The history of artificial intelligence (AI) has witnessed the significant impact of high-quality data on various deep learning models, such as ImageNet for AlexNet and ResNet. Recently, instead of designing more complex neural architectures as model-centric approaches, the attention of AI community has shifted to data-centric ones, which focuses on better processing data to strengthen the ability of neural models. Graph learning, which operates on ubiquitous topological data, also plays an important role in the era of deep learning. In this survey, we comprehensively review graph learning approaches from the data-centric perspective, and aim to answer three crucial questions: (1) when to modify graph data, (2) what part of the graph data needs modification to unlock the potential of various graph models, and (3) how to safeguard graph models from problematic data influence. Accordingly, we propose a novel taxonomy based on the stages in the graph learning pipeline, and highlight the processing methods for different data structures in the graph data, i.e., topology, feature and label. Furthermore, we analyze some potential problems embedded in graph data and discuss how to solve them in a data-centric manner. Finally, we provide some promising future directions for data-centric graph learning.
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.
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.
Deep neural networks for graphs have emerged as a powerful tool for learning on complex non-euclidean data, which is becoming increasingly common for a variety of different applications. Yet, although their potential has been widely recognised in the machine learning community, graph learning is largely unexplored for downstream tasks such as robotics applications. To fully unlock their potential, hence, we propose a review of graph neural architectures from a robotics perspective. The paper covers the fundamentals of graph-based models, including their architecture, training procedures, and applications. It also discusses recent advancements and challenges that arise in applied settings, related for example to the integration of perception, decision-making, and control. Finally, the paper provides an extensive review of various robotic applications that benefit from learning on graph structures, such as bodies and contacts modelling, robotic manipulation, action recognition, fleet motion planning, and many more. This survey aims to provide readers with a thorough understanding of the capabilities and limitations of graph neural architectures in robotics, and to highlight potential avenues for future research.
Within the graph learning community, conventional wisdom dictates that spectral convolutional networks may only be deployed on undirected graphs: Only there could the existence of a well-defined graph Fourier transform be guaranteed, so that information may be translated between spatial- and spectral domains. Here we show this traditional reliance on the graph Fourier transform to be superfluous and -- making use of certain advanced tools from complex analysis and spectral theory -- extend spectral convolutions to directed graphs. We provide a frequency-response interpretation of newly developed filters, investigate the influence of the basis used to express filters and discuss the interplay with characteristic operators on which networks are based. In order to thoroughly test the developed theory, we conduct experiments in real world settings, showcasing that directed spectral convolutional networks provide new state of the art results for heterophilic node classification on many datasets and -- as opposed to baselines -- may be rendered stable to resolution-scale varying topological perturbations.
It is by now a well known fact in the graph learning community that the presence of bottlenecks severely limits the ability of graph neural networks to propagate information over long distances. What so far has not been appreciated is that, counter-intuitively, also the presence of strongly connected sub-graphs may severely restrict information flow in common architectures. Motivated by this observation, we introduce the concept of multi-scale consistency. At the node level this concept refers to the retention of a connected propagation graph even if connectivity varies over a given graph. At the graph-level, multi-scale consistency refers to the fact that distinct graphs describing the same object at different resolutions should be assigned similar feature vectors. As we show, both properties are not satisfied by poular graph neural network architectures. To remedy these shortcomings, we introduce ResolvNet, a flexible graph neural network based on the mathematical concept of resolvents. We rigorously establish its multi-scale consistency theoretically and verify it in extensive experiments on real world data: Here networks based on this ResolvNet architecture prove expressive; out-performing baselines significantly on many tasks; in- and outside the multi-scale setting.
