Hypergraphs, capable of representing high-order interactions via hyperedges, have become a powerful tool for modeling real-world biological and social systems. Inherent relationships within these real-world systems, such as the encoding relationship between genes and their protein products, drive the establishment of interconnections between multiple hypergraphs. Here, we demonstrate how to utilize those interconnections between multiple hypergraphs to synthesize integrated information from multiple higher-order systems, thereby enhancing understanding of underlying structures. We propose a model based on the stochastic block model, which integrates information from multiple hypergraphs to reveal latent high-order structures. Real-world hyperedges exhibit preferential attachment, where certain nodes dominate hyperedge formation. To characterize this phenomenon, our model introduces hyperedge internal degree to quantify nodes' contributions to hyperedge formation. This model is capable of mining communities, predicting missing hyperedges of arbitrary sizes within hypergraphs, and inferring inter-hypergraph edges between hypergraphs. We apply our model to high-order datasets to evaluate its performance. Experimental results demonstrate strong performance of our model in community detection, hyperedge prediction, and inter-hypergraph edge prediction tasks. Moreover, we show that our model enables analysis of multiple hypergraphs of different types and supports the analysis of a single hypergraph in the absence of inter-hypergraph edges. Our work provides a practical and flexible tool for analyzing multiple hypergraphs, greatly advancing the understanding of the organization in real-world high-order systems.
Hyperedge prediction is a fundamental task to predict future high-order relations based on the observed network structure. Existing hyperedge prediction methods, however, suffer from the data sparsity problem. To alleviate this problem, negative sampling methods can be used, which leverage non-existing hyperedges as contrastive information for model training. However, the following important challenges have been rarely studied: (C1) lack of guidance for generating negatives and (C2) possibility of producing false negatives. To address them, we propose a novel hyperedge prediction method, HyGEN, that employs (1) a negative hyperedge generator that employs positive hyperedges as a guidance to generate more realistic ones and (2) a regularization term that prevents the generated hyperedges from being false negatives. Extensive experiments on six real-world hypergraphs reveal that HyGEN consistently outperforms four state-of-the-art hyperedge prediction methods.
Groups with complex set intersection relations are a natural way to model a wide array of data, from the formation of social groups to the complex protein interactions which form the basis of biological life. One approach to representing such higher order relationships is as a hypergraph. However, efforts to apply machine learning techniques to hypergraph structured datasets have been limited thus far. In this paper, we address the problem of link prediction in knowledge hypergraphs as well as simple hypergraphs and develop a novel, simple, and effective optimization architecture that addresses both tasks. Additionally, we introduce a novel feature extraction technique using node level clustering and we show how integrating data from node-level labels can improve system performance. Our self-supervised approach achieves significant improvement over state of the art baselines on several hyperedge prediction and knowledge hypergraph completion benchmarks.
Hyperedge prediction is crucial in hypergraph analysis for understanding complex multi-entity interactions in various web-based applications, including social networks and e-commerce systems. Traditional methods often face difficulties in generating high-quality negative samples due to the imbalance between positive and negative instances. To address this, we present the Scalable and Effective Negative Sample Generation for Hyperedge Prediction (SEHP) framework, which utilizes diffusion models to tackle these challenges. SEHP employs a boundary-aware loss function that iteratively refines negative samples, moving them closer to decision boundaries to improve classification performance. SEHP samples positive instances to form sub-hypergraphs for scalable batch processing. By using structural information from sub-hypergraphs as conditions within the diffusion process, SEHP effectively captures global patterns. To enhance efficiency, our approach operates directly in latent space, avoiding the need for discrete ID generation and resulting in significant speed improvements while preserving accuracy. Extensive experiments show that SEHP outperforms existing methods in accuracy, efficiency, and scalability, representing a substantial advancement in hyperedge prediction techniques. Our code is available here.
