recent advancements have explored integrating large language models for graph-based tasks. In this paper, we propose a novel approach named Learnable Graph Pooling Token (LGPT), which addresses the limitations of the scalability issues in node-level projection and information loss in graph-level projection. LGPT enables flexible and efficient graph representation by introducing learnable parameters that act as tokens in large language models, balancing fine-grained and global graph information. Additionally, we investigate an Early Query Fusion technique, which fuses query context before constructing the graph representation, leading to more effective graph embeddings. Our method achieves a 4.13\% performance improvement on the GraphQA benchmark without training the large language model, demonstrating significant gains in handling complex textual-attributed graph data.

We show that standard Transformers without graph-specific modifications can lead to promising results in graph learning both in theory and practice. Given a graph, we simply treat all nodes and edges as independent tokens, augment them with token embeddings, and feed them to a Transformer. With an appropriate choice of token embeddings, we prove that this approach is theoretically at least as expressive as an invariant graph network (2-IGN) composed of equivariant linear layers, which is already more expressive than all message-passing Graph Neural Networks (GNN). When trained on a large-scale graph dataset (PCQM4Mv2), our method coined Tokenized Graph Transformer (TokenGT) achieves significantly better results compared to GNN baselines and competitive results compared to Transformer variants with sophisticated graph-specific inductive bias. Our implementation is available at https://github.com/jw9730/tokengt.

Language Models (LMs) are increasingly challenging the dominance of domain-specific models, including Graph Neural Networks (GNNs) and Graph Transformers (GTs), in graph learning tasks. Following this trend, we propose a novel approach that empowers off-the-shelf LMs to achieve performance comparable to state-of-the-art GNNs on node classification tasks, without requiring any architectural modification. By preserving the LM's original architecture, our approach retains a key benefit of LM instruction tuning: the ability to jointly train on diverse datasets, fostering greater flexibility and efficiency. To achieve this, we introduce two key augmentation strategies: (1) Enriching LMs' input using topological and semantic retrieval methods, which provide richer contextual information, and (2) guiding the LMs' classification process through a lightweight GNN classifier that effectively prunes class candidates. Our experiments on real-world datasets show that backbone Flan-T5 models equipped with these augmentation strategies outperform state-of-the-art text-output node classifiers and are comparable to top-performing vector-output node classifiers. By bridging the gap between specialized task-specific node classifiers and general LMs, this work paves the way for more versatile and widely applicable graph learning models. We will open-source the code upon publication.

This paper builds off recent work from Kiperwasser & Goldberg (2016) using neural attention in a simple graph-based dependency parser. We use a larger but more thoroughly regularized parser than other recent BiLSTM-based approaches, with biaffine classifiers to predict arcs and labels. Our parser gets state of the art or near state of the art performance on standard treebanks for six different languages, achieving 95.7% UAS and 94.1% LAS on the most popular English PTB dataset. This makes it the highest-performing graph-based parser on this benchmark---outperforming Kiperwasser Goldberg (2016) by 1.8% and 2.2%---and comparable to the highest performing transition-based parser (Kuncoro et al., 2016), which achieves 95.8% UAS and 94.6% LAS. We also show which hyperparameter choices had a significant effect on parsing accuracy, allowing us to achieve large gains over other graph-based approaches.

Pre-trained sequence-to-sequence language models have led to widespread success in many natural language generation tasks. However, there has been relatively less work on analyzing their ability to generate structured outputs such as graphs. Unlike natural language, graphs have distinct structural and semantic properties in the context of a downstream NLP task, e.g., generating a graph that is connected and acyclic can be attributed to its structural constraints, while the semantics of a graph can refer to how meaningfully an edge represents the relation between two node concepts. In this work, we study pre-trained language models that generate explanation graphs in an end-to-end manner and analyze their ability to learn the structural constraints and semantics of such graphs. We first show that with limited supervision, pre-trained language models often generate graphs that either violate these constraints or are semantically incoherent. Since curating large amount of human-annotated graphs is expensive and tedious, we propose simple yet effective ways of graph perturbations via node and edge edit operations that lead to structurally and semantically positive and negative graphs. Next, we leverage these graphs in different contrastive learning models with Max-Margin and InfoNCE losses. Our methods lead to significant improvements in both structural and semantic accuracy of explanation graphs and also generalize to other similar graph generation tasks. Lastly, we show that human errors are the best negatives for contrastive learning and also that automatically generating more such human-like negative graphs can lead to further improvements. Our code and models are publicly available at https://github.com/swarnaHub/ExplagraphGen

The CLEVR dataset has been used extensively in language grounded visual reasoning in Machine Learning (ML) and Natural Language Processing (NLP) domains. We present a graph parser library for CLEVR, that provides functionalities for object-centric attributes and relationships extraction, and construction of structural graph representations for dual modalities. Structural order-invariant representations enable geometric learning and can aid in downstream tasks like language grounding to vision, robotics, compositionality, interpretability, and computational grammar construction. We provide three extensible main components - parser, embedder, and visualizer that can be tailored to suit specific learning setups. We also provide out-of-the-box functionality for seamless integration with popular deep graph neural network (GNN) libraries. Additionally, we discuss downstream usage and applications of the library, and how it accelerates research for the NLP research community.

Relation Extraction is a way of obtaining the semantic relationship between entities in text. The state-of-the-art methods use linguistic tools to build a graph for the text in which the entities appear and then a Graph Convolutional Network (GCN) is employed to encode the pre-built graphs. Although their performance is promising, the reliance on linguistic tools results in a non end-to-end process. In this work, we propose a novel model, the Self-determined Graph Convolutional Network (SGCN), which determines a weighted graph using a self-attention mechanism, rather using any linguistic tool. Then, the self-determined graph is encoded using a GCN. We test our model on the TACRED dataset and achieve the state-of-the-art result. Our experiments show that SGCN outperforms the traditional GCN, which uses dependency parsing tools to build the graph.

Vision-Language Models (VLMs) generate discourse-level, multi-sentence visual descriptions, challenging text scene graph parsers built for single-sentence caption-to-graph mapping. Current approaches typically merge sentence-level parsing outputs for discourse input, often missing phenomena like cross-sentence coreference, resulting in fragmented graphs and degraded downstream VLM task performance. We introduce a new task, Discourse-level text Scene Graph parsing (DiscoSG), and release DiscoSG-DS, a dataset of 400 expert-annotated and 8,430 synthesised multi-sentence caption-graph pairs. Each caption averages 9 sentences, and each graph contains at least 3 times more triples than those in existing datasets. Fine-tuning GPT-4o on DiscoSG-DS yields over 40% higher SPICE metric than the best sentence-merging baseline. However, its high inference cost and licensing restrict open-source use. Smaller fine-tuned open-source models (e.g., Flan-T5) perform well on simpler graphs yet degrade on denser, more complex graphs. To bridge this gap, we introduce DiscoSG-Refiner, a lightweight open-source parser that drafts a seed graph and iteratively refines it with a novel learned graph-editing model, achieving 30% higher SPICE than the baseline while delivering 86 times faster inference than GPT-4o. It generalises from simple to dense graphs, thereby consistently improving downstream VLM tasks, including discourse-level caption evaluation and hallucination detection, outperforming alternative open-source parsers. Code and data are available at https://github.com/ShaoqLin/DiscoSG .

In this paper, we conduct a holistic exploration of the Universal Decompositional Semantic (UDS) Parsing. We first introduce a cascade model for UDS parsing that decomposes the complex parsing task into semantically appropriate subtasks. Our approach outperforms the prior models, while significantly reducing inference time. We also incorporate syntactic information and further optimized the architecture. Besides, different ways for data augmentation are explored, which further improve the UDS Parsing. Lastly, we conduct experiments to investigate the efficacy of ChatGPT in handling the UDS task, revealing that it excels in attribute parsing but struggles in relation parsing, and using ChatGPT for data augmentation yields suboptimal results. Our code is available at https://github.com/hexuandeng/HExp4UDS.

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.

Bidirectional masked Transformers have become the core theme in the current NLP landscape. Despite their impressive benchmarks, a recurring theme in recent research has been to question such models' capacity for syntactic generalization. In this work, we seek to address this question by adding a supervised, token-level supertagging objective to standard unsupervised pretraining, enabling the explicit incorporation of syntactic biases into the network's training dynamics. Our approach is straightforward to implement, induces a marginal computational overhead and is general enough to adapt to a variety of settings. We apply our methodology on Lassy Large, an automatically annotated corpus of written Dutch. Our experiments suggest that our syntax-aware model performs on par with established baselines, despite Lassy Large being one order of magnitude smaller than commonly used corpora.

Graph neural networks (GNNs) are effective models for representation learning on relational data. However, standard GNNs are limited in their expressive power, as they cannot distinguish graphs beyond the capability of the Weisfeiler-Leman graph isomorphism heuristic. In order to break this expressiveness barrier, GNNs have been enhanced with random node initialization (RNI), where the idea is to train and run the models with randomized initial node features. In this work, we analyze the expressive power of GNNs with RNI, and prove that these models are universal, a first such result for GNNs not relying on computationally demanding higher-order properties. This universality result holds even with partially randomized initial node features, and preserves the invariance properties of GNNs in expectation. We then empirically analyze the effect of RNI on GNNs, based on carefully constructed datasets. Our empirical findings support the superior performance of GNNs with RNI over standard GNNs.

Graph neural networks (GNNs) have become the preferred models for node classification in graph data due to their robust capabilities in integrating graph structures and attributes. However, these models heavily depend on a substantial amount of high-quality labeled data for training, which is often costly to obtain. With the rise of large language models (LLMs), a promising approach is to utilize their exceptional zero-shot capabilities and extensive knowledge for node labeling. Despite encouraging results, this approach either requires numerous queries to LLMs or suffers from reduced performance due to noisy labels generated by LLMs. To address these challenges, we introduce Locle, an active self-training framework that does Label-free node Classification with LLMs cost-Effectively. Locle iteratively identifies small sets of "critical" samples using GNNs and extracts informative pseudo-labels for them with both LLMs and GNNs, serving as additional supervision signals to enhance model training. Specifically, Locle comprises three key components: (i) an effective active node selection strategy for initial annotations; (ii) a careful sample selection scheme to identify "critical" nodes based on label disharmonicity and entropy; and (iii) a label refinement module that combines LLMs and GNNs with a rewired topology. Extensive experiments on five benchmark text-attributed graph datasets demonstrate that Locle significantly outperforms state-of-the-art methods under the same query budget to LLMs in terms of label-free node classification. Notably, on the DBLP dataset with 14.3k nodes, Locle achieves an 8.08% improvement in accuracy over the state-of-the-art at a cost of less than one cent. Our code is available at https://github.com/HKBU-LAGAS/Locle.

Graph neural networks (GNNs) have gained significant attention in recent years for their ability to process data that may be represented as graphs. This has prompted several studies to explore their representational capability based on the graph isomorphism task. Notably, these works inherently assume a countable node feature representation, potentially limiting their applicability. Interestingly, only a few study GNNs with uncountable node feature representation. In the paper, a new perspective on the representational capability of GNNs is investigated across all levelsx2014node-level, neighborhood-level, and graph-levelx2014when the space of node feature representation is uncountable. Specifically, the injective and metric requirements of previous works are softly relaxed by employing a pseudometric distance on the space of input to create a soft-injective function such that distinct inputs may produce similar outputs if and only if the pseudometric deems the inputs to be sufficiently similar on some representation. As a consequence, a simple and computationally efficient soft-isomorphic relational graph convolution network (SIR-GCN) that emphasizes the contextualized transformation of neighborhood feature representations via anisotropic and dynamic message functions is proposed. Furthermore, a mathematical discussion on the relationship between SIR-GCN and key GNNs in literature is laid out to put the contribution into context, establishing SIR-GCN as a generalization of classical GNN methodologies. To close, experiments on synthetic and benchmark datasets demonstrate the relative superiority of SIR-GCN, outperforming comparable models in node and graph property prediction tasks.