Temporal heterogeneous networks (THNs) are evolving networks that characterize many real-world applications such as citation and events networks, recommender systems, and knowledge graphs. Although different Graph Neural Networks (GNNs) have been successfully applied to dynamic graphs, most of them only support homogeneous graphs or suffer from model design heavily influenced by specific THNs prediction tasks. Furthermore, there is a lack of temporal heterogeneous networked data in current standard graph benchmark datasets. Hence, in this work, we propose DURENDAL, a graph deep learning framework for THNs. DURENDAL can help to easily repurpose any heterogeneous graph learning model to evolving networks by combining design principles from snapshot-based and multirelational message-passing graph learning models. We introduce two different schemes to update embedding representations for THNs, discussing the strengths and weaknesses of both strategies. We also extend the set of benchmarks for TNHs by introducing two novel high-resolution temporal heterogeneous graph datasets derived from an emerging Web3 platform and a well-established e-commerce website. Overall, we conducted the experimental evaluation of the framework over four temporal heterogeneous network datasets on future link prediction tasks in an evaluation setting that takes into account the evolving nature of the data. Experiments show the prediction power of DURENDAL compared to current solutions for evolving and dynamic graphs, and the effectiveness of its model design.
Designing a single model to address multiple tasks has been a long-standing objective in artificial intelligence. Recently, large language models have demonstrated exceptional capability in solving different tasks within the language domain. However, a unified model for various graph tasks remains underexplored, primarily due to the challenges unique to the graph learning domain. First, graph data from different areas carry distinct attributes and follow different distributions. Such discrepancy makes it hard to represent graphs in a single representation space. Second, tasks on graphs diversify into node, link, and graph tasks, requiring distinct embedding strategies. Finally, an appropriate graph prompting paradigm for in-context learning is unclear. We propose \textbf{One for All (OFA)}, the first general framework that can use a single graph model to address the above challenges. Specifically, OFA proposes text-attributed graphs to unify different graph data by describing nodes and edges with natural language and uses language models to encode the diverse and possibly cross-domain text attributes to feature vectors in the same embedding space. Furthermore, OFA introduces the concept of nodes-of-interest to standardize different tasks with a single task representation. For in-context learning on graphs, OFA introduces a novel graph prompting paradigm that appends prompting substructures to the input graph, which enables it to address varied tasks without fine-tuning. We train the OFA model using graph data from multiple domains (including citation networks, molecular graphs, knowledge graphs, etc.) simultaneously and evaluate its ability in supervised, few-shot, and zero-shot learning scenarios. OFA performs well across different tasks, making it the first general-purpose across-domains classification model on graphs.
How to utilize the pseudo labels has always been a research hotspot in machine learning. However, most methods use pseudo labels as supervised training, and lack of valid assessing for their accuracy. Moreover, applications of pseudo labels in graph neural networks (GNNs) oversee the difference between graph learning and other machine learning tasks such as message passing mechanism. Aiming to address the first issue, we found through a large number of experiments that the pseudo labels are more accurate if they are selected by not overlapping partial labels and defined as negative node pairs relations. Therefore, considering the extraction based on pseudo and partial labels, negative edges are constructed between two nodes by the negative pseudo partial labels extraction (NP$^2$E) module. With that, a signed graph are built containing highly accurate pseudo labels information from the original graph, which effectively assists GNN in learning at the message-passing level, provide one solution to the second issue. Empirical results about link prediction and node classification tasks on several benchmark datasets demonstrate the effectiveness of our method. State-of-the-art performance is achieved on the both tasks.
knowledge graph-based recommendation methods have achieved great success in the field of recommender systems. However, over-reliance on high-quality knowledge graphs is a bottleneck for such methods. Specifically, the long-tailed distribution of entities of KG and noise issues in the real world will make item-entity dependent relations deviate from reflecting true characteristics and significantly harm the performance of modeling user preference. Contrastive learning, as a novel method that is employed for data augmentation and denoising, provides inspiration to fill this research gap. However, the mainstream work only focuses on the long-tail properties of the number of items clicked, while ignoring that the long-tail properties of total number of clicks per user may also affect the performance of the recommendation model. Therefore, to tackle these problems, motivated by the Debiased Contrastive Learning of Unsupervised Sentence Representations (DCLR), we propose Two-Level Debiased Contrastive Graph Learning (TDCGL) model. Specifically, we design the Two-Level Debiased Contrastive Learning (TDCL) and deploy it in the KG, which is conducted not only on User-Item pairs but also on User-User pairs for modeling higher-order relations. Also, to reduce the bias caused by random sampling in contrastive learning, with the exception of the negative samples obtained by random sampling, we add a noise-based generation of negation to ensure spatial uniformity. Considerable experiments on open-source datasets demonstrate that our method has excellent anti-noise capability and significantly outperforms state-of-the-art baselines. In addition, ablation studies about the necessity for each level of TDCL are conducted.