Incomplete knowledge of metabolic processes hinders the accuracy of GEnome-scale Metabolic models (GEMs), which in turn impedes advancements in systems biology and metabolic engineering. Existing gap-filling methods typically rely on phenotypic data to minimize the disparity between computational predictions and experimental results. However, there is still a lack of an automatic and precise gap-filling method for initial state GEMs before experimental data and annotated genomes become available. In this study, we introduce CLOSEgaps, a deep learning-driven tool that addresses the gap-filling issue by modeling it as a hyperedge prediction problem within GEMs. Specifically, CLOSEgaps maps metabolic networks as hypergraphs and learns their hyper-topology features to identify missing reactions and gaps by leveraging hypothetical reactions. This innovative approach allows for the characterization and curation of both known and hypothetical reactions within metabolic networks. Extensive results demonstrate that CLOSEgaps accurately gap-filling over 96% of artificially introduced gaps for various GEMs. Furthermore, CLOSEgaps enhances phenotypic predictions for 24 GEMs and also finds a notable improvement in producing four crucial metabolites (Lactate, Ethanol, Propionate, and Succinate) in two organisms. As a broadly applicable solution for any GEM, CLOSEgaps represents a promising model to automate the gap-filling process and uncover missing connections between reactions and observed metabolic phenotypes.
Hyperlink prediction aims to predict interactions among multiple entries, constituting a practical yet challenging problem in the literature. While a handful of solutions have been proposed, they generally operate on the entire hypergraph. A practical subgraph-based solution not only enables better identification of localized characteristics of the central hyperedge but also alleviates scalability concerns. In this study, we present SSF, an innovative hyperlink prediction methodology based on Subgraph Structural Features. The rationale behind SSF is that hyperedges and non-hyperedges exhibit distinct local patterns, which can be unveiled through the assimilation of subgraph structural features. To this end, we utilize well-established structural heuristics such as walks and loops as the fundamental building blocks. We commence by extracting a subgraph encompassing each focal hyperedge, subsequently integrating an edge weakening scheme to facilitate feature extraction from the initial subgraph and its variations. The extracted feature vector is interpretable, and the designed edge weakening scheme empowers SSF with an adaptive capability to handle hypergraphs with varying densities. Lastly, a multilayer perceptron classifier is trained for prediction. Experiment results on ten real-world hypergraph networks demonstrate the effectiveness of the proposed approach.
Hypergraphs are crucial for modelling higher-order interactions in real-world data. Hypergraph neural networks (HNNs) effectively utilise these structures by message passing to generate informative node features for various downstream tasks like node classification. However, the message passing module in existing HNNs typically requires a computationally intensive training process, which limits their practical use. To tackle this challenge, we propose an alternative approach by decoupling the usage of hypergraph structural information from the model learning stage. This leads to a novel training-free message passing module, named TF-MP-Module, which can be precomputed in the data preprocessing stage, thereby reducing the computational burden. We refer to the hypergraph neural network equipped with our TF-MP-Module as TF-HNN. We theoretically support the efficiency and effectiveness of TF-HNN by showing that: 1) It is more training-efficient compared to existing HNNs; 2) It utilises as much information as existing HNNs for node feature generation; and 3) It is robust against the oversmoothing issue while using long-range interactions. Experiments based on seven real-world hypergraph benchmarks in node classification and hyperlink prediction show that, compared to state-of-the-art HNNs, TF-HNN exhibits both competitive performance and superior training efficiency. Specifically, on the large-scale benchmark, Trivago, TF-HNN outperforms the node classification accuracy of the best baseline by 10% with just 1% of the training time of that baseline.