While Language Models have become workhorses for NLP, their interplay with textual knowledge graphs (KGs) - structured memories of general or domain knowledge - is actively researched. Current embedding methodologies for such graphs typically either (i) linearize graphs for embedding them using sequential Language Models (LMs), which underutilize structural information, or (ii) use Graph Neural Networks (GNNs) to preserve graph structure, while GNNs cannot represent textual features as well as a pre-trained LM could. In this work we introduce a novel language model, the Graph Language Model (GLM), that integrates the strengths of both approaches, while mitigating their weaknesses. The GLM parameters are initialized from a pretrained LM, to facilitate nuanced understanding of individual concepts and triplets. Simultaneously, its architectural design incorporates graph biases, thereby promoting effective knowledge distribution within the graph. Empirical evaluations on relation classification tasks on ConceptNet subgraphs reveal that GLM embeddings surpass both LM- and GNN-based baselines in supervised and zero-shot settings.

Recently, research on Text-Attributed Graphs (TAGs) has gained significant attention due to the prevalence of free-text node features in real-world applications and the advancements in Large Language Models (LLMs) that bolster TAG methodologies. However, current TAG approaches face two primary challenges: (i) Heavy reliance on label information and (ii) Limited cross-domain zero/few-shot transferability. These issues constrain the scaling of both data and model size, owing to high labor costs and scaling laws, complicating the development of graph foundation models with strong transferability. In this work, we propose the GraphCLIP framework to address these challenges by learning graph foundation models with strong cross-domain zero/few-shot transferability through a self-supervised contrastive graph-summary pretraining method. Specifically, we generate and curate large-scale graph-summary pair data with the assistance of LLMs, and introduce a novel graph-summary pretraining method, combined with invariant learning, to enhance graph foundation models with strong cross-domain zero-shot transferability. For few-shot learning, we propose a novel graph prompt tuning technique aligned with our pretraining objective to mitigate catastrophic forgetting and minimize learning costs. Extensive experiments show the superiority of GraphCLIP in both zero-shot and few-shot settings, while evaluations across various downstream tasks confirm the versatility of GraphCLIP. Our code is available at: https://github.com/ZhuYun97/GraphCLIP

Recent prevailing works on graph machine learning typically follow a similar methodology that involves designing advanced variants of graph neural networks (GNNs) to maintain the superior performance of GNNs on different graphs. In this paper, we aim to streamline the GNN design process and leverage the advantages of Large Language Models (LLMs) to improve the performance of GNNs on downstream tasks. We formulate a new paradigm, coined "LLMs-as-Consultants," which integrates LLMs with GNNs in an interactive manner. A framework named LOGIN (LLM Consulted GNN training) is instantiated, empowering the interactive utilization of LLMs within the GNN training process. First, we attentively craft concise prompts for spotted nodes, carrying comprehensive semantic and topological information, and serving as input to LLMs. Second, we refine GNNs by devising a complementary coping mechanism that utilizes the responses from LLMs, depending on their correctness. We empirically evaluate the effectiveness of LOGIN on node classification tasks across both homophilic and heterophilic graphs. The results illustrate that even basic GNN architectures, when employed within the proposed LLMs-as-Consultants paradigm, can achieve comparable performance to advanced GNNs with intricate designs. Our codes are available at https://github.com/QiaoYRan/LOGIN.

Graph Neural Architecture Search (GNAS) facilitates the automatic design of Graph Neural Networks (GNNs) tailored to specific downstream graph learning tasks. However, existing GNAS approaches often require manual adaptation to new graph search spaces, necessitating substantial code optimization and domain-specific knowledge. To address this challenge, we present LLM4GNAS, a toolkit for GNAS that leverages the generative capabilities of Large Language Models (LLMs). LLM4GNAS includes an algorithm library for graph neural architecture search algorithms based on LLMs, enabling the adaptation of GNAS methods to new search spaces through the modification of LLM prompts. This approach reduces the need for manual intervention in algorithm adaptation and code modification. The LLM4GNAS toolkit is extensible and robust, incorporating LLM-enhanced graph feature engineering, LLM-enhanced graph neural architecture search, and LLM-enhanced hyperparameter optimization. Experimental results indicate that LLM4GNAS outperforms existing GNAS methods on tasks involving both homogeneous and heterogeneous graphs.

The success of deep learning notoriously requires larger amounts of costly annotated data. This has led to the development of self-supervised learning (SSL) that aims to alleviate this limitation by creating domain specific pretext tasks on unlabeled data. Simultaneously, there are increasing interests in generalizing deep learning to the graph domain in the form of graph neural networks (GNNs). GNNs can naturally utilize unlabeled nodes through the simple neighborhood aggregation that is unable to thoroughly make use of unlabeled nodes. Thus, we seek to harness SSL for GNNs to fully exploit the unlabeled data. Different from data instances in the image and text domains, nodes in graphs present unique structure information and they are inherently linked indicating not independent and identically distributed (or i.i.d.). Such complexity is a double-edged sword for SSL on graphs. On the one hand, it determines that it is challenging to adopt solutions from the image and text domains to graphs and dedicated efforts are desired. On the other hand, it provides rich information that enables us to build SSL from a variety of perspectives. Thus, in this paper, we first deepen our understandings on when, why, and which strategies of SSL work with GNNs by empirically studying numerous basic SSL pretext tasks on graphs. Inspired by deep insights from the empirical studies, we propose a new direction SelfTask to build advanced pretext tasks that are able to achieve state-of-the-art performance on various real-world datasets. The specific experimental settings to reproduce our results can be found in https://github.com/ChandlerBang/SelfTask-GNN.

Large language models generate code one token at a time. Their autoregressive generation process lacks the feedback of observing the program's output. Training LLMs to suggest edits directly can be challenging due to the scarcity of rich edit data. To address these problems, we propose neural diffusion models that operate on syntax trees of any context-free grammar. Similar to image diffusion models, our method also inverts ``noise'' applied to syntax trees. Rather than generating code sequentially, we iteratively edit it while preserving syntactic validity, which makes it easy to combine this neural model with search. We apply our approach to inverse graphics tasks, where our model learns to convert images into programs that produce those images. Combined with search, our model is able to write graphics programs, see the execution result, and debug them to meet the required specifications. We additionally show how our system can write graphics programs for hand-drawn sketches.

Given a graph with textual attributes, we enable users to `chat with their graph': that is, to ask questions about the graph using a conversational interface. In response to a user's questions, our method provides textual replies and highlights the relevant parts of the graph. While existing works integrate large language models (LLMs) and graph neural networks (GNNs) in various ways, they mostly focus on either conventional graph tasks (such as node, edge, and graph classification), or on answering simple graph queries on small or synthetic graphs. In contrast, we develop a flexible question-answering framework targeting real-world textual graphs, applicable to multiple applications including scene graph understanding, common sense reasoning, and knowledge graph reasoning. Toward this goal, we first develop a Graph Question Answering (GraphQA) benchmark with data collected from different tasks. Then, we propose our G-Retriever method, introducing the first retrieval-augmented generation (RAG) approach for general textual graphs, which can be fine-tuned to enhance graph understanding via soft prompting. To resist hallucination and to allow for textual graphs that greatly exceed the LLM's context window size, G-Retriever performs RAG over a graph by formulating this task as a Prize-Collecting Steiner Tree optimization problem. Empirical evaluations show that our method outperforms baselines on textual graph tasks from multiple domains, scales well with larger graph sizes, and mitigates hallucination.~Our codes and datasets are available at: \url{https://github.com/XiaoxinHe/G-Retriever}

While great success has been achieved in building vision models with Contrastive Language-Image Pre-training (CLIP) over internet-scale image-text pairs, building transferable Graph Neural Networks (GNNs) with CLIP pipeline is challenging because of the scarcity of labeled data and text supervision, different levels of downstream tasks, and the conceptual gaps between domains. In this work, to address these issues, we propose a multi-modal prompt learning paradigm to effectively adapt pre-trained GNN to downstream tasks and data, given only a few semantically labeled samples, each with extremely weak text supervision. Our new paradigm embeds the graphs directly in the same space as the Large Language Models (LLMs) by learning both graph prompts and text prompts simultaneously. We demonstrate the superior performance of our paradigm in few-shot, multi-task-level, and cross-domain settings. Moreover, we build the first CLIP-style zero-shot classification prototype that can generalize GNNs to unseen classes with extremely weak text supervision. The code is available at https://github.com/Violet24K/Morpher.

Large language models (LLMs) have demonstrated remarkable in-context reasoning capabilities across a wide range of tasks, particularly with unstructured inputs such as language or images. However, LLMs struggle to handle structured data, such as graphs, due to their lack of understanding of non-Euclidean structures. As a result, without additional fine-tuning, their performance significantly lags behind that of graph neural networks (GNNs) in graph learning tasks. In this paper, we show that learning on graph data can be conceptualized as a retrieval-augmented generation (RAG) process, where specific instances (e.g., nodes or edges) act as queries, and the graph itself serves as the retrieved context. Building on this insight, we propose a series of RAG frameworks to enhance the in-context learning capabilities of LLMs for graph learning tasks. Comprehensive evaluations demonstrate that our proposed RAG frameworks significantly improve LLM performance on graph-based tasks, particularly in scenarios where a pretrained LLM must be used without modification or accessed via an API.

Graph pooling compresses graph information into a compact representation. State-of-the-art graph pooling methods follow a hierarchical approach, which reduces the graph size step-by-step. These methods must balance memory efficiency with preserving node information, depending on whether they use node dropping or node clustering. Additionally, fixed pooling ratios or numbers of pooling layers are predefined for all graphs, which prevents personalized pooling structures from being captured for each individual graph. In this work, inspired by bottom-up grammar induction, we propose an efficient graph parsing algorithm to infer the pooling structure, which then drives graph pooling. The resulting Graph Parsing Network (GPN) adaptively learns personalized pooling structure for each individual graph. GPN benefits from the discrete assignments generated by the graph parsing algorithm, allowing good memory efficiency while preserving node information intact. Experimental results on standard benchmarks demonstrate that GPN outperforms state-of-the-art graph pooling methods in graph classification tasks while being able to achieve competitive performance in node classification tasks. We also conduct a graph reconstruction task to show GPN's ability to preserve node information and measure both memory and time efficiency through relevant tests.

Representation learning on text-attributed graphs (TAGs) has become a critical research problem in recent years. A typical example of a TAG is a paper citation graph, where the text of each paper serves as node attributes. Initial graph neural network (GNN) pipelines handled these text attributes by transforming them into shallow or hand-crafted features, such as skip-gram or bag-of-words features. Recent efforts have focused on enhancing these pipelines with language models (LMs), which typically demand intricate designs and substantial computational resources. With the advent of powerful large language models (LLMs) such as GPT or Llama2, which demonstrate an ability to reason and to utilize general knowledge, there is a growing need for techniques which combine the textual modelling abilities of LLMs with the structural learning capabilities of GNNs. Hence, in this work, we focus on leveraging LLMs to capture textual information as features, which can be used to boost GNN performance on downstream tasks. A key innovation is our use of explanations as features: we prompt an LLM to perform zero-shot classification, request textual explanations for its decision-making process, and design an LLM-to-LM interpreter to translate these explanations into informative features for downstream GNNs. Our experiments demonstrate that our method achieves state-of-the-art results on well-established TAG datasets, including Cora, PubMed, ogbn-arxiv, as well as our newly introduced dataset, tape-arxiv23. Furthermore, our method significantly speeds up training, achieving a 2.88 times improvement over the closest baseline on ogbn-arxiv. Lastly, we believe the versatility of the proposed method extends beyond TAGs and holds the potential to enhance other tasks involving graph-text data. Our codes and datasets are available at: https://github.com/XiaoxinHe/TAPE.

Code retrieval is a crucial component in modern software development, particularly in large-scale projects. However, existing approaches relying on sequence-based models often fail to fully exploit the structural dependencies inherent in code, leading to suboptimal retrieval performance, particularly with structurally complex code fragments. In this paper, we introduce GNN-Coder, a novel framework based on Graph Neural Network (GNN) to utilize Abstract Syntax Tree (AST). We make the first attempt to study how GNN-integrated Transformer can promote the development of semantic retrieval tasks by capturing the structural and semantic features of code. We further propose an innovative graph pooling method tailored for AST, utilizing the number of child nodes as a key feature to highlight the intrinsic topological relationships within the AST. This design effectively integrates both sequential and hierarchical representations, enhancing the model's ability to capture code structure and semantics. Additionally, we introduce the Mean Angular Margin (MAM), a novel metric for quantifying the uniformity of code embedding distributions, providing a standardized measure of feature separability. The proposed method achieves a lower MAM, indicating a more discriminative feature representation. This underscores GNN-Coder's superior ability to distinguish between code snippets, thereby enhancing retrieval accuracy. Experimental results show that GNN-Coder significantly boosts retrieval performance, with a 1\%-10\% improvement in MRR on the CSN dataset, and a notable 20\% gain in zero-shot performance on the CosQA dataset.