Pulmonary diseases rank prominently among the principal causes of death worldwide. Curing them will require, among other things, a better understanding of the complex 3D tree-shaped structures within the pulmonary system, such as airways, arteries, and veins. Traditional approaches using high-resolution image stacks and standard CNNs on dense voxel grids face challenges in computational efficiency, limited resolution, local context, and inadequate preservation of shape topology. Our method addresses these issues by shifting from dense voxel to sparse point representation, offering better memory efficiency and global context utilization. However, the inherent sparsity in point representation can lead to a loss of crucial connectivity in tree-shaped structures. To mitigate this, we introduce graph learning on skeletonized structures, incorporating differentiable feature fusion for improved topology and long-distance context capture. Furthermore, we employ an implicit function for efficient conversion of sparse representations into dense reconstructions end-to-end. The proposed method not only delivers state-of-the-art performance in labeling accuracy, both overall and at key locations, but also enables efficient inference and the generation of closed surface shapes. Addressing data scarcity in this field, we have also curated a comprehensive dataset to validate our approach. Data and code are available at \url{https://github.com/M3DV/pulmonary-tree-labeling}.
Large language models (LLMs) are gaining increasing attention for their capability to process graphs with rich text attributes, especially in a zero-shot fashion. Recent studies demonstrate that LLMs obtain decent text classification performance on common text-rich graph benchmarks, and the performance can be improved by appending encoded structural information as natural languages into prompts. We aim to understand why the incorporation of structural information inherent in graph data can improve the prediction performance of LLMs. First, we rule out the concern of data leakage by curating a novel leakage-free dataset and conducting a comparative analysis alongside a previously widely-used dataset. Second, as past work usually encodes the ego-graph by describing the graph structure in natural language, we ask the question: do LLMs understand the graph structure in accordance with the intent of the prompt designers? Third, we investigate why LLMs can improve their performance after incorporating structural information. Our exploration of these questions reveals that (i) there is no substantial evidence that the performance of LLMs is significantly attributed to data leakage; (ii) instead of understanding prompts as graph structures as intended by the prompt designers, LLMs tend to process prompts more as contextual paragraphs and (iii) the most efficient elements of the local neighborhood included in the prompt are phrases that are pertinent to the node label, rather than the graph structure.
In the field of 3D scene understanding, 3D scene graphs have emerged as a new scene representation that combines geometric and semantic information about objects and their relationships. However, learning semantic 3D scene graphs in a fully supervised manner is inherently difficult as it requires not only object-level annotations but also relationship labels. While pre-training approaches have helped to boost the performance of many methods in various fields, pre-training for 3D scene graph prediction has received little attention. Furthermore, we find in this paper that classical contrastive point cloud-based pre-training approaches are ineffective for 3D scene graph learning. To this end, we present SGRec3D, a novel self-supervised pre-training method for 3D scene graph prediction. We propose to reconstruct the 3D input scene from a graph bottleneck as a pretext task. Pre-training SGRec3D does not require object relationship labels, making it possible to exploit large-scale 3D scene understanding datasets, which were off-limits for 3D scene graph learning before. Our experiments demonstrate that in contrast to recent point cloud-based pre-training approaches, our proposed pre-training improves the 3D scene graph prediction considerably, which results in SOTA performance, outperforming other 3D scene graph models by +10% on object prediction and +4% on relationship prediction. Additionally, we show that only using a small subset of 10% labeled data during fine-tuning is sufficient to outperform the same model without pre-training.