Temporal hypergraphs provide a powerful paradigm for modeling time-dependent, higher-order interactions in complex systems. Representation learning for hypergraphs is essential for extracting patterns of the higher-order interactions that are critically important in real-world problems in social network analysis, neuroscience, finance, etc. However, existing methods are typically designed only for specific tasks or static hypergraphs. We present CAT-Walk, an inductive method that learns the underlying dynamic laws that govern the temporal and structural processes underlying a temporal hypergraph. CAT-Walk introduces a temporal, higher-order walk on hypergraphs, SetWalk, that extracts higher-order causal patterns. CAT-Walk uses a novel adaptive and permutation invariant pooling strategy, SetMixer, along with a set-based anonymization process that hides the identity of hyperedges. Finally, we present a simple yet effective neural network model to encode hyperedges. Our evaluation on 10 hypergraph benchmark datasets shows that CAT-Walk attains outstanding performance on temporal hyperedge prediction benchmarks in both inductive and transductive settings. It also shows competitive performance with state-of-the-art methods for node classification. (https://github.com/ubc-systopia/CATWalk)
Many networked datasets with units interacting in groups of two or more, encoded with hypergraphs, are accompanied by extra information about nodes, such as the role of an individual in a workplace. Here we show how these node attributes can be used to improve our understanding of the structure resulting from higher-order interactions. We consider the problem of community detection in hypergraphs and develop a principled model that combines higher-order interactions and node attributes to better represent the observed interactions and to detect communities more accurately than using either of these types of information alone. The method learns automatically from the input data the extent to which structure and attributes contribute to explain the data, down weighing or discarding attributes if not informative. Our algorithmic implementation is efficient and scales to large hypergraphs and interactions of large numbers of units. We apply our method to a variety of systems, showing strong performance in hyperedge prediction tasks and in selecting community divisions that correlate with attributes when these are informative, but discarding them otherwise. Our approach illustrates the advantage of using informative node attributes when available with higher-order data.
Although pretraining has garnered significant attention and popularity in recent years, its application in graph-based recommender systems is relatively limited. It is challenging to exploit prior knowledge by pretraining in widely used ID-dependent datasets. On one hand, user-item interaction history in one dataset can hardly be transferred to other datasets through pretraining, where IDs are different. On the other hand, pretraining and finetuning on the same dataset leads to a high risk of overfitting. In this paper, we propose a novel multitask pretraining framework named Unified Pretraining for Recommendation via Task Hypergraphs. For a unified learning pattern to handle diverse requirements and nuances of various pretext tasks, we design task hypergraphs to generalize pretext tasks to hyperedge prediction. A novel transitional attention layer is devised to discriminatively learn the relevance between each pretext task and recommendation. Experimental results on three benchmark datasets verify the superiority of UPRTH. Additional detailed investigations are conducted to demonstrate the effectiveness of the proposed framework.
Hypergraphs can naturally model group-wise relations (e.g., a group of users who co-purchase an item) as hyperedges. Hyperedge prediction is to predict future or unobserved hyperedges, which is a fundamental task in many real-world applications (e.g., group recommendation). Despite the recent breakthrough of hyperedge prediction methods, the following challenges have been rarely studied: (C1) How to aggregate the nodes in each hyperedge candidate for accurate hyperedge prediction? and (C2) How to mitigate the inherent data sparsity problem in hyperedge prediction? To tackle both challenges together, in this paper, we propose a novel hyperedge prediction framework (CASH) that employs (1) context-aware node aggregation to precisely capture complex relations among nodes in each hyperedge for (C1) and (2) self-supervised contrastive learning in the context of hyperedge prediction to enhance hypergraph representations for (C2). Furthermore, as for (C2), we propose a hyperedge-aware augmentation method to fully exploit the latent semantics behind the original hypergraph and consider both node-level and group-level contrasts (i.e., dual contrasts) for better node and hyperedge representations. Extensive experiments on six real-world hypergraphs reveal that CASH consistently outperforms all competing methods in terms of the accuracy in hyperedge prediction and each of the proposed strategies is effective in improving the model accuracy of CASH. For the detailed information of CASH, we provide the code and datasets at: https://github.com/yy-ko/cash.
In this paper, we provide a theory of using graph neural networks (GNNs) for \textit{multi-node representation learning}, where we are interested in learning a representation for a set of more than one node such as a link. Existing GNNs are mainly designed to learn single-node representations. When we want to learn a node-set representation involving multiple nodes, a common practice in previous works is to directly aggregate the single-node representations obtained by a GNN. In this paper, we show a fundamental limitation of such an approach, namely the inability to capture the dependence among multiple nodes in a node set, and argue that directly aggregating individual node representations fails to produce an effective joint representation for multiple nodes. A straightforward solution is to distinguish target nodes from others. Formalizing this idea, we propose \text{labeling trick}, which first labels nodes in the graph according to their relationships with the target node set before applying a GNN and then aggregates node representations obtained in the labeled graph for multi-node representations. The labeling trick also unifies a few previous successful works for multi-node representation learning, including SEAL, Distance Encoding, ID-GNN, and NBFNet. Besides node sets in graphs, we also extend labeling tricks to posets, subsets and hypergraphs. Experiments verify that the labeling trick technique can boost GNNs on various tasks, including undirected link prediction, directed link prediction, hyperedge prediction, and subgraph prediction. Our work explains the superior performance of previous node-labeling-based methods and establishes a theoretical foundation for using GNNs for multi-node representation learning.