We present an approach for assessing how multilingual large language models (LLMs) learn syntax in terms of multi-formalism syntactic structures. We aim to recover constituent and dependency structures by casting parsing as sequence labeling. To do so, we select a few LLMs and study them on 13 diverse UD treebanks for dependency parsing and 10 treebanks for constituent parsing. Our results show that: (i) the framework is consistent across encodings, (ii) pre-trained word vectors do not favor constituency representations of syntax over dependencies, (iii) sub-word tokenization is needed to represent syntax, in contrast to character-based models, and (iv) occurrence of a language in the pretraining data is more important than the amount of task data when recovering syntax from the word vectors.

We introduce a convolutional neural network that operates directly on graphs. These networks allow end-to-end learning of prediction pipelines whose inputs are graphs of arbitrary size and shape. The architecture we present generalizes standard molecular feature extraction methods based on circular fingerprints. We show that these data-driven features are more interpretable, and have better predictive performance on a variety of tasks.

Graphs can model complex relationships between objects, enabling a myriad of Web applications such as online page/article classification and social recommendation. While graph neural networks(GNNs) have emerged as a powerful tool for graph representation learning, in an end-to-end supervised setting, their performance heavily rely on a large amount of task-specific supervision. To reduce labeling requirement, the "pre-train, fine-tune" and "pre-train, prompt" paradigms have become increasingly common. In particular, prompting is a popular alternative to fine-tuning in natural language processing, which is designed to narrow the gap between pre-training and downstream objectives in a task-specific manner. However, existing study of prompting on graphs is still limited, lacking a universal treatment to appeal to different downstream tasks. In this paper, we propose GraphPrompt, a novel pre-training and prompting framework on graphs. GraphPrompt not only unifies pre-training and downstream tasks into a common task template, but also employs a learnable prompt to assist a downstream task in locating the most relevant knowledge from the pre-train model in a task-specific manner. Finally, we conduct extensive experiments on five public datasets to evaluate and analyze GraphPrompt.

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.

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.

Recent improvements in KG-to-text generation are due to additional auxiliary pre-training tasks designed to give the fine-tune task a boost in performance. These tasks require extensive computational resources while only suggesting marginal improvements. Here, we demonstrate that by fusing graph-aware elements into existing pre-trained language models, we are able to outperform state-of-the-art models and close the gap imposed by additional pre-training tasks. We do so by proposing a mask structure to capture neighborhood information and a novel type encoder that adds a bias to the graph-attention weights depending on the connection type. Experiments on two KG-to-text benchmark datasets show our models are competitive while involving fewer parameters and no additional pre-training tasks. By formulating the problem as a framework, we can interchange the various proposed components and begin interpreting KG-to-text generative models based on the topological and type information found in a graph.

We present UDify, a multilingual multi-task model capable of accurately predicting universal part-of-speech, morphological features, lemmas, and dependency trees simultaneously for all 124 Universal Dependencies treebanks across 75 languages. By leveraging a multilingual BERT self-attention model pretrained on 104 languages, we found that fine-tuning it on all datasets concatenated together with simple softmax classifiers for each UD task can result in state-of-the-art UPOS, UFeats, Lemmas, UAS, and LAS scores, without requiring any recurrent or language-specific components. We evaluate UDify for multilingual learning, showing that low-resource languages benefit the most from cross-linguistic annotations. We also evaluate for zero-shot learning, with results suggesting that multilingual training provides strong UD predictions even for languages that neither UDify nor BERT have ever been trained on. Code for UDify is available at https://github.com/hyperparticle/udify.

In this paper, we describe our submission to the BabyLM Challenge 2023 shared task on data-efficient language model (LM) pretraining (Warstadt et al., 2023). We train transformer-based masked language models that incorporate unsupervised predictions about hierarchical sentence structure into the model architecture. Concretely, we use the Structformer architecture (Shen et al., 2021) and variants thereof. StructFormer models have been shown to perform well on unsupervised syntactic induction based on limited pretraining data, and to yield performance improvements over a vanilla transformer architecture (Shen et al., 2021). Evaluation of our models on 39 tasks provided by the BabyLM challenge shows promising improvements of models that integrate a hierarchical bias into the architecture at some particular tasks, even though they fail to consistently outperform the RoBERTa baseline model provided by the shared task organizers on all tasks.

Graph Neural Networks (GNNs) have advanced graph structure understanding via recursive information exchange and aggregation among graph nodes. To improve model robustness, self-supervised learning (SSL) has emerged as a promising approach for data augmentation. However, existing methods for generating pre-trained graph embeddings often rely on fine-tuning with specific downstream task labels, which limits their usability in scenarios where labeled data is scarce or unavailable. To address this, our research focuses on advancing the generalization capabilities of graph models in challenging zero-shot learning scenarios. Inspired by the success of large language models (LLMs), we aim to develop a graph-oriented LLM that can achieve high generalization across diverse downstream datasets and tasks, even without any information available from the downstream graph data. In this work, we present the GraphGPT framework that aligns LLMs with graph structural knowledge with a graph instruction tuning paradigm. Our framework incorporates a text-graph grounding component to establish a connection between textual information and graph structures. Additionally, we propose a dual-stage instruction tuning paradigm, accompanied by a lightweight graph-text alignment projector. This paradigm explores self-supervised graph structural signals and task-specific graph instructions, to guide LLMs in understanding complex graph structures and improving their adaptability across different downstream tasks. Our framework is evaluated on supervised and zero-shot graph learning tasks, demonstrating superior generalization and outperforming state-of-the-art baselines.

This paper proposes a simple, yet effective framework, called GiT, simultaneously applicable for various vision tasks only with a vanilla ViT. Motivated by the universality of the Multi-layer Transformer architecture (e.g, GPT) widely used in large language models (LLMs), we seek to broaden its scope to serve as a powerful vision foundation model (VFM). However, unlike language modeling, visual tasks typically require specific modules, such as bounding box heads for detection and pixel decoders for segmentation, greatly hindering the application of powerful multi-layer transformers in the vision domain. To solve this, we design a universal language interface that empowers the successful auto-regressive decoding to adeptly unify various visual tasks, from image-level understanding (e.g., captioning), over sparse perception (e.g., detection), to dense prediction (e.g., segmentation). Based on the above designs, the entire model is composed solely of a ViT, without any specific additions, offering a remarkable architectural simplification. GiT is a multi-task visual model, jointly trained across five representative benchmarks without task-specific fine-tuning. Interestingly, our GiT builds a new benchmark in generalist performance, and fosters mutual enhancement across tasks, leading to significant improvements compared to isolated training. This reflects a similar impact observed in LLMs. Further enriching training with 27 datasets, GiT achieves strong zero-shot results over various tasks. Due to its simple design, this paradigm holds promise for narrowing the architectural gap between vision and language. Code and models will be available at https://github.com/Haiyang-W/GiT.

Pre-trained language models have demonstrated impressive performance in both natural language processing and program understanding, which represent the input as a token sequence without explicitly modeling its structure. Some prior works show that pre-trained language models can capture the syntactic rules of natural languages without finetuning on syntax understanding tasks. However, there is limited understanding of how well pre-trained models understand the code structure so far. In this work, we perform the first thorough benchmarking of the state-of-the-art pre-trained models for identifying the syntactic structures of programs. Specifically, we introduce CodeSyntax, a large-scale dataset of programs annotated with the syntactic relationships in their corresponding abstract syntax trees. Our key observation is that existing language models pretrained on code still lack the understanding of code syntax. In fact, these pre-trained programming language models fail to match the performance of simple baselines based on positional offsets and keywords. We also present a natural language benchmark to highlight the differences between natural languages and programming languages in terms of syntactic structure understanding. Our findings point out key limitations of existing pre-training methods for programming languages, and suggest the importance of modeling code syntactic structures.

Universally modeling all typical information extraction tasks (UIE) with one generative language model (GLM) has revealed great potential by the latest study, where various IE predictions are unified into a linearized hierarchical expression under a GLM. Syntactic structure information, a type of effective feature which has been extensively utilized in IE community, should also be beneficial to UIE. In this work, we propose a novel structure-aware GLM, fully unleashing the power of syntactic knowledge for UIE. A heterogeneous structure inductor is explored to unsupervisedly induce rich heterogeneous structural representations by post-training an existing GLM. In particular, a structural broadcaster is devised to compact various latent trees into explicit high-order forests, helping to guide a better generation during decoding. We finally introduce a task-oriented structure fine-tuning mechanism, further adjusting the learned structures to most coincide with the end-task's need. Over 12 IE benchmarks across 7 tasks our system shows significant improvements over the baseline UIE system. Further in-depth analyses show that our GLM learns rich task-adaptive structural bias that greatly resolves the UIE crux, the long-range dependence issue and boundary identifying. Source codes are open at https://github.com/ChocoWu/LasUIE.

Linear sequences of words are implicitly represented in our brains by hierarchical structures that organize the composition of words in sentences. Linguists formalize different frameworks to model this hierarchy; two of the most common syntactic frameworks are Constituency and Dependency. Constituency represents sentences as nested groups of phrases, while dependency represents a sentence by assigning relations between its words. Recently, the pursuit of intelligent machines has produced Language Models (LMs) capable of solving many language tasks with a human-level performance. Many studies now question whether LMs implicitly represent syntactic hierarchies. This thesis focuses on producing constituency and dependency structures from LMs in an unsupervised setting. I review the critical methods in this field and highlight a line of work that utilizes a numerical representation for binary constituency trees (Syntactic Distance). I present a detailed study on StructFormer (SF) (Shen et al., 2021), which retrofits a transformer encoder architecture with a parser network to produce constituency and dependency structures. I present six experiments to analyze and address this field's challenges; experiments include investigating the effect of repositioning the parser network within the SF architecture, evaluating subword-based induced trees, and benchmarking the models developed in the thesis experiments on linguistic tasks. Models benchmarking is performed by participating in the BabyLM challenge, published at CoNLL 2023 (Momen et al., 2023). The results of this thesis encourage further development in the direction of retrofitting transformer-based models to induce syntactic structures, supported by the acceptable performance of SF in different experimental settings and the observed limitations that require innovative solutions to advance the state of syntactic structure induction.

Graph neural networks have shown significant success in the field of graph representation learning. Graph convolutions perform neighborhood aggregation and represent one of the most important graph operations. Nevertheless, one layer of these neighborhood aggregation methods only consider immediate neighbors, and the performance decreases when going deeper to enable larger receptive fields. Several recent studies attribute this performance deterioration to the over-smoothing issue, which states that repeated propagation makes node representations of different classes indistinguishable. In this work, we study this observation systematically and develop new insights towards deeper graph neural networks. First, we provide a systematical analysis on this issue and argue that the key factor compromising the performance significantly is the entanglement of representation transformation and propagation in current graph convolution operations. After decoupling these two operations, deeper graph neural networks can be used to learn graph node representations from larger receptive fields. We further provide a theoretical analysis of the above observation when building very deep models, which can serve as a rigorous and gentle description of the over-smoothing issue. Based on our theoretical and empirical analysis, we propose Deep Adaptive Graph Neural Network (DAGNN) to adaptively incorporate information from large receptive fields. A set of experiments on citation, co-authorship, and co-purchase datasets have confirmed our analysis and insights and demonstrated the superiority of our proposed methods.

Generalizing to unseen graph tasks without task-pecific supervision remains challenging. Graph Neural Networks (GNNs) are limited by fixed label spaces, while Large Language Models (LLMs) lack structural inductive biases. Recent advances in Large Reasoning Models (LRMs) provide a zero-shot alternative via explicit, long chain-of-thought reasoning. Inspired by this, we propose a GNN-free approach that reformulates graph tasks--node classification, link prediction, and graph classification--as textual reasoning problems solved by LRMs. We introduce the first datasets with detailed reasoning traces for these tasks and develop Graph-R1, a reinforcement learning framework that leverages task-specific rethink templates to guide reasoning over linearized graphs. Experiments demonstrate that Graph-R1 outperforms state-of-the-art baselines in zero-shot settings, producing interpretable and effective predictions. Our work highlights the promise of explicit reasoning for graph learning and provides new resources for future research.

