In many applications, we desire neural networks to exhibit invariance or equivariance to certain groups due to symmetries inherent in the data. Recently, frame-averaging methods emerged to be a unified framework for attaining symmetries efficiently by averaging over input-dependent subsets of the group, i.e., frames. What we currently lack is a principled understanding of the design of frames. In this work, we introduce a canonicalization perspective that provides an essential and complete view of the design of frames. Canonicalization is a classic approach for attaining invariance by mapping inputs to their canonical forms. We show that there exists an inherent connection between frames and canonical forms. Leveraging this connection, we can efficiently compare the complexity of frames as well as determine the optimality of certain frames. Guided by this principle, we design novel frames for eigenvectors that are strictly superior to existing methods -- some are even optimal -- both theoretically and empirically. The reduction to the canonicalization perspective further uncovers equivalences between previous methods. These observations suggest that canonicalization provides a fundamental understanding of existing frame-averaging methods and unifies existing equivariant and invariant learning methods. Code is available at https://github.com/PKU-ML/canonicalization.
Knowledge Graph Embedding (KGE) techniques are crucial in learning compact representations of entities and relations within a knowledge graph, facilitating efficient reasoning and knowledge discovery. While existing methods typically focus either on training KGE models solely based on graph structure or fine-tuning pre-trained language models with classification data in KG, KG-FIT leverages LLM-guided refinement to construct a semantically coherent hierarchical structure of entity clusters. By incorporating this hierarchical knowledge along with textual information during the fine-tuning process, KG-FIT effectively captures both global semantics from the LLM and local semantics from the KG. Extensive experiments on the benchmark datasets FB15K-237, YAGO3-10, and PrimeKG demonstrate the superiority of KG-FIT over state-of-the-art pre-trained language model-based methods, achieving improvements of 14.4%, 13.5%, and 11.9% in the Hits@10 metric for the link prediction task, respectively. Furthermore, KG-FIT yields substantial performance gains of 12.6%, 6.7%, and 17.7% compared to the structure-based base models upon which it is built. These results highlight the effectiveness of KG-FIT in incorporating open-world knowledge from LLMs to significantly enhance the expressiveness and informativeness of KG embeddings.
Graph NAS has emerged as a promising approach for autonomously designing GNN architectures by leveraging the correlations between graphs and architectures. Existing methods fail to generalize under distribution shifts that are ubiquitous in real-world graph scenarios, mainly because the graph-architecture correlations they exploit might be spurious and varying across distributions. We propose to handle the distribution shifts in the graph architecture search process by discovering and exploiting the causal relationship between graphs and architectures to search for the optimal architectures that can generalize under distribution shifts. The problem remains unexplored with following challenges: how to discover the causal graph-architecture relationship that has stable predictive abilities across distributions, and how to handle distribution shifts with the discovered causal graph-architecture relationship to search the generalized graph architectures. To address these challenges, we propose Causal-aware Graph Neural Architecture Search (CARNAS), which is able to capture the causal graph-architecture relationship during the architecture search process and discover the generalized graph architecture under distribution shifts. Specifically, we propose Disentangled Causal Subgraph Identification to capture the causal subgraphs that have stable prediction abilities across distributions. Then, we propose Graph Embedding Intervention to intervene on causal subgraphs within the latent space, ensuring that these subgraphs encapsulate essential features for prediction while excluding non-causal elements. Additionally, we propose Invariant Architecture Customization to reinforce the causal invariant nature of the causal subgraphs, which are utilized to tailor generalized graph architectures. Extensive experiments demonstrate that CARNAS achieves advanced out-of-distribution generalization ability.
Fuzzy clustering algorithms can be roughly categorized into two main groups: Fuzzy C-Means (FCM) based methods and mixture model based methods. However, for almost all existing FCM based methods, how to automatically selecting proper membership degree hyper-parameter values remains a challenging and unsolved problem. Mixture model based methods, while circumventing the difficulty of manually adjusting membership degree hyper-parameters inherent in FCM based methods, often have a preference for specific distributions, such as the Gaussian distribution. In this paper, we propose a novel FCM based clustering model that is capable of automatically learning an appropriate membership degree hyper-parameter value and handling data with non-Gaussian clusters. Moreover, by removing the graph embedding regularization, the proposed FCM model can degenerate into the simplified generalized Gaussian mixture model. Therefore, the proposed FCM model can be also seen as the generalized Gaussian mixture model with graph embedding. Extensive experiments are conducted on both synthetic and real-world datasets to demonstrate the effectiveness of the proposed model.