In this work, we introduce a hypergraph representation learning framework called Hypergraph Neural Networks (HNN) that jointly learns hyperedge embeddings along with a set of hyperedge-dependent embeddings for each node in the hypergraph. HNN derives multiple embeddings per node in the hypergraph where each embedding for a node is dependent on a specific hyperedge of that node. Notably, HNN is accurate, data-efficient, flexible with many interchangeable components, and useful for a wide range of hypergraph learning tasks. We evaluate the effectiveness of the HNN framework for hyperedge prediction and hypergraph node classification. We find that HNN achieves an overall mean gain of 7.72% and 11.37% across all baseline models and graphs for hyperedge prediction and hypergraph node classification, respectively.
Hypergraphs (i.e., sets of hyperedges) naturally represent group relations (e.g., researchers co-authoring a paper and ingredients used together in a recipe), each of which corresponds to a hyperedge (i.e., a subset of nodes). Predicting future or missing hyperedges bears significant implications for many applications (e.g., collaboration and recipe recommendation). What makes hyperedge prediction particularly challenging is the vast number of non-hyperedge subsets, which grows exponentially with the number of nodes. Since it is prohibitive to use all of them as negative examples for model training, it is inevitable to sample a very small portion of them, and to this end, heuristic sampling schemes have been employed. However, trained models suffer from poor generalization capability for examples of different natures. In this paper, we propose AHP, an adversarial training-based hyperedge-prediction method. It learns to sample negative examples without relying on any heuristic schemes. Using six real hypergraphs, we show that AHP generalizes better to negative examples of various natures. It yields up to 28.2% higher AUROC than the best existing methods and often even outperforms its variants with sampling schemes tailored to test sets.
Hypergraphs, encoding structured interactions among any number of system units, have recently proven a successful tool to describe many real-world biological and social networks. Here we propose a framework based on statistical inference to characterize the structural organization of hypergraphs. The method allows to infer missing hyperedges of any size in a principled way, and to jointly detect overlapping communities in presence of higher-order interactions. Furthermore, our model has an efficient numerical implementation, and it runs faster than dyadic algorithms on pairwise records projected from higher-order data. We apply our method to a variety of real-world systems, showing strong performance in hyperedge prediction tasks, detecting communities well aligned with the information carried by interactions, and robustness against addition of noisy hyperedges. Our approach illustrates the fundamental advantages of a hypergraph probabilistic model when modeling relational systems with higher-order interactions.
The explosion of digital information and the growing involvement of people in social networks led to enormous research activity to develop methods that can extract meaningful information from interaction data. Commonly, interactions are represented by edges in a network or a graph, which implicitly assumes that the interactions are pairwise and static. However, real-world interactions deviate from these assumptions: (i) interactions can be multi-way, involving more than two nodes or individuals (e.g., family relationships, protein interactions), and (ii) interactions can change over a period of time (e.g., change of opinions and friendship status). While pairwise interactions have been studied in a dynamic network setting and multi-way interactions have been studied using hypergraphs in static networks, there exists no method, at present, that can predict multi-way interactions or hyperedges in dynamic settings. Existing related methods cannot answer temporal queries like what type of interaction will occur next and when it will occur. This paper proposes a temporal point process model for hyperedge prediction to address these problems. Our proposed model uses dynamic representation learning techniques for nodes in a neural point process framework to forecast hyperedges. We present several experimental results and set benchmark results. As far as our knowledge, this is the first work that uses the temporal point process to forecast hyperedges in dynamic networks.