Transformers have recently emerged as powerful neural networks for graph learning, showcasing state-of-the-art performance on several graph property prediction tasks. However, these results have been limited to small-scale graphs, where the computational feasibility of the global attention mechanism is possible. The next goal is to scale up these architectures to handle very large graphs on the scale of millions or even billions of nodes. With large-scale graphs, global attention learning is proven impractical due to its quadratic complexity w.r.t. the number of nodes. On the other hand, neighborhood sampling techniques become essential to manage large graph sizes, yet finding the optimal trade-off between speed and accuracy with sampling techniques remains challenging. This work advances representation learning on single large-scale graphs with a focus on identifying model characteristics and critical design constraints for developing scalable graph transformer (GT) architectures. We argue such GT requires layers that can adeptly learn both local and global graph representations while swiftly sampling the graph topology. As such, a key innovation of this work lies in the creation of a fast neighborhood sampling technique coupled with a local attention mechanism that encompasses a 4-hop reception field, but achieved through just 2-hop operations. This local node embedding is then integrated with a global node embedding, acquired via another self-attention layer with an approximate global codebook, before finally sent through a downstream layer for node predictions. The proposed GT framework, named LargeGT, overcomes previous computational bottlenecks and is validated on three large-scale node classification benchmarks. We report a 3x speedup and 16.8% performance gain on ogbn-products and snap-patents, while we also scale LargeGT on ogbn-papers100M with a 5.9% performance improvement.

Large language models (LLMs) such as GPT-4 have emerged as frontrunners, showcasing unparalleled prowess in diverse applications, including answering queries, code generation, and more. Parallelly, graph-structured data, an intrinsic data type, is pervasive in real-world scenarios. Merging the capabilities of LLMs with graph-structured data has been a topic of keen interest. This paper bifurcates such integrations into two predominant categories. The first leverages LLMs for graph learning, where LLMs can not only augment existing graph algorithms but also stand as prediction models for various graph tasks. Conversely, the second category underscores the pivotal role of graphs in advancing LLMs. Mirroring human cognition, we solve complex tasks by adopting graphs in either reasoning or collaboration. Integrating with such structures can significantly boost the performance of LLMs in various complicated tasks. We also discuss and propose open questions for integrating LLMs with graph-structured data for the future direction of the field.

Recently, there has been a surge of interest in extending the success of large language models (LLMs) from texts to molecules. Most existing approaches adopt a graph neural network to represent a molecule as a series of node tokens for molecule-language alignment, which, however, have overlooked the inherent hierarchical structures in molecules. Notably, higher-order molecular structures contain rich semantics of functional groups, which encode crucial biochemical functionalities of the molecules. We show that neglecting the hierarchical information in tokenization will lead to subpar molecule-language alignment and severe hallucination. To address this limitation, we propose HIerarchical GrapH Tokenization (HIGHT). HIGHT employs a hierarchical graph tokenizer that encodes the hierarchy of atom, motif, and molecular levels of informative tokens to improve the molecular perception of LLMs. HIGHT also adopts an augmented instruction tuning dataset, enriched with the hierarchical graph information, to further enhance the molecule-language alignment. Extensive experiments on 14 real-world benchmarks verify the effectiveness of HIGHT in reducing hallucination by 40%, and significant improvements in various molecule-language downstream tasks. The project is available at https: //higraphllm.github.io/.

Graph Convolutional Networks (GCNs) have shown strong performance in learning text representations for various tasks such as text classification, due to its expressive power in modeling graph structure data (e.g., a literature citation network). Most existing GCNs are limited to deal with documents included in a pre-defined graph, i.e., it cannot be generalized to out-of-graph documents. To address this issue, we propose to transform the document graph into a word graph, to decouple data samples (i.e., documents in training and test sets) and a GCN model by using a document-independent graph. Such word-level GCN could therefore naturally inference out-of-graph documents in an inductive way. The proposed Word-level Graph (WGraph) can not only implicitly learning word presentation with commonly-used word co-occurrences in corpora, but also incorporate extra global semantic dependency derived from inter-document relationships (e.g., literature citations). An inductive Word-grounded Graph Convolutional Network (WGCN) is proposed to learn word and document representations based on WGraph in a supervised manner. Experiments on text classification with and without citation networks evidence that the proposed WGCN model outperforms existing methods in terms of effectiveness and efficiency.

Graph Neural Networks (GNNs) have empowered the advance in graph-structured data analysis. Recently, the rise of Large Language Models (LLMs) like GPT-4 has heralded a new era in deep learning. However, their application to graph data poses distinct challenges due to the inherent difficulty of translating graph structures to language. To this end, we introduce the Large Language and Graph Assistant (LLaGA), an innovative model that effectively integrates LLM capabilities to handle the complexities of graph-structured data. LLaGA retains the general-purpose nature of LLMs while adapting graph data into a format compatible with LLM input. LLaGA achieves this by reorganizing graph nodes to structure-aware sequences and then mapping these into the token embedding space through a versatile projector. LLaGA excels in versatility, generalizability and interpretability, allowing it to perform consistently well across different datasets and tasks, extend its ability to unseen datasets or tasks, and provide explanations for graphs. Our extensive experiments across popular graph benchmarks show that LLaGA delivers outstanding performance across four datasets and three tasks using one single model, surpassing state-of-the-art graph models in both supervised and zero-shot scenarios. Our code is available at https://github.com/VITA-Group/LLaGA.

Large language models (LLMs) like ChatGPT, exhibit powerful zero-shot and instruction-following capabilities, have catalyzed a revolutionary transformation across diverse fields, especially for open-ended tasks. While the idea is less explored in the graph domain, despite the availability of numerous powerful graph models (GMs), they are restricted to tasks in a pre-defined form. Although several methods applying LLMs to graphs have been proposed, they fail to simultaneously handle the pre-defined and open-ended tasks, with LLM as a node feature enhancer or as a standalone predictor. To break this dilemma, we propose to bridge the pretrained GM and LLM by a Translator, named GraphTranslator, aiming to leverage GM to handle the pre-defined tasks effectively and utilize the extended interface of LLMs to offer various open-ended tasks for GM. To train such Translator, we propose a Producer capable of constructing the graph-text alignment data along node information, neighbor information and model information. By translating node representation into tokens, GraphTranslator empowers an LLM to make predictions based on language instructions, providing a unified perspective for both pre-defined and open-ended tasks. Extensive results demonstrate the effectiveness of our proposed GraphTranslator on zero-shot node classification. The graph question answering experiments reveal our GraphTranslator potential across a broad spectrum of open-ended tasks through language instructions. Our code is available at: https://github.com/alibaba/GraphTranslator.

In recent years, there have been remarkable advancements in node classification achieved by Graph Neural Networks (GNNs). However, they necessitate abundant high-quality labels to ensure promising performance. In contrast, Large Language Models (LLMs) exhibit impressive zero-shot proficiency on text-attributed graphs. Yet, they face challenges in efficiently processing structural data and suffer from high inference costs. In light of these observations, this work introduces a label-free node classification on graphs with LLMs pipeline, LLM-GNN. It amalgamates the strengths of both GNNs and LLMs while mitigating their limitations. Specifically, LLMs are leveraged to annotate a small portion of nodes and then GNNs are trained on LLMs' annotations to make predictions for the remaining large portion of nodes. The implementation of LLM-GNN faces a unique challenge: how can we actively select nodes for LLMs to annotate and consequently enhance the GNN training? How can we leverage LLMs to obtain annotations of high quality, representativeness, and diversity, thereby enhancing GNN performance with less cost? To tackle this challenge, we develop an annotation quality heuristic and leverage the confidence scores derived from LLMs to advanced node selection. Comprehensive experimental results validate the effectiveness of LLM-GNN. In particular, LLM-GNN can achieve an accuracy of 74.9% on a vast-scale dataset \products with a cost less than 1 dollar.

Recent advances in Graph Neural Networks (GNNs) and Graph Transformers (GTs) have been driven by innovations in architectures and Positional Encodings (PEs), which are critical for augmenting node features and capturing graph topology. PEs are essential for GTs, where topological information would otherwise be lost without message-passing. However, PEs are often tested alongside novel architectures, making it difficult to isolate their effect on established models. To address this, we present a comprehensive benchmark of PEs in a unified framework that includes both message-passing GNNs and GTs. We also establish theoretical connections between MPNNs and GTs and introduce a sparsified GRIT attention mechanism to examine the influence of global connectivity. Our findings demonstrate that previously untested combinations of GNN architectures and PEs can outperform existing methods and offer a more comprehensive picture of the state-of-the-art. To support future research and experimentation in our framework, we make the code publicly available.

Existing PTLM-based models for TSC can be categorized into two groups: 1) fine-tuning-based models that adopt PTLM as the context encoder; 2) prompting-based models that transfer the classification task to the text/word generation task. In this paper, we present a new perspective of leveraging PTLM for TSC: simultaneously leveraging the merits of both language modeling and explicit target-context interactions via contextual target attributes. Specifically, we design the domain- and target-constrained cloze test, which can leverage the PTLMs' strong language modeling ability to generate the given target's attributes pertaining to the review context. The attributes contain the background and property information of the target, which can help to enrich the semantics of the review context and the target. To exploit the attributes for tackling TSC, we first construct a heterogeneous information graph by treating the attributes as nodes and combining them with (1) the syntax graph automatically produced by the off-the-shelf dependency parser and (2) the semantics graph of the review context, which is derived from the self-attention mechanism. Then we propose a heterogeneous information gated graph convolutional network to model the interactions among the attribute information, the syntactic information, and the contextual information. The experimental results on three benchmark datasets demonstrate the superiority of our model, which achieves new state-of-the-art performance.

Recent advances in large language models (LLMs) have intensified efforts to fuse heterogeneous open-source models into a unified system that inherits their complementary strengths. Existing logit-based fusion methods maintain inference efficiency but treat vocabulary dimensions independently, overlooking semantic dependencies encoded by cross-dimension interactions. These dependencies reflect how token types interact under a model's internal reasoning and are essential for aligning models with diverse generation behaviors. To explicitly model these dependencies, we propose InfiGFusion, the first structure-aware fusion framework with a novel Graph-on-Logits Distillation (GLD) loss. Specifically, we retain the top-k logits per output and aggregate their outer products across sequence positions to form a global co-activation graph, where nodes represent vocabulary channels and edges quantify their joint activations. To ensure scalability and efficiency, we design a sorting-based closed-form approximation that reduces the original O(n^4) cost of Gromov-Wasserstein distance to O(n log n), with provable approximation guarantees. Experiments across multiple fusion settings show that GLD consistently improves fusion quality and stability. InfiGFusion outperforms SOTA models and fusion baselines across 11 benchmarks spanning reasoning, coding, and mathematics. It shows particular strength in complex reasoning tasks, with +35.6 improvement on Multistep Arithmetic and +37.06 on Causal Judgement over SFT, demonstrating superior multi-step and relational inference.

This paper studies learning on text-attributed graphs (TAGs), where each node is associated with a text description. An ideal solution for such a problem would be integrating both the text and graph structure information with large language models and graph neural networks (GNNs). However, the problem becomes very challenging when graphs are large due to the high computational complexity brought by training large language models and GNNs together. In this paper, we propose an efficient and effective solution to learning on large text-attributed graphs by fusing graph structure and language learning with a variational Expectation-Maximization (EM) framework, called GLEM. Instead of simultaneously training large language models and GNNs on big graphs, GLEM proposes to alternatively update the two modules in the E-step and M-step. Such a procedure allows training the two modules separately while simultaneously allowing the two modules to interact and mutually enhance each other. Extensive experiments on multiple data sets demonstrate the efficiency and effectiveness of the proposed approach.