Bio-inspired neuromorphic cameras asynchronously record pixel brightness changes and generate sparse event streams. They can capture dynamic scenes with little motion blur and more details in extreme illumination conditions. Due to the multidimensional address-event structure, most existing vision algorithms cannot properly handle asynchronous event streams. While several event representations and processing methods have been developed to address such an issue, they are typically driven by a large number of events, leading to substantial overheads in runtime and memory. In this paper, we propose a new graph representation of the event data and couple it with a Graph Transformer to perform accurate neuromorphic classification. Extensive experiments show that our approach leads to better results and excels at the challenging realistic situations where only a small number of events and limited computational resources are available, paving the way for neuromorphic applications embedded into mobile facilities.
Graph Neural Networks (GNNs) have garnered considerable interest due to their exceptional performance in a wide range of graph machine learning tasks. Nevertheless, the majority of GNN-based approaches have been examined using well-annotated benchmark datasets, leading to suboptimal performance in real-world graph learning scenarios. To bridge this gap, the present paper investigates the problem of graph transfer learning in the presence of label noise, which transfers knowledge from a noisy source graph to an unlabeled target graph. We introduce a novel technique termed Balance Alignment and Information-aware Examination (ALEX) to address this challenge. ALEX first employs singular value decomposition to generate different views with crucial structural semantics, which help provide robust node representations using graph contrastive learning. To mitigate both label shift and domain shift, we estimate a prior distribution to build subgraphs with balanced label distributions. Building on this foundation, an adversarial domain discriminator is incorporated for the implicit domain alignment of complex multi-modal distributions. Furthermore, we project node representations into a different space, optimizing the mutual information between the projected features and labels. Subsequently, the inconsistency of similarity structures is evaluated to identify noisy samples with potential overfitting. Comprehensive experiments on various benchmark datasets substantiate the outstanding superiority of the proposed ALEX in different settings.
Protein-protein interactions (PPIs) are critical for various biological processes, and understanding their dynamics is essential for decoding molecular mechanisms and advancing fields such as cancer research and drug discovery. Mutations in PPIs can disrupt protein binding affinity and lead to functional changes and disease. Predicting the impact of mutations on binding affinity is valuable but experimentally challenging. Computational methods, including physics-based and machine learning-based approaches, have been developed to address this challenge. Machine learning-based methods, fueled by extensive PPI datasets such as Ab-Bind, PINT, SKEMPI, and others, have shown promise in predicting binding affinity changes. However, accurate predictions and generalization of these models across different datasets remain challenging. Geometric graph learning has emerged as a powerful approach, combining graph theory and machine learning, to capture structural features of biomolecules. We present GGL-PPI, a novel method that integrates geometric graph learning and machine learning to predict mutation-induced binding free energy changes. GGL-PPI leverages atom-level graph coloring and multi-scale weighted colored geometric subgraphs to extract informative features, demonstrating superior performance on three validation datasets, namely AB-Bind, SKEMPI 1.0, and SKEMPI 2.0 datasets. Evaluation on a blind test set highlights the unbiased predictions of GGL-PPI for both direct and reverse mutations. The findings underscore the potential of GGL-PPI in accurately predicting binding free energy changes, contributing to our understanding of PPIs and aiding drug design efforts.
How can we enhance the node features acquired from Pretrained Models (PMs) to better suit downstream graph learning tasks? Graph Neural Networks (GNNs) have become the state-of-the-art approach for many high-impact, real-world graph applications. For feature-rich graphs, a prevalent practice involves utilizing a PM directly to generate features, without incorporating any domain adaptation techniques. Nevertheless, this practice is suboptimal because the node features extracted from PM are graph-agnostic and prevent GNNs from fully utilizing the potential correlations between the graph structure and node features, leading to a decline in GNNs performance. In this work, we seek to improve the node features obtained from a PM for downstream graph tasks and introduce TOUCHUP-G, which has several advantages. It is (a) General: applicable to any downstream graph task, including link prediction which is often employed in recommender systems; (b) Multi-modal: able to improve raw features of any modality (e.g. images, texts, audio); (c) Principled: it is closely related to a novel metric, feature homophily, which we propose to quantify the potential correlations between the graph structure and node features and we show that TOUCHUP-G can effectively shrink the discrepancy between the graph structure and node features; (d) Effective: achieving state-of-the-art results on four real-world datasets spanning different tasks and modalities.