We present a generalization of Transformers to any-order permutation invariant data (sets, graphs, and hypergraphs). We begin by observing that Transformers generalize DeepSets, or first-order (set-input) permutation invariant MLPs. Then, based on recently characterized higher-order invariant MLPs, we extend the concept of self-attention to higher orders and propose higher-order Transformers for order-$k$ data ($k=2$ for graphs and $k>2$ for hypergraphs). Unfortunately, higher-order Transformers turn out to have prohibitive complexity $\mathcal{O}(n^{2k})$ to the number of input nodes $n$. To address this problem, we present sparse higher-order Transformers that have quadratic complexity to the number of input hyperedges, and further adopt the kernel attention approach to reduce the complexity to linear. In particular, we show that the sparse second-order Transformers with kernel attention are theoretically more expressive than message passing operations while having an asymptotically identical complexity. Our models achieve significant performance improvement over invariant MLPs and message-passing graph neural networks in large-scale graph regression and set-to-(hyper)graph prediction tasks. Our implementation is available at https://github.com/jw9730/hot.
Hypergraph offers a framework to depict the multilateral relationships in real-world complex data. Predicting higher-order relationships, i.e hyperedge, becomes a fundamental problem for the full understanding of complicated interactions. The development of graph neural network (GNN) has greatly advanced the analysis of ordinary graphs with pair-wise relations. However, these methods could not be easily extended to the case of hypergraph. In this paper, we generalize the challenges of GNN in representing higher-order data in principle, which are edge- and node-level ambiguities. To overcome the challenges, we present SNALS that utilizes bipartite graph neural network with structural features to collectively tackle the two ambiguity issues. SNALS captures the joint interactions of a hyperedge by its local environment, which is retrieved by collecting the spectrum information of their connections. As a result, SNALS achieves nearly 30% performance increase compared with most recent GNN-based models. In addition, we applied SNALS to predict genetic higher-order interactions on 3D genome organization data. SNALS showed consistently high prediction accuracy across different chromosomes, and generated novel findings on 4-way gene interaction, which is further validated by existing literature.
Link prediction in graphs is studied by modeling the dyadic interactions among two nodes. The relationships can be more complex than simple dyadic interactions and could require the user to model super-dyadic associations among nodes. Such interactions can be modeled using a hypergraph, which is a generalization of a graph where a hyperedge can connect more than two nodes. In this work, we consider the problem of hyperedge prediction in a $k-$uniform hypergraph. We utilize the tensor-based representation of hypergraphs and propose a novel interpretation of the tensor eigenvectors. This is further used to propose a hyperedge prediction algorithm. The proposed algorithm utilizes the \textit{Fiedler} eigenvector computed using tensor eigenvalue decomposition of hypergraph Laplacian. The \textit{Fiedler} eigenvector is used to evaluate the construction cost of new hyperedges, which is further utilized to determine the most probable hyperedges to be constructed. The functioning and efficacy of the proposed method are illustrated using some example hypergraphs and a few real datasets. The code for the proposed method is available on https://github.com/d-maurya/hypred_ tensorEVD
Hypergraphs provide a natural way of representing group relations, whose complexity motivates an extensive array of prior work to adopt some form of abstraction and simplification of higher-order interactions. However, the following question has yet to be addressed: How much abstraction of group interactions is sufficient in solving a hypergraph task, and how different such results become across datasets? This question, if properly answered, provides a useful engineering guideline on how to trade off between complexity and accuracy of solving a downstream task. To this end, we propose a method of incrementally representing group interactions using a notion of n-projected graph whose accumulation contains information on up to n-way interactions, and quantify the accuracy of solving a task as n grows for various datasets. As a downstream task, we consider hyperedge prediction, an extension of link prediction, which is a canonical task for evaluating graph models. Through experiments on 15 real-world datasets, we draw the following messages: (a) Diminishing returns: small n is enough to achieve accuracy comparable with near-perfect approximations, (b) Troubleshooter: as the task becomes more challenging, larger n brings more benefit, and (c) Irreducibility: datasets whose pairwise interactions do not tell much about higher-order interactions lose much accuracy when reduced to pairwise abstractions.