Transportation mode share analysis is important to various real-world transportation tasks as it helps researchers understand the travel behaviors and choices of passengers. A typical example is the prediction of communities' travel mode share by accounting for their sociodemographics like age, income, etc., and travel modes' attributes (e.g. travel cost and time). However, there exist only limited efforts in integrating the structure of the urban built environment, e.g., road networks, into the mode share models to capture the impacts of the built environment. This task usually requires manual feature engineering or prior knowledge of the urban design features. In this study, we propose deep hybrid models (DHM), which directly combine road networks and sociodemographic features as inputs for travel mode share analysis. Using graph embedding (GE) techniques, we enhance travel demand models with a more powerful representation of urban structures. In experiments of mode share prediction in Chicago, results demonstrate that DHM can provide valuable spatial insights into the sociodemographic structure, improving the performance of travel demand models in estimating different mode shares at the city level. Specifically, DHM improves the results by more than 20\% while retaining the interpretation power of the choice models, demonstrating its superiority in interpretability, prediction accuracy, and geographical insights.
Knowledge graph embedding (KGE) methods have achieved great success in handling various knowledge graph (KG) downstream tasks. However, KGE methods may learn biased representations on low-quality KGs that are prevalent in the real world. Some recent studies propose adversarial attacks to investigate the vulnerabilities of KGE methods, but their attackers are target-oriented with the KGE method and the target triples to predict are given in advance, which lacks practicability. In this work, we explore untargeted attacks with the aim of reducing the global performances of KGE methods over a set of unknown test triples and conducting systematic analyses on KGE robustness. Considering logic rules can effectively summarize the global structure of a KG, we develop rule-based attack strategies to enhance the attack efficiency. In particular,we consider adversarial deletion which learns rules, applying the rules to score triple importance and delete important triples, and adversarial addition which corrupts the learned rules and applies them for negative triples as perturbations. Extensive experiments on two datasets over three representative classes of KGE methods demonstrate the effectiveness of our proposed untargeted attacks in diminishing the link prediction results. And we also find that different KGE methods exhibit different robustness to untargeted attacks. For example, the robustness of methods engaged with graph neural networks and logic rules depends on the density of the graph. But rule-based methods like NCRL are easily affected by adversarial addition attacks to capture negative rules
Heterogeneous, interconnected, systems-level, molecular data have become increasingly available and key in precision medicine. We need to utilize them to better stratify patients into risk groups, discover new biomarkers and targets, repurpose known and discover new drugs to personalize medical treatment. Existing methodologies are limited and a paradigm shift is needed to achieve quantitative and qualitative breakthroughs. In this perspective paper, we survey the literature and argue for the development of a comprehensive, general framework for embedding of multi-scale molecular network data that would enable their explainable exploitation in precision medicine in linear time. Network embedding methods map nodes to points in low-dimensional space, so that proximity in the learned space reflects the network's topology-function relationships. They have recently achieved unprecedented performance on hard problems of utilizing few omic data in various biomedical applications. However, research thus far has been limited to special variants of the problems and data, with the performance depending on the underlying topology-function network biology hypotheses, the biomedical applications and evaluation metrics. The availability of multi-omic data, modern graph embedding paradigms and compute power call for a creation and training of efficient, explainable and controllable models, having no potentially dangerous, unexpected behaviour, that make a qualitative breakthrough. We propose to develop a general, comprehensive embedding framework for multi-omic network data, from models to efficient and scalable software implementation, and to apply it to biomedical informatics. It will lead to a paradigm shift in computational and biomedical understanding of data and diseases that will open up ways to solving some of the major bottlenecks in precision medicine and other domains.