Audiovisual data is everywhere in this digital age, which raises higher requirements for the deep learning models developed on them. To well handle the information of the multi-modal data is the key to a better audiovisual modal. We observe that these audiovisual data naturally have temporal attributes, such as the time information for each frame in the video. More concretely, such data is inherently multi-modal according to both audio and visual cues, which proceed in a strict chronological order. It indicates that temporal information is important in multi-modal acoustic event modeling for both intra- and inter-modal. However, existing methods deal with each modal feature independently and simply fuse them together, which neglects the mining of temporal relation and thus leads to sub-optimal performance. With this motivation, we propose a Temporal Multi-modal graph learning method for Acoustic event Classification, called TMac, by modeling such temporal information via graph learning techniques. In particular, we construct a temporal graph for each acoustic event, dividing its audio data and video data into multiple segments. Each segment can be considered as a node, and the temporal relationships between nodes can be considered as timestamps on their edges. In this case, we can smoothly capture the dynamic information in intra-modal and inter-modal. Several experiments are conducted to demonstrate TMac outperforms other SOTA models in performance. Our code is available at https://github.com/MGitHubL/TMac.
Graphs are a widely used data structure for collecting and analyzing relational data. However, when the graph structure is distributed across several parties, its analysis is particularly challenging. In particular, due to the sensitivity of the data each party might want to keep their partial knowledge of the graph private, while still willing to collaborate with the other parties for tasks of mutual benefit, such as data curation or the removal of poisoned data. To address this challenge, we propose Crypto'Graph, an efficient protocol for privacy-preserving link prediction on distributed graphs. More precisely, it allows parties partially sharing a graph with distributed links to infer the likelihood of formation of new links in the future. Through the use of cryptographic primitives, Crypto'Graph is able to compute the likelihood of these new links on the joint network without revealing the structure of the private individual graph of each party, even though they know the number of nodes they have, since they share the same graph but not the same links. Crypto'Graph improves on previous works by enabling the computation of a certain number of similarity metrics without any additional cost. The use of Crypto'Graph is illustrated for defense against graph poisoning attacks, in which it is possible to identify potential adversarial links without compromising the privacy of the graphs of individual parties. The effectiveness of Crypto'Graph in mitigating graph poisoning attacks and achieving high prediction accuracy on a graph neural network node classification task is demonstrated through extensive experimentation on a real-world dataset.
Continual graph learning (CGL) is purposed to continuously update a graph model with graph data being fed in a streaming manner. Since the model easily forgets previously learned knowledge when training with new-coming data, the catastrophic forgetting problem has been the major focus in CGL. Recent replay-based methods intend to solve this problem by updating the model using both (1) the entire new-coming data and (2) a sampling-based memory bank that stores replayed graphs to approximate the distribution of historical data. After updating the model, a new replayed graph sampled from the incoming graph will be added to the existing memory bank. Despite these methods are intuitive and effective for the CGL, two issues are identified in this paper. Firstly, most sampling-based methods struggle to fully capture the historical distribution when the storage budget is tight. Secondly, a significant data imbalance exists in terms of the scales of the complex new-coming graph data and the lightweight memory bank, resulting in unbalanced training. To solve these issues, a Condense and Train (CaT) framework is proposed in this paper. Prior to each model update, the new-coming graph is condensed to a small yet informative synthesised replayed graph, which is then stored in a Condensed Graph Memory with historical replay graphs. In the continual learning phase, a Training in Memory scheme is used to update the model directly with the Condensed Graph Memory rather than the whole new-coming graph, which alleviates the data imbalance problem. Extensive experiments conducted on four benchmark datasets successfully demonstrate superior performances of the proposed CaT framework in terms of effectiveness and efficiency. The code has been released on https://github.com/superallen13/CaT-CGL.