Graphs are essential data structures for modeling complex interactions in domains such as social networks, molecular structures, and biological systems. Graph-level tasks, which predict properties or classes for the entire graph, are critical for applications, such as molecular property prediction and subgraph counting. Graph Neural Networks (GNNs) have shown promise in these tasks, but their evaluations are often limited to narrow datasets, tasks, and inconsistent experimental setups, restricting their generalizability. To address these limitations, we propose a unified evaluation framework for graph-level GNNs. This framework provides a standardized setting to evaluate GNNs across diverse datasets, various graph tasks (e.g., graph classification and regression), and challenging scenarios, including noisy, imbalanced, and few-shot graphs. Additionally, we propose a novel GNN model with enhanced expressivity and generalization capabilities. Specifically, we enhance the expressivity of GNNs through a k-path rooted subgraph approach, enabling the model to effectively count subgraphs (e.g., paths and cycles). Moreover, we introduce a unified graph contrastive learning algorithm for graphs across diverse domains, which adaptively removes unimportant edges to augment graphs, thereby significantly improving generalization performance. Extensive experiments demonstrate that our model achieves superior performance against fourteen effective baselines across twenty-seven graph datasets, establishing it as a robust and generalizable model for graph-level tasks.

Graph Neural Networks (GNNs) are an effective framework for representation learning of graphs. GNNs follow a neighborhood aggregation scheme, where the representation vector of a node is computed by recursively aggregating and transforming representation vectors of its neighboring nodes. Many GNN variants have been proposed and have achieved state-of-the-art results on both node and graph classification tasks. However, despite GNNs revolutionizing graph representation learning, there is limited understanding of their representational properties and limitations. Here, we present a theoretical framework for analyzing the expressive power of GNNs to capture different graph structures. Our results characterize the discriminative power of popular GNN variants, such as Graph Convolutional Networks and GraphSAGE, and show that they cannot learn to distinguish certain simple graph structures. We then develop a simple architecture that is provably the most expressive among the class of GNNs and is as powerful as the Weisfeiler-Lehman graph isomorphism test. We empirically validate our theoretical findings on a number of graph classification benchmarks, and demonstrate that our model achieves state-of-the-art performance.

Information flows by routes inside the network via mechanisms implemented in the model. These routes can be represented as graphs where nodes correspond to token representations and edges to operations inside the network. We automatically build these graphs in a top-down manner, for each prediction leaving only the most important nodes and edges. In contrast to the existing workflows relying on activation patching, we do this through attribution: this allows us to efficiently uncover existing circuits with just a single forward pass. Additionally, the applicability of our method is far beyond patching: we do not need a human to carefully design prediction templates, and we can extract information flow routes for any prediction (not just the ones among the allowed templates). As a result, we can talk about model behavior in general, for specific types of predictions, or different domains. We experiment with Llama 2 and show that the role of some attention heads is overall important, e.g. previous token heads and subword merging heads. Next, we find similarities in Llama 2 behavior when handling tokens of the same part of speech. Finally, we show that some model components can be specialized on domains such as coding or multilingual texts.

We introduce a self-supervised approach for learning node and graph level representations by contrasting structural views of graphs. We show that unlike visual representation learning, increasing the number of views to more than two or contrasting multi-scale encodings do not improve performance, and the best performance is achieved by contrasting encodings from first-order neighbors and a graph diffusion. We achieve new state-of-the-art results in self-supervised learning on 8 out of 8 node and graph classification benchmarks under the linear evaluation protocol. For example, on Cora (node) and Reddit-Binary (graph) classification benchmarks, we achieve 86.8% and 84.5% accuracy, which are 5.5% and 2.4% relative improvements over previous state-of-the-art. When compared to supervised baselines, our approach outperforms them in 4 out of 8 benchmarks. Source code is released at: https://github.com/kavehhassani/mvgrl

We propose STRuCT-LLM, a unified framework for training large language models (LLMs) to perform structured reasoning over both relational and graph-structured data. Our approach jointly optimizes Text-to-SQL and Text-to-Cypher tasks using reinforcement learning (RL) combined with Chain-of-Thought (CoT) supervision. To support fine-grained optimization in graph-based parsing, we introduce a topology-aware reward function based on graph edit distance. Unlike prior work that treats relational and graph formalisms in isolation, STRuCT-LLM leverages shared abstractions between SQL and Cypher to induce cross-formalism transfer, enabling SQL training to improve Cypher performance and vice versa - even without shared schemas. Our largest model (QwQ-32B) achieves substantial relative improvements across tasks: on semantic parsing, Spider improves by 13.5\% and Text2Cypher by 73.1\%. The model also demonstrates strong zero-shot generalization, improving performance on downstream tabular QA (TableBench: 8.5\%) and knowledge graph QA (CR-LT-KGQA: 1.7\%) without any QA-specific supervision. These results demonstrate both the effectiveness of executable queries as scaffolds for structured reasoning and the synergistic benefits of jointly training on SQL and Cypher (code available at https://github.com/bouv/STRuCT-LLM).

Graph transformers (GTs) have emerged as a promising architecture that is theoretically more expressive than message-passing graph neural networks (GNNs). However, typical GT models have at least quadratic complexity and thus cannot scale to large graphs. While there are several linear GTs recently proposed, they still lag behind GNN counterparts on several popular graph datasets, which poses a critical concern on their practical expressivity. To balance the trade-off between expressivity and scalability of GTs, we propose Polynormer, a polynomial-expressive GT model with linear complexity. Polynormer is built upon a novel base model that learns a high-degree polynomial on input features. To enable the base model permutation equivariant, we integrate it with graph topology and node features separately, resulting in local and global equivariant attention models. Consequently, Polynormer adopts a linear local-to-global attention scheme to learn high-degree equivariant polynomials whose coefficients are controlled by attention scores. Polynormer has been evaluated on 13 homophilic and heterophilic datasets, including large graphs with millions of nodes. Our extensive experiment results show that Polynormer outperforms state-of-the-art GNN and GT baselines on most datasets, even without the use of nonlinear activation functions.

Graph-to-text generation has benefited from pre-trained language models (PLMs) in achieving better performance than structured graph encoders. However, they fail to fully utilize the structure information of the input graph. In this paper, we aim to further improve the performance of the pre-trained language model by proposing a structured graph-to-text model with a two-step fine-tuning mechanism which first fine-tunes the model on Wikipedia before adapting to the graph-to-text generation. In addition to using the traditional token and position embeddings to encode the knowledge graph (KG), we propose a novel tree-level embedding method to capture the inter-dependency structures of the input graph. This new approach has significantly improved the performance of all text generation metrics for the English WebNLG 2017 dataset.

Programming language processing (similar to natural language processing) is a hot research topic in the field of software engineering; it has also aroused growing interest in the artificial intelligence community. However, different from a natural language sentence, a program contains rich, explicit, and complicated structural information. Hence, traditional NLP models may be inappropriate for programs. In this paper, we propose a novel tree-based convolutional neural network (TBCNN) for programming language processing, in which a convolution kernel is designed over programs' abstract syntax trees to capture structural information. TBCNN is a generic architecture for programming language processing; our experiments show its effectiveness in two different program analysis tasks: classifying programs according to functionality, and detecting code snippets of certain patterns. TBCNN outperforms baseline methods, including several neural models for NLP.

The ability to accurately represent sentences is central to language understanding. We describe a convolutional architecture dubbed the Dynamic Convolutional Neural Network (DCNN) that we adopt for the semantic modelling of sentences. The network uses Dynamic k-Max Pooling, a global pooling operation over linear sequences. The network handles input sentences of varying length and induces a feature graph over the sentence that is capable of explicitly capturing short and long-range relations. The network does not rely on a parse tree and is easily applicable to any language. We test the DCNN in four experiments: small scale binary and multi-class sentiment prediction, six-way question classification and Twitter sentiment prediction by distant supervision. The network achieves excellent performance in the first three tasks and a greater than 25% error reduction in the last task with respect to the strongest baseline.

Semantic matching is of central importance to many natural language tasks bordes2014semantic,RetrievalQA. A successful matching algorithm needs to adequately model the internal structures of language objects and the interaction between them. As a step toward this goal, we propose convolutional neural network models for matching two sentences, by adapting the convolutional strategy in vision and speech. The proposed models not only nicely represent the hierarchical structures of sentences with their layer-by-layer composition and pooling, but also capture the rich matching patterns at different levels. Our models are rather generic, requiring no prior knowledge on language, and can hence be applied to matching tasks of different nature and in different languages. The empirical study on a variety of matching tasks demonstrates the efficacy of the proposed model on a variety of matching tasks and its superiority to competitor models.

We propose a recipe on how to build a general, powerful, scalable (GPS) graph Transformer with linear complexity and state-of-the-art results on a diverse set of benchmarks. Graph Transformers (GTs) have gained popularity in the field of graph representation learning with a variety of recent publications but they lack a common foundation about what constitutes a good positional or structural encoding, and what differentiates them. In this paper, we summarize the different types of encodings with a clearer definition and categorize them as being local, global or relative. The prior GTs are constrained to small graphs with a few hundred nodes, here we propose the first architecture with a complexity linear in the number of nodes and edges O(N+E) by decoupling the local real-edge aggregation from the fully-connected Transformer. We argue that this decoupling does not negatively affect the expressivity, with our architecture being a universal function approximator on graphs. Our GPS recipe consists of choosing 3 main ingredients: (i) positional/structural encoding, (ii) local message-passing mechanism, and (iii) global attention mechanism. We provide a modular framework GraphGPS that supports multiple types of encodings and that provides efficiency and scalability both in small and large graphs. We test our architecture on 16 benchmarks and show highly competitive results in all of them, show-casing the empirical benefits gained by the modularity and the combination of different strategies.

We tackle NED by comparing entities in short sentences with graphs. Creating a context vector from graphs through deep learning is a challenging problem that has never been applied to NED. Our main contribution is to present an experimental study of recent neural techniques, as well as a discussion about which graph features are most important for the disambiguation task. In addition, a new dataset () is created to allow a clean and scalable evaluation of NED with entries, and to be used as a reference in future research. In the end our results show that a Bi-LSTM encoding of the graph triplets performs best, improving upon the baseline models and scoring an F1 value of 91.6% on the test set

Deep learning has revolutionized many machine learning tasks in recent years, ranging from image classification and video processing to speech recognition and natural language understanding. The data in these tasks are typically represented in the Euclidean space. However, there is an increasing number of applications where data are generated from non-Euclidean domains and are represented as graphs with complex relationships and interdependency between objects. The complexity of graph data has imposed significant challenges on existing machine learning algorithms. Recently, many studies on extending deep learning approaches for graph data have emerged. In this survey, we provide a comprehensive overview of graph neural networks (GNNs) in data mining and machine learning fields. We propose a new taxonomy to divide the state-of-the-art graph neural networks into four categories, namely recurrent graph neural networks, convolutional graph neural networks, graph autoencoders, and spatial-temporal graph neural networks. We further discuss the applications of graph neural networks across various domains and summarize the open source codes, benchmark data sets, and model evaluation of graph neural networks. Finally, we propose potential research directions in this rapidly growing field.

There are two major classes of natural language grammar -- the dependency grammar that models one-to-one correspondences between words and the constituency grammar that models the assembly of one or several corresponded words. While previous unsupervised parsing methods mostly focus on only inducing one class of grammars, we introduce a novel model, StructFormer, that can simultaneously induce dependency and constituency structure. To achieve this, we propose a new parsing framework that can jointly generate a constituency tree and dependency graph. Then we integrate the induced dependency relations into the transformer, in a differentiable manner, through a novel dependency-constrained self-attention mechanism. Experimental results show that our model can achieve strong results on unsupervised constituency parsing, unsupervised dependency parsing, and masked language modeling at the same time.

Advances in Visually Rich Document Understanding (VrDU) have enabled information extraction and question answering over documents with complex layouts. Two tropes of architectures have emerged -- transformer-based models inspired by LLMs, and Graph Neural Networks. In this paper, we introduce DocGraphLM, a novel framework that combines pre-trained language models with graph semantics. To achieve this, we propose 1) a joint encoder architecture to represent documents, and 2) a novel link prediction approach to reconstruct document graphs. DocGraphLM predicts both directions and distances between nodes using a convergent joint loss function that prioritizes neighborhood restoration and downweighs distant node detection. Our experiments on three SotA datasets show consistent improvement on IE and QA tasks with the adoption of graph features. Moreover, we report that adopting the graph features accelerates convergence in the learning process during training, despite being solely constructed through link prediction.