Knowledge graph embedding (KGE) has caught significant interest for its effectiveness in knowledge graph completion (KGC), specifically link prediction (LP), with recent KGE models cracking the LP benchmarks. Despite the rapidly growing literature, insufficient attention has been paid to the cooperation between humans and AI on KG. However, humans' capability to analyze graphs conceptually may further improve the efficacy of KGE models with semantic information. To this effect, we carefully designed a human-AI team (HAIT) system dubbed KG-HAIT, which harnesses the human insights on KG by leveraging fully human-designed ad-hoc dynamic programming (DP) on KG to produce human insightful feature (HIF) vectors that capture the subgraph structural feature and semantic similarities. By integrating HIF vectors into the training of KGE models, notable improvements are observed across various benchmarks and metrics, accompanied by accelerated model convergence. Our results underscore the effectiveness of human-designed DP in the task of LP, emphasizing the pivotal role of collaboration between humans and AI on KG. We open avenues for further exploration and innovation through KG-HAIT, paving the way towards more effective and insightful KG analysis techniques.
Recent advances in knowledge graph embedding (KGE) rely on Euclidean/hyperbolic orthogonal relation transformations to model intrinsic logical patterns and topological structures. However, existing approaches are confined to rigid relational orthogonalization with restricted dimension and homogeneous geometry, leading to deficient modeling capability. In this work, we move beyond these approaches in terms of both dimension and geometry by introducing a powerful framework named GoldE, which features a universal orthogonal parameterization based on a generalized form of Householder reflection. Such parameterization can naturally achieve dimensional extension and geometric unification with theoretical guarantees, enabling our framework to simultaneously capture crucial logical patterns and inherent topological heterogeneity of knowledge graphs. Empirically, GoldE achieves state-of-the-art performance on three standard benchmarks. Codes are available at https://github.com/xxrep/GoldE.
Inductive representation learning on temporal heterogeneous graphs is crucial for scalable deep learning on heterogeneous information networks (HINs) which are time-varying, such as citation networks. However, most existing approaches are not inductive and thus cannot handle new nodes or edges. Moreover, previous temporal graph embedding methods are often trained with the temporal link prediction task to simulate the link formation process of temporal graphs, while ignoring the evolution of high-order topological structures on temporal graphs. To fill these gaps, we propose a Continuous-Time Representation Learning (CTRL) model on temporal HINs. To preserve heterogeneous node features and temporal structures, CTRL integrates three parts in a single layer, they are 1) a \emph{heterogeneous attention} unit that measures the semantic correlation between nodes, 2) a \emph{edge-based Hawkes process} to capture temporal influence between heterogeneous nodes, and 3) \emph{dynamic centrality} that indicates the dynamic importance of a node. We train the CTRL model with a future event (a subgraph) prediction task to capture the evolution of the high-order network structure. Extensive experiments have been conducted on three benchmark datasets. The results demonstrate that our model significantly boosts performance and outperforms various state-of-the-art approaches. Ablation studies are conducted to demonstrate the effectiveness of the model design.
Last year has witnessed the considerable interest of Large Language Models (LLMs) for their potential applications in recommender systems, which may mitigate the persistent issue of data sparsity. Though large efforts have been made for user-item graph augmentation with better graph-based recommendation performance, they may fail to deal with the dynamic graph recommendation task, which involves both structural and temporal graph dynamics with inherent complexity in processing time-evolving data. To bridge this gap, in this paper, we propose a novel framework, called DynLLM, to deal with the dynamic graph recommendation task with LLMs. Specifically, DynLLM harnesses the power of LLMs to generate multi-faceted user profiles based on the rich textual features of historical purchase records, including crowd segments, personal interests, preferred categories, and favored brands, which in turn supplement and enrich the underlying relationships between users and items. Along this line, to fuse the multi-faceted profiles with temporal graph embedding, we engage LLMs to derive corresponding profile embeddings, and further employ a distilled attention mechanism to refine the LLM-generated profile embeddings for alleviating noisy signals, while also assessing and adjusting the relevance of each distilled facet embedding for seamless integration with temporal graph embedding from continuous time dynamic graphs (CTDGs). Extensive experiments on two real e-commerce datasets have validated the superior improvements of DynLLM over a wide range of state-of-the-art baseline methods.