Relational pooling is a framework for building more expressive and permutation-invariant graph neural networks. However, there is limited understanding of the exact enhancement in the expressivity of RP and its connection with the Weisfeiler Lehman hierarchy. Starting from RP, we propose to explicitly assign labels to nodes as additional features to improve expressive power of message passing neural networks. The method is then extended to higher dimensional WL, leading to a novel k,l-WL algorithm, a more general framework than k-WL. Theoretically, we analyze the expressivity of k,l-WL with respect to k and l and unifies it with a great number of subgraph GNNs. Complexity reduction methods are also systematically discussed to build powerful and practical k,l-GNN instances. We theoretically and experimentally prove that our method is universally compatible and capable of improving the expressivity of any base GNN model. Our k,l-GNNs achieve superior performance on many synthetic and real-world datasets, which verifies the effectiveness of our framework.

Large Language Models (LLMs) have demonstrated remarkable generalization and instruction-following capabilities with instruction tuning. The advancements in LLMs and instruction tuning have led to the development of Large Vision-Language Models (LVLMs). However, the competency of the LLMs and instruction tuning have been less explored in the molecular domain. Thus, we propose LLaMo: Large Language Model-based Molecular graph assistant, which is an end-to-end trained large molecular graph-language model. To bridge the discrepancy between the language and graph modalities, we present the multi-level graph projector that transforms graph representations into graph tokens by abstracting the output representations of each GNN layer and motif representations with the cross-attention mechanism. We also introduce machine-generated molecular graph instruction data to instruction-tune the large molecular graph-language model for general-purpose molecule and language understanding. Our extensive experiments demonstrate that LLaMo shows the best performance on diverse tasks, such as molecular description generation, property prediction, and IUPAC name prediction. The code of LLaMo is available at https://github.com/mlvlab/LLaMo.

In the field of deep learning, Graph Neural Networks (GNNs) and Graph Transformer models, with their outstanding performance and flexible architectural designs, have become leading technologies for processing structured data, especially graph data. Traditional GNNs often face challenges in capturing information from distant vertices effectively. In contrast, Graph Transformer models are particularly adept at managing long-distance node relationships. Despite these advantages, Graph Transformer models still encounter issues with computational and storage efficiency when scaled to large graph datasets. To address these challenges, we propose an innovative Graph Neural Network (GNN) architecture that integrates a Top-m attention mechanism aggregation component and a neighborhood aggregation component, effectively enhancing the model's ability to aggregate relevant information from both local and extended neighborhoods at each layer. This method not only improves computational efficiency but also enriches the node features, facilitating a deeper analysis of complex graph structures. Additionally, to assess the effectiveness of our proposed model, we have applied it to citation sentiment prediction, a novel task previously unexplored in the GNN field. Accordingly, we constructed a dedicated citation network, ArXivNet. In this dataset, we specifically annotated the sentiment polarity of the citations (positive, neutral, negative) to enable in-depth sentiment analysis. Our approach has shown superior performance across a variety of tasks including vertex classification, link prediction, sentiment prediction, graph regression, and visualization. It outperforms existing methods in terms of effectiveness, as demonstrated by experimental results on multiple datasets.

Parsing sentences into syntax trees can benefit downstream applications in NLP. Transition-based parsers build trees by executing actions in a state transition system. They are computationally efficient, and can leverage machine learning to predict actions based on partial trees. However, existing transition-based parsers are predominantly based on the shift-reduce transition system, which does not align with how humans are known to parse sentences. Psycholinguistic research suggests that human parsing is strongly incremental: humans grow a single parse tree by adding exactly one token at each step. In this paper, we propose a novel transition system called attach-juxtapose. It is strongly incremental; it represents a partial sentence using a single tree; each action adds exactly one token into the partial tree. Based on our transition system, we develop a strongly incremental parser. At each step, it encodes the partial tree using a graph neural network and predicts an action. We evaluate our parser on Penn Treebank (PTB) and Chinese Treebank (CTB). On PTB, it outperforms existing parsers trained with only constituency trees; and it performs on par with state-of-the-art parsers that use dependency trees as additional training data. On CTB, our parser establishes a new state of the art. Code is available at https://github.com/princeton-vl/attach-juxtapose-parser.

We present DeepWalk, a novel approach for learning latent representations of vertices in a network. These latent representations encode social relations in a continuous vector space, which is easily exploited by statistical models. DeepWalk generalizes recent advancements in language modeling and unsupervised feature learning (or deep learning) from sequences of words to graphs. DeepWalk uses local information obtained from truncated random walks to learn latent representations by treating walks as the equivalent of sentences. We demonstrate DeepWalk's latent representations on several multi-label network classification tasks for social networks such as BlogCatalog, Flickr, and YouTube. Our results show that DeepWalk outperforms challenging baselines which are allowed a global view of the network, especially in the presence of missing information. DeepWalk's representations can provide F_1 scores up to 10% higher than competing methods when labeled data is sparse. In some experiments, DeepWalk's representations are able to outperform all baseline methods while using 60% less training data. DeepWalk is also scalable. It is an online learning algorithm which builds useful incremental results, and is trivially parallelizable. These qualities make it suitable for a broad class of real world applications such as network classification, and anomaly detection.

It is always well believed that modeling relationships between objects would be helpful for representing and eventually describing an image. Nevertheless, there has not been evidence in support of the idea on image description generation. In this paper, we introduce a new design to explore the connections between objects for image captioning under the umbrella of attention-based encoder-decoder framework. Specifically, we present Graph Convolutional Networks plus Long Short-Term Memory (dubbed as GCN-LSTM) architecture that novelly integrates both semantic and spatial object relationships into image encoder. Technically, we build graphs over the detected objects in an image based on their spatial and semantic connections. The representations of each region proposed on objects are then refined by leveraging graph structure through GCN. With the learnt region-level features, our GCN-LSTM capitalizes on LSTM-based captioning framework with attention mechanism for sentence generation. Extensive experiments are conducted on COCO image captioning dataset, and superior results are reported when comparing to state-of-the-art approaches. More remarkably, GCN-LSTM increases CIDEr-D performance from 120.1% to 128.7% on COCO testing set.

The existing definitions of graph convolution, either from spatial or spectral perspectives, are inflexible and not unified. Defining a general convolution operator in the graph domain is challenging due to the lack of canonical coordinates, the presence of irregular structures, and the properties of graph symmetries. In this work, we propose a novel and general graph convolution framework by parameterizing the kernels as continuous functions of pseudo-coordinates derived via graph positional encoding. We name this Continuous Kernel Graph Convolution (CKGConv). Theoretically, we demonstrate that CKGConv is flexible and expressive. CKGConv encompasses many existing graph convolutions, and exhibits a stronger expressiveness, as powerful as graph transformers in terms of distinguishing non-isomorphic graphs. Empirically, we show that CKGConv-based Networks outperform existing graph convolutional networks and perform comparably to the best graph transformers across a variety of graph datasets. The code and models are publicly available at https://github.com/networkslab/CKGConv.

We present an approach to modifying Transformer architectures by integrating graph-aware relational reasoning into the attention mechanism, merging concepts from graph neural networks and language modeling. Building on the inherent connection between attention and graph theory, we reformulate the Transformer's attention mechanism as a graph operation and propose Graph-Aware Isomorphic Attention. This method leverages advanced graph modeling strategies, including Graph Isomorphism Networks (GIN) and Principal Neighborhood Aggregation (PNA), to enrich the representation of relational structures. Our approach captures complex dependencies and generalizes across tasks, as evidenced by a reduced generalization gap and improved learning performance. Additionally, we expand the concept of graph-aware attention to introduce Sparse GIN-Attention, a fine-tuning approach that employs sparse GINs. By interpreting attention matrices as sparse adjacency graphs, this technique enhances the adaptability of pre-trained foundational models with minimal computational overhead, endowing them with graph-aware capabilities. Sparse GIN-Attention fine-tuning achieves improved training dynamics and better generalization compared to alternative methods like low-rank adaption (LoRA). We discuss latent graph-like structures within traditional attention mechanisms, offering a new lens through which Transformers can be understood. By evolving Transformers as hierarchical GIN models for relational reasoning. This perspective suggests profound implications for foundational model development, enabling the design of architectures that dynamically adapt to both local and global dependencies. Applications in bioinformatics, materials science, language modeling, and beyond could benefit from this synthesis of relational and sequential data modeling, setting the stage for interpretable and generalizable modeling strategies.

Recent research on integrating Large Language Models (LLMs) with Graph Neural Networks (GNNs) typically follows two approaches: LLM-centered models, which convert graph data into tokens for LLM processing, and GNN-centered models, which use LLMs to encode text features into node and edge representations for GNN input. LLM-centered models often struggle to capture graph structures effectively, while GNN-centered models compress variable-length textual data into fixed-size vectors, limiting their ability to understand complex semantics. Additionally, GNN-centered approaches require converting tasks into a uniform, manually-designed format, restricting them to classification tasks and preventing language output. To address these limitations, we introduce a new architecture that deeply integrates GNN with LLM, featuring three key innovations: (1) Structure-Aware Transformers, which incorporate GNN's message-passing capabilities directly into LLM's transformer layers, allowing simultaneous processing of textual and structural information and generating outputs from both GNN and LLM; (2) Graph-Text Cross-Attention, which processes full, uncompressed text from graph nodes and edges, ensuring complete semantic integration; and (3) GNN-LLM Twin Predictor, enabling LLM's flexible autoregressive generation alongside GNN's scalable one-pass prediction. GL-Fusion achieves outstand performance on various tasks. Notably, it achieves state-of-the-art performance on OGBN-Arxiv and OGBG-Code2.

Understanding which information is encoded in deep models of spoken and written language has been the focus of much research in recent years, as it is crucial for debugging and improving these architectures. Most previous work has focused on probing for speaker characteristics, acoustic and phonological information in models of spoken language, and for syntactic information in models of written language. Here we focus on the encoding of syntax in several self-supervised and visually grounded models of spoken language. We employ two complementary probing methods, combined with baselines and reference representations to quantify the degree to which syntactic structure is encoded in the activations of the target models. We show that syntax is captured most prominently in the middle layers of the networks, and more explicitly within models with more parameters.

Graph Structure Learning (GSL) focuses on capturing intrinsic dependencies and interactions among nodes in graph-structured data by generating novel graph structures. Graph Neural Networks (GNNs) have emerged as promising GSL solutions, utilizing recursive message passing to encode node-wise inter-dependencies. However, many existing GSL methods heavily depend on explicit graph structural information as supervision signals, leaving them susceptible to challenges such as data noise and sparsity. In this work, we propose GraphEdit, an approach that leverages large language models (LLMs) to learn complex node relationships in graph-structured data. By enhancing the reasoning capabilities of LLMs through instruction-tuning over graph structures, we aim to overcome the limitations associated with explicit graph structural information and enhance the reliability of graph structure learning. Our approach not only effectively denoises noisy connections but also identifies node-wise dependencies from a global perspective, providing a comprehensive understanding of the graph structure. We conduct extensive experiments on multiple benchmark datasets to demonstrate the effectiveness and robustness of GraphEdit across various settings. We have made our model implementation available at: https://github.com/HKUDS/GraphEdit.

Search is an ability foundational in many important tasks, and recent studies have shown that large language models (LLMs) struggle to perform search robustly. It is unknown whether this inability is due to a lack of data, insufficient model parameters, or fundamental limitations of the transformer architecture. In this work, we use the foundational graph connectivity problem as a testbed to generate effectively limitless high-coverage data to train small transformers and test whether they can learn to perform search. We find that, when given the right training distribution, the transformer is able to learn to search. We analyze the algorithm that the transformer has learned through a novel mechanistic interpretability technique that enables us to extract the computation graph from the trained model. We find that for each vertex in the input graph, transformers compute the set of vertices reachable from that vertex. Each layer then progressively expands these sets, allowing the model to search over a number of vertices exponential in the number of layers. However, we find that as the input graph size increases, the transformer has greater difficulty in learning the task. This difficulty is not resolved even as the number of parameters is increased, suggesting that increasing model scale will not lead to robust search abilities. We also find that performing search in-context (i.e., chain-of-thought) does not resolve this inability to learn to search on larger graphs.

Automatically describing the content of an image is a fundamental problem in artificial intelligence that connects computer vision and natural language processing. In this paper, we present a generative model based on a deep recurrent architecture that combines recent advances in computer vision and machine translation and that can be used to generate natural sentences describing an image. The model is trained to maximize the likelihood of the target description sentence given the training image. Experiments on several datasets show the accuracy of the model and the fluency of the language it learns solely from image descriptions. Our model is often quite accurate, which we verify both qualitatively and quantitatively. Finally, given the recent surge of interest in this task, a competition was organized in 2015 using the newly released COCO dataset. We describe and analyze the various improvements we applied to our own baseline and show the resulting performance in the competition, which we won ex-aequo with a team from Microsoft Research, and provide an open source implementation in TensorFlow.

Graph representation learning has emerged as a powerful technique for addressing real-world problems. Various downstream graph learning tasks have benefited from its recent developments, such as node classification, similarity search, and graph classification. However, prior arts on graph representation learning focus on domain specific problems and train a dedicated model for each graph dataset, which is usually non-transferable to out-of-domain data. Inspired by the recent advances in pre-training from natural language processing and computer vision, we design Graph Contrastive Coding (GCC) -- a self-supervised graph neural network pre-training framework -- to capture the universal network topological properties across multiple networks. We design GCC's pre-training task as subgraph instance discrimination in and across networks and leverage contrastive learning to empower graph neural networks to learn the intrinsic and transferable structural representations. We conduct extensive experiments on three graph learning tasks and ten graph datasets. The results show that GCC pre-trained on a collection of diverse datasets can achieve competitive or better performance to its task-specific and trained-from-scratch counterparts. This suggests that the pre-training and fine-tuning paradigm presents great potential for graph representation learning.

The advancement of Large Language Models (LLMs) has remarkably pushed the boundaries towards artificial general intelligence (AGI), with their exceptional ability on understanding diverse types of information, including but not limited to images and audio. Despite this progress, a critical gap remains in empowering LLMs to proficiently understand and reason on graph data. Recent studies underscore LLMs' underwhelming performance on fundamental graph reasoning tasks. In this paper, we endeavor to unearth the obstacles that impede LLMs in graph reasoning, pinpointing the common practice of converting graphs into natural language descriptions (Graph2Text) as a fundamental bottleneck. To overcome this impediment, we introduce GraphLLM, a pioneering end-to-end approach that synergistically integrates graph learning models with LLMs. This synergy equips LLMs with the ability to proficiently interpret and reason on graph data, harnessing the superior expressive power of graph learning models. Our empirical evaluations across four fundamental graph reasoning tasks validate the effectiveness of GraphLLM. The results exhibit a substantial average accuracy enhancement of 54.44%, alongside a noteworthy context reduction of 96.45% across various graph reasoning tasks.

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.

Although Large Language Models (LLMs) have demonstrated remarkable progress, their proficiency in graph-related tasks remains notably limited, hindering the development of truly general-purpose models. Previous attempts, including pretraining graph foundation models or employing supervised fine-tuning, often face challenges such as the scarcity of large-scale, universally represented graph data. We introduce G1, a simple yet effective approach demonstrating that Reinforcement Learning (RL) on synthetic graph-theoretic tasks can significantly scale LLMs' graph reasoning abilities. To enable RL training, we curate Erd\~os, the largest graph reasoning dataset to date comprising 50 diverse graph-theoretic tasks of varying difficulty levels, 100k training data and 5k test data, all drived from real-world graphs. With RL on Erd\~os, G1 obtains substantial improvements in graph reasoning, where our finetuned 3B model even outperforms Qwen2.5-72B-Instruct (24x size). RL-trained models also show strong zero-shot generalization to unseen tasks, domains, and graph encoding schemes, including other graph-theoretic benchmarks as well as real-world node classification and link prediction tasks, without compromising general reasoning abilities. Our findings offer an efficient, scalable path for building strong graph reasoners by finetuning LLMs with RL on graph-theoretic tasks, which combines the strengths of pretrained LLM capabilities with abundant, automatically generated synthetic data, suggesting that LLMs possess graph understanding abilities that RL can elicit successfully.

Graph-structured data are the commonly used and have wide application scenarios in the real world. For these diverse applications, the vast variety of learning tasks, graph domains, and complex graph learning procedures present challenges for human experts when designing versatile graph learning approaches. Facing these challenges, large language models (LLMs) offer a potential solution due to the extensive knowledge and the human-like intelligence. This paper proposes a novel conceptual prototype for designing versatile graph learning methods with LLMs, with a particular focus on the "where" and "how" perspectives. From the "where" perspective, we summarize four key graph learning procedures, including task definition, graph data feature engineering, model selection and optimization, deployment and serving. We then explore the application scenarios of LLMs in these procedures across a wider spectrum. In the "how" perspective, we align the abilities of LLMs with the requirements of each procedure. Finally, we point out the promising directions that could better leverage the strength of LLMs towards versatile graph learning methods.

Attention-based graph neural networks (GNNs), such as graph attention networks (GATs), have become popular neural architectures for processing graph-structured data and learning node embeddings. Despite their empirical success, these models rely on labeled data and the theoretical properties of these models have yet to be fully understood. In this work, we propose a novel attention-based node embedding framework for graphs. Our framework builds upon a hierarchical kernel for multisets of subgraphs around nodes (e.g. neighborhoods) and each kernel leverages the geometry of a smooth statistical manifold to compare pairs of multisets, by "projecting" the multisets onto the manifold. By explicitly computing node embeddings with a manifold of Gaussian mixtures, our method leads to a new attention mechanism for neighborhood aggregation. We provide theoretical insights into generalizability and expressivity of our embeddings, contributing to a deeper understanding of attention-based GNNs. We propose both efficient unsupervised and supervised methods for learning the embeddings. Through experiments on several node classification benchmarks, we demonstrate that our proposed method outperforms existing attention-based graph models like GATs. Our code is available at https://github.com/BorgwardtLab/fisher_information_embedding.

Graph Convolutional Networks (GCN) have achieved state-of-art results on single text classification tasks like sentiment analysis, emotion detection, etc. However, the performance is achieved by testing and reporting on resource-rich languages like English. Applying GCN for multi-task text classification is an unexplored area. Moreover, training a GCN or adopting an English GCN for Indian languages is often limited by data availability, rich morphological variation, syntax, and semantic differences. In this paper, we study the use of GCN for the Telugu language in single and multi-task settings for four natural language processing (NLP) tasks, viz. sentiment analysis (SA), emotion identification (EI), hate-speech (HS), and sarcasm detection (SAR). In order to evaluate the performance of GCN with one of the Indian languages, Telugu, we analyze the GCN based models with extensive experiments on four downstream tasks. In addition, we created an annotated Telugu dataset, TEL-NLP, for the four NLP tasks. Further, we propose a supervised graph reconstruction method, Multi-Task Text GCN (MT-Text GCN) on the Telugu that leverages to simultaneously (i) learn the low-dimensional word and sentence graph embeddings from word-sentence graph reconstruction using graph autoencoder (GAE) and (ii) perform multi-task text classification using these latent sentence graph embeddings. We argue that our proposed MT-Text GCN achieves significant improvements on TEL-NLP over existing Telugu pretrained word embeddings, and multilingual pretrained Transformer models: mBERT, and XLM-R. On TEL-NLP, we achieve a high F1-score for four NLP tasks: SA (0.84), EI (0.55), HS (0.83) and SAR (0.66). Finally, we show our model's quantitative and qualitative analysis on the four NLP tasks in Telugu.

Abstract meaning representation (AMR) highlights the core semantic information of text in a graph structure. Recently, pre-trained language models (PLMs) have advanced tasks of AMR parsing and AMR-to-text generation, respectively. However, PLMs are typically pre-trained on textual data, thus are sub-optimal for modeling structural knowledge. To this end, we investigate graph self-supervised training to improve the structure awareness of PLMs over AMR graphs. In particular, we introduce two graph auto-encoding strategies for graph-to-graph pre-training and four tasks to integrate text and graph information during pre-training. We further design a unified framework to bridge the gap between pre-training and fine-tuning tasks. Experiments on both AMR parsing and AMR-to-text generation show the superiority of our model. To our knowledge, we are the first to consider pre-training on semantic graphs.

The Transformer architecture has become a dominant choice in many domains, such as natural language processing and computer vision. Yet, it has not achieved competitive performance on popular leaderboards of graph-level prediction compared to mainstream GNN variants. Therefore, it remains a mystery how Transformers could perform well for graph representation learning. In this paper, we solve this mystery by presenting Graphormer, which is built upon the standard Transformer architecture, and could attain excellent results on a broad range of graph representation learning tasks, especially on the recent OGB Large-Scale Challenge. Our key insight to utilizing Transformer in the graph is the necessity of effectively encoding the structural information of a graph into the model. To this end, we propose several simple yet effective structural encoding methods to help Graphormer better model graph-structured data. Besides, we mathematically characterize the expressive power of Graphormer and exhibit that with our ways of encoding the structural information of graphs, many popular GNN variants could be covered as the special cases of Graphormer.

This work studies self-supervised graph learning for text-attributed graphs (TAGs) where nodes are represented by textual attributes. Unlike traditional graph contrastive methods that perturb the numerical feature space and alter the graph's topological structure, we aim to improve view generation through language supervision. This is driven by the prevalence of textual attributes in real applications, which complement graph structures with rich semantic information. However, this presents challenges because of two major reasons. First, text attributes often vary in length and quality, making it difficulty to perturb raw text descriptions without altering their original semantic meanings. Second, although text attributes complement graph structures, they are not inherently well-aligned. To bridge the gap, we introduce GAugLLM, a novel framework for augmenting TAGs. It leverages advanced large language models like Mistral to enhance self-supervised graph learning. Specifically, we introduce a mixture-of-prompt-expert technique to generate augmented node features. This approach adaptively maps multiple prompt experts, each of which modifies raw text attributes using prompt engineering, into numerical feature space. Additionally, we devise a collaborative edge modifier to leverage structural and textual commonalities, enhancing edge augmentation by examining or building connections between nodes. Empirical results across five benchmark datasets spanning various domains underscore our framework's ability to enhance the performance of leading contrastive methods as a plug-in tool. Notably, we observe that the augmented features and graph structure can also enhance the performance of standard generative methods, as well as popular graph neural networks. The open-sourced implementation of our GAugLLM is available at Github.

We introduce the MultiLang Code Parser Dataset (MLCPD), a large-scale, language-agnostic dataset unifying syntactic and structural representations of code across ten major programming languages. MLCPD contains over seven million parsed source files normalized under our proposed universal Abstract Syntax Tree (AST) schema, enabling consistent cross-language reasoning, structural learning, and multilingual software analysis. Unlike existing corpora that focus purely on token-level code or isolated parsers, MLCPD provides both hierarchical tree representations and rich metadata for every file, ensuring lossless syntactic coverage and structural uniformity. Each entry includes a normalized schema, language-level metadata, and abstracted node semantics stored in Parquet format for scalable retrieval. Empirical analyses reveal strong cross-language structural regularities-demonstrating that syntactic graphs from languages as diverse as Python, Java, and Go can be aligned under a shared schema. We release the dataset publicly on Hugging Face and the accompanying codebase on GitHub, which includes complete pipelines for dataset reproduction, grammar compilation, and a visualization tool for exploring the unified AST across languages. Together, these resources establish MLCPD as an open, reproducible foundation for future research in cross-language representation learning and program analysis.