Traditional knowledge graph embedding (KGE) methods typically require preserving the entire knowledge graph (KG) with significant training costs when new knowledge emerges. To address this issue, the continual knowledge graph embedding (CKGE) task has been proposed to train the KGE model by learning emerging knowledge efficiently while simultaneously preserving decent old knowledge. However, the explicit graph structure in KGs, which is critical for the above goal, has been heavily ignored by existing CKGE methods. On the one hand, existing methods usually learn new triples in a random order, destroying the inner structure of new KGs. On the other hand, old triples are preserved with equal priority, failing to alleviate catastrophic forgetting effectively. In this paper, we propose a competitive method for CKGE based on incremental distillation (IncDE), which considers the full use of the explicit graph structure in KGs. First, to optimize the learning order, we introduce a hierarchical strategy, ranking new triples for layer-by-layer learning. By employing the inter- and intra-hierarchical orders together, new triples are grouped into layers based on the graph structure features. Secondly, to preserve the old knowledge effectively, we devise a novel incremental distillation mechanism, which facilitates the seamless transfer of entity representations from the previous layer to the next one, promoting old knowledge preservation. Finally, we adopt a two-stage training paradigm to avoid the over-corruption of old knowledge influenced by under-trained new knowledge. Experimental results demonstrate the superiority of IncDE over state-of-the-art baselines. Notably, the incremental distillation mechanism contributes to improvements of 0.2%-6.5% in the mean reciprocal rank (MRR) score.
Causal networks are useful in a wide variety of applications, from medical diagnosis to root-cause analysis in manufacturing. In practice, however, causal networks are often incomplete with missing causal relations. This paper presents a novel approach, called CausalLP, that formulates the issue of incomplete causal networks as a knowledge graph completion problem. More specifically, the task of finding new causal relations in an incomplete causal network is mapped to the task of knowledge graph link prediction. The use of knowledge graphs to represent causal relations enables the integration of external domain knowledge; and as an added complexity, the causal relations have weights representing the strength of the causal association between entities in the knowledge graph. Two primary tasks are supported by CausalLP: causal explanation and causal prediction. An evaluation of this approach uses a benchmark dataset of simulated videos for causal reasoning, CLEVRER-Humans, and compares the performance of multiple knowledge graph embedding algorithms. Two distinct dataset splitting approaches are used for evaluation: (1) random-based split, which is the method typically employed to evaluate link prediction algorithms, and (2) Markov-based split, a novel data split technique that utilizes the Markovian property of causal relations. Results show that using weighted causal relations improves causal link prediction over the baseline without weighted relations.
This study investigates the robustness of graph embedding methods for community detection in the face of network perturbations, specifically edge deletions. Graph embedding techniques, which represent nodes as low-dimensional vectors, are widely used for various graph machine learning tasks due to their ability to capture structural properties of networks effectively. However, the impact of perturbations on the performance of these methods remains relatively understudied. The research considers state-of-the-art graph embedding methods from two families: matrix factorization (e.g., LE, LLE, HOPE, M-NMF) and random walk-based (e.g., DeepWalk, LINE, node2vec). Through experiments conducted on both synthetic and real-world networks, the study reveals varying degrees of robustness within each family of graph embedding methods. The robustness is found to be influenced by factors such as network size, initial community partition strength, and the type of perturbation. Notably, node2vec and LLE consistently demonstrate higher robustness for community detection across different scenarios, including networks with degree and community size heterogeneity. These findings highlight the importance of selecting an appropriate graph embedding method based on the specific characteristics of the network and the task at hand, particularly in scenarios where robustness to perturbations is crucial.
A wide range of graph embedding objectives decompose into two components: one that enforces similarity, attracting the embeddings of nodes that are perceived as similar, and another that enforces dissimilarity, repelling the embeddings of nodes that are perceived as dissimilar. Without repulsion, the embeddings would collapse into trivial solutions. Skip-Gram Negative Sampling (SGNS) is a popular and efficient repulsion approach that prevents collapse by repelling each node from a sample of dissimilar nodes. In this work, we show that when repulsion is most needed and the embeddings approach collapse, SGNS node-wise repulsion is, in the aggregate, an approximate re-centering of the node embedding dimensions. Such dimension operations are more scalable than node operations and produce a simpler geometric interpretation of the repulsion. Our theoretical result establishes dimension regularization as an effective and more efficient, compared to skip-gram node contrast, approach to enforcing dissimilarity among embeddings of nodes. We use this result to propose a flexible algorithm augmentation framework that improves the scalability of any existing algorithm using SGNS. The framework prioritizes node attraction and replaces SGNS with dimension regularization. We instantiate this generic framework for LINE and node2vec and show that the augmented algorithms preserve downstream link-prediction performance while reducing GPU memory usage by up to 33.3% and training time by 23.4%. Moreover, we show that completely removing repulsion (a special case of our augmentation framework) in LINE reduces training time by 70.9% on average, while increasing link prediction performance, especially for graphs that are globally sparse but locally dense. In general, however, repulsion is needed, and dimension regularization provides an efficient alternative to SGNS.