The combination of strong visual backbones and Large Language Model (LLM) reasoning has led to Large Multimodal Models (LMMs) becoming the current standard for a wide range of vision and language (VL) tasks. However, recent research has shown that even the most advanced LMMs still struggle to capture aspects of compositional visual reasoning, such as attributes and relationships between objects. One solution is to utilize scene graphs (SGs)--a formalization of objects and their relations and attributes that has been extensively used as a bridge between the visual and textual domains. Yet, scene graph data requires scene graph annotations, which are expensive to collect and thus not easily scalable. Moreover, finetuning an LMM based on SG data can lead to catastrophic forgetting of the pretraining objective. To overcome this, inspired by chain-of-thought methods, we propose Compositional Chain-of-Thought (CCoT), a novel zero-shot Chain-of-Thought prompting method that utilizes SG representations in order to extract compositional knowledge from an LMM. Specifically, we first generate an SG using the LMM, and then use that SG in the prompt to produce a response. Through extensive experiments, we find that the proposed CCoT approach not only improves LMM performance on several vision and language VL compositional benchmarks but also improves the performance of several popular LMMs on general multimodal benchmarks, without the need for fine-tuning or annotated ground-truth SGs. Code: https://github.com/chancharikmitra/CCoT

We introduce GraphNet, a dataset of 2.7K real-world deep learning computational graphs with rich metadata, spanning six major task categories across multiple deep learning frameworks. To evaluate tensor compiler performance on these samples, we propose the benchmark metric Speedup Score S(t), which jointly considers runtime speedup and execution correctness under tunable tolerance levels, offering a reliable measure of general optimization capability. Furthermore, we extend S(t) to the Error-aware Speedup Score ES(t), which incorporates error information and helps compiler developers identify key performance bottlenecks. In this report, we benchmark the default tensor compilers, CINN for PaddlePaddle and TorchInductor for PyTorch, on computer vision (CV) and natural language processing (NLP) samples to demonstrate the practicality of GraphNet. The full construction pipeline with graph extraction and compiler evaluation tools is available at https://github.com/PaddlePaddle/GraphNet .

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.

Visual grounding is a ubiquitous building block in many vision-language tasks and yet remains challenging due to large variations in visual and linguistic features of grounding entities, strong context effect and the resulting semantic ambiguities. Prior works typically focus on learning representations of individual phrases with limited context information. To address their limitations, this paper proposes a language-guided graph representation to capture the global context of grounding entities and their relations, and develop a cross-modal graph matching strategy for the multiple-phrase visual grounding task. In particular, we introduce a modular graph neural network to compute context-aware representations of phrases and object proposals respectively via message propagation, followed by a graph-based matching module to generate globally consistent localization of grounding phrases. We train the entire graph neural network jointly in a two-stage strategy and evaluate it on the Flickr30K Entities benchmark. Extensive experiments show that our method outperforms the prior state of the arts by a sizable margin, evidencing the efficacy of our grounding framework. Code is available at "https://github.com/youngfly11/LCMCG-PyTorch".

Transformers serve as the backbone architectures of Foundational Models, where a domain-specific tokenizer helps them adapt to various domains. Graph Transformers (GTs) have recently emerged as a leading model in geometric deep learning, outperforming Graph Neural Networks (GNNs) in various graph learning tasks. However, the development of tokenizers for graphs has lagged behind other modalities, with existing approaches relying on heuristics or GNNs co-trained with Transformers. To address this, we introduce GQT (Graph Quantized Tokenizer), which decouples tokenizer training from Transformer training by leveraging multi-task graph self-supervised learning, yielding robust and generalizable graph tokens. Furthermore, the GQT utilizes Residual Vector Quantization (RVQ) to learn hierarchical discrete tokens, resulting in significantly reduced memory requirements and improved generalization capabilities. By combining the GQT with token modulation, a Transformer encoder achieves state-of-the-art performance on 16 out of 18 benchmarks, including large-scale homophilic and heterophilic datasets. The code is available at: https://github.com/limei0307/graph-tokenizer

We propose a simple approach for weighting self-connecting edges in a Graph Convolutional Network (GCN) and show its impact on depression detection from transcribed clinical interviews. To this end, we use a GCN for modeling non-consecutive and long-distance semantics to classify the transcriptions into depressed or control subjects. The proposed method aims to mitigate the limiting assumptions of locality and the equal importance of self-connections vs. edges to neighboring nodes in GCNs, while preserving attractive features such as low computational cost, data agnostic, and interpretability capabilities. We perform an exhaustive evaluation in two benchmark datasets. Results show that our approach consistently outperforms the vanilla GCN model as well as previously reported results, achieving an F1=0.84 on both datasets. Finally, a qualitative analysis illustrates the interpretability capabilities of the proposed approach and its alignment with previous findings in psychology.

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.

We introduceGraphGPT, a novel self-supervised generative pre-trained model for graph learning based on the Graph Eulerian Transformer (GET). First, we propose GET, which combines a standard transformer encoder or decoder architecture with an innovative graph-to-sequence transformation method. This method converts graphs or sampled subgraphs into sequences of tokens representing nodes, edges, and attributes in a reversible manner using Eulerian paths. We pre-train GET using either of the two self-supervised tasks: next-token prediction (NTP) and scheduled masked-token prediction (SMTP). The pre-trained model is then fine-tuned for downstream tasks such as graph-, edge-, and node-level prediction. Despite its simplicity, GraphGPT achieves performance comparable to or surpassing state-of-the-art methods on multiple large-scale Open Graph Benchmark (OGB) datasets. It demonstrates exceptional results on the molecular property prediction dataset PCQM4Mv2 and the protein-protein interaction dataset ogbl-ppa. Notably, generative pre-training enables scaling GraphGPT to 2 billion parameters while maintaining performance gains - a breakthrough that overcomes the scalability limitations of traditional Graph Neural Networks (GNNs) and prior graph transformers (GTs). To advance research in graph foundation models and facilitate scientific discovery in chemistry, materials science, and related fields, we will release the source code (https://github.com/alibaba/graph-gpt) and pre-trained checkpoints.

Universal Dependencies is an open community effort to create cross-linguistically consistent treebank annotation for many languages within a dependency-based lexicalist framework. The annotation consists in a linguistically motivated word segmentation; a morphological layer comprising lemmas, universal part-of-speech tags, and standardized morphological features; and a syntactic layer focusing on syntactic relations between predicates, arguments and modifiers. In this paper, we describe version 2 of the guidelines (UD v2), discuss the major changes from UD v1 to UD v2, and give an overview of the currently available treebanks for 90 languages.

This paper introduces Graph Convolutional Recurrent Network (GCRN), a deep learning model able to predict structured sequences of data. Precisely, GCRN is a generalization of classical recurrent neural networks (RNN) to data structured by an arbitrary graph. Such structured sequences can represent series of frames in videos, spatio-temporal measurements on a network of sensors, or random walks on a vocabulary graph for natural language modeling. The proposed model combines convolutional neural networks (CNN) on graphs to identify spatial structures and RNN to find dynamic patterns. We study two possible architectures of GCRN, and apply the models to two practical problems: predicting moving MNIST data, and modeling natural language with the Penn Treebank dataset. Experiments show that exploiting simultaneously graph spatial and dynamic information about data can improve both precision and learning speed.

Humans describe complex scenes with compositionality, using simple text descriptions enriched with links and relationships. While vision-language research has aimed to develop models with compositional understanding capabilities, this is not reflected yet in existing datasets which, for the most part, still use plain text to describe images. In this work, we propose a new annotation strategy, graph-based captioning (GBC) that describes an image using a labelled graph structure, with nodes of various types. The nodes in GBC are created using, in a first stage, object detection and dense captioning tools nested recursively to uncover and describe entity nodes, further linked together in a second stage by highlighting, using new types of nodes, compositions and relations among entities. Since all GBC nodes hold plain text descriptions, GBC retains the flexibility found in natural language, but can also encode hierarchical information in its edges. We demonstrate that GBC can be produced automatically, using off-the-shelf multimodal LLMs and open-vocabulary detection models, by building a new dataset, GBC10M, gathering GBC annotations for about 10M images of the CC12M dataset. We use GBC10M to showcase the wealth of node captions uncovered by GBC, as measured with CLIP training. We show that using GBC nodes' annotations -- notably those stored in composition and relation nodes -- results in significant performance boost on downstream models when compared to other dataset formats. To further explore the opportunities provided by GBC, we also propose a new attention mechanism that can leverage the entire GBC graph, with encouraging experimental results that show the extra benefits of incorporating the graph structure. Our datasets are released at https://huggingface.co/graph-based-captions.

We present Simplified Text-Attributed Graph Embeddings (STAGE), a straightforward yet effective method for enhancing node features in Graph Neural Network (GNN) models that encode Text-Attributed Graphs (TAGs). Our approach leverages Large-Language Models (LLMs) to generate embeddings for textual attributes. STAGE achieves competitive results on various node classification benchmarks while also maintaining a simplicity in implementation relative to current state-of-the-art (SoTA) techniques. We show that utilizing pre-trained LLMs as embedding generators provides robust features for ensemble GNN training, enabling pipelines that are simpler than current SoTA approaches which require multiple expensive training and prompting stages. We also implement diffusion-pattern GNNs in an effort to make this pipeline scalable to graphs beyond academic benchmarks.

Hypergraph Neural Networks (HGNNs) have recently attracted much attention and exhibited satisfactory performance due to their superiority in high-order correlation modeling. However, it is noticed that the high-order modeling capability of hypergraph also brings increased computation complexity, which hinders its practical industrial deployment. In practice, we find that one key barrier to the efficient deployment of HGNNs is the high-order structural dependencies during inference. In this paper, we propose to bridge the gap between the HGNNs and inference-efficient Multi-Layer Perceptron (MLPs) to eliminate the hypergraph dependency of HGNNs and thus reduce computational complexity as well as improve inference speed. Specifically, we introduce LightHGNN and LightHGNN^+ for fast inference with low complexity. LightHGNN directly distills the knowledge from teacher HGNNs to student MLPs via soft labels, and LightHGNN^+ further explicitly injects reliable high-order correlations into the student MLPs to achieve topology-aware distillation and resistance to over-smoothing. Experiments on eight hypergraph datasets demonstrate that even without hypergraph dependency, the proposed LightHGNNs can still achieve competitive or even better performance than HGNNs and outperform vanilla MLPs by 16.3 on average. Extensive experiments on three graph datasets further show the average best performance of our LightHGNNs compared with all other methods. Experiments on synthetic hypergraphs with 5.5w vertices indicate LightHGNNs can run 100times faster than HGNNs, showcasing their ability for latency-sensitive deployments.

This paper integrates graph-to-sequence into an end-to-end text-to-speech framework for syntax-aware modelling with syntactic information of input text. Specifically, the input text is parsed by a dependency parsing module to form a syntactic graph. The syntactic graph is then encoded by a graph encoder to extract the syntactic hidden information, which is concatenated with phoneme embedding and input to the alignment and flow-based decoding modules to generate the raw audio waveform. The model is experimented on two languages, English and Mandarin, using single-speaker, few samples of target speakers, and multi-speaker datasets, respectively. Experimental results show better prosodic consistency performance between input text and generated audio, and also get higher scores in the subjective prosodic evaluation, and show the ability of voice conversion. Besides, the efficiency of the model is largely boosted through the design of the AI chip operator with 5x acceleration.

Task planning in language agents is emerging as an important research topic alongside the development of large language models (LLMs). It aims to break down complex user requests in natural language into solvable sub-tasks, thereby fulfilling the original requests. In this context, the sub-tasks can be naturally viewed as a graph, where the nodes represent the sub-tasks, and the edges denote the dependencies among them. Consequently, task planning is a decision-making problem that involves selecting a connected path or subgraph within the corresponding graph and invoking it. In this paper, we explore graph learning-based methods for task planning, a direction that is orthogonal to the prevalent focus on prompt design. Our interest in graph learning stems from a theoretical discovery: the biases of attention and auto-regressive loss impede LLMs' ability to effectively navigate decision-making on graphs, which is adeptly addressed by graph neural networks (GNNs). This theoretical insight led us to integrate GNNs with LLMs to enhance overall performance. Extensive experiments demonstrate that GNN-based methods surpass existing solutions even without training, and minimal training can further enhance their performance. The performance gain increases with a larger task graph size.

Graph neural networks (GNNs) learn the representation of graph-structured data, and their expressiveness can be further enhanced by inferring node relations for propagation. Attention-based GNNs infer neighbor importance to manipulate the weight of its propagation. Despite their popularity, the discussion on deep graph attention and its unique challenges has been limited. In this work, we investigate some problematic phenomena related to deep graph attention, including vulnerability to over-smoothed features and smooth cumulative attention. Through theoretical and empirical analyses, we show that various attention-based GNNs suffer from these problems. Motivated by our findings, we propose AEROGNN, a novel GNN architecture designed for deep graph attention. AERO-GNN provably mitigates the proposed problems of deep graph attention, which is further empirically demonstrated with (a) its adaptive and less smooth attention functions and (b) higher performance at deep layers (up to 64). On 9 out of 12 node classification benchmarks, AERO-GNN outperforms the baseline GNNs, highlighting the advantages of deep graph attention. Our code is available at https://github.com/syleeheal/AERO-GNN.