Distinguished from traditional knowledge graphs (KGs), temporal knowledge graphs (TKGs) must explore and reason over temporally evolving facts adequately. However, existing TKG approaches still face two main challenges, i.e., the limited capability to model arbitrary timestamps continuously and the lack of rich inference patterns under temporal constraints. In this paper, we propose an innovative TKGE method (PTBox) via polynomial decomposition-based temporal representation and box embedding-based entity representation to tackle the above-mentioned problems. Specifically, we decompose time information by polynomials and then enhance the model's capability to represent arbitrary timestamps flexibly by incorporating the learnable temporal basis tensor. In addition, we model every entity as a hyperrectangle box and define each relation as a transformation on the head and tail entity boxes. The entity boxes can capture complex geometric structures and learn robust representations, improving the model's inductive capability for rich inference patterns. Theoretically, our PTBox can encode arbitrary time information or even unseen timestamps while capturing rich inference patterns and higher-arity relations of the knowledge base. Extensive experiments on real-world datasets demonstrate the effectiveness of our method.
Knowledge graphs (KGs), which store an extensive number of relational facts (head, relation, tail), serve various applications. While many downstream tasks highly rely on the expressive modeling and predictive embedding of KGs, most of the current KG representation learning methods, where each entity is embedded as a vector in the Euclidean space and each relation is embedded as a transformation, follow an entity ranking protocol. On one hand, such an embedding design cannot capture many-to-many relations. On the other hand, in many retrieval cases, the users wish to get an exact set of answers without any ranking, especially when the results are expected to be precise, e.g., which genes cause an illness. Such scenarios are commonly referred to as "set retrieval". This work presents a pioneering study on the KG set retrieval problem. We show that the set retrieval highly depends on expressive modeling of many-to-many relations, and propose a new KG embedding model SpherE to address this problem. SpherE is based on rotational embedding methods, but each entity is embedded as a sphere instead of a vector. While inheriting the high interpretability of rotational-based models, our SpherE can more expressively model one-to-many, many-to-one, and many-to-many relations. Through extensive experiments, we show that our SpherE can well address the set retrieval problem while still having a good predictive ability to infer missing facts. The code is available at https://github.com/Violet24K/SpherE.
A Knowledge Graph (KG) is the directed graphical representation of entities and relations in the real world. KG can be applied in diverse Natural Language Processing (NLP) tasks where knowledge is required. The need to scale up and complete KG automatically yields Knowledge Graph Embedding (KGE), a shallow machine learning model that is suffering from memory and training time consumption issues. To mitigate the computational load, we propose a parameter-sharing method, i.e., using conjugate parameters for complex numbers employed in KGE models. Our method improves memory efficiency by 2x in relation embedding while achieving comparable performance to the state-of-the-art non-conjugate models, with faster, or at least comparable, training time. We demonstrated the generalizability of our method on two best-performing KGE models $5^{\bigstar}\mathrm{E}$ and $\mathrm{ComplEx}$ on five benchmark datasets.
Most previous heterogeneous graph embedding models represent elements in a heterogeneous graph as vector representations in a low-dimensional Euclidean space. However, because heterogeneous graphs inherently possess complex structures, such as hierarchical or power-law structures, distortions can occur when representing them in Euclidean space. To overcome this limitation, we propose Hyperbolic Heterogeneous Graph Attention Networks (HHGAT) that learn vector representations in hyperbolic spaces with meta-path instances. We conducted experiments on three real-world heterogeneous graph datasets, demonstrating that HHGAT outperforms state-of-the-art heterogeneous graph embedding models in node classification and clustering tasks.
Knowledge Graph (KG) is a graph based data structure to represent facts of the world where nodes represent real world entities or abstract concept and edges represent relation between the entities. Graph as representation for knowledge has several drawbacks like data sparsity, computational complexity and manual feature engineering. Knowledge Graph embedding tackles the drawback by representing entities and relation in low dimensional vector space by capturing the semantic relation between them. There are different KG embedding models. Here, we discuss translation based and neural network based embedding models which differ based on semantic property, scoring function and architecture they use. Further, we discuss application of KG in some domains that use deep learning models and leverage social media data.