知识图谱

Recent embedding-based methods have achieved great successes in exploiting entity alignment from knowledge graph (KG) embeddings of multiple modalities. In this paper, we study embedding-based entity alignment (EEA) from a perspective of generative models. We show that EEA shares similarities with typical generative models and prove the effectiveness of the recently developed generative adversarial network (GAN)-based EEA methods theoretically. We then reveal that their incomplete objective limits the capacity on both entity alignment and entity synthesis (i.e., generating new entities). We mitigate this problem by introducing a generative EEA (GEEA) framework with the proposed mutual variational autoencoder (M-VAE) as the generative model. M-VAE enables entity conversion between KGs and generation of new entities from random noise vectors. We demonstrate the power of GEEA with theoretical analysis and empirical experiments on both entity alignment and entity synthesis tasks. The source code and datasets are available at github.com/zjukg/GEEA.

It is believed that in knowledge distillation (KD), the role of the teacher is to provide an estimate for the unknown Bayes conditional probability distribution (BCPD) to be used in the student training process. Conventionally, this estimate is obtained by training the teacher using maximum log-likelihood (MLL) method. To improve this estimate for KD, in this paper we introduce the concept of conditional mutual information (CMI) into the estimation of BCPD and propose a novel estimator called the maximum CMI (MCMI) method. Specifically, in MCMI estimation, both the log-likelihood and CMI of the teacher are simultaneously maximized when the teacher is trained. In fact, maximizing the teacher's CMI value ensures that the teacher can effectively capture the contextual information within the images, and for visualizing this information, we deploy Eigen-CAM. Via conducting a thorough set of experiments, we show that by employing a teacher trained via MCMI estimation rather than one trained via MLL estimation in various state-of-the-art KD frameworks, the student's classification accuracy consistently increases, with the gain of up to 3.32\%. This suggests that the teacher's BCPD estimate provided by MCMI method is more accurate than that provided by MLL method. In addition, we show that such improvements in the student's accuracy are more drastic in zero-shot and few-shot settings. Notably, the student's accuracy increases with the gain of up to 5.72\% when 5\% of the training samples are available to student (few-shot), and increases from 0\% to as high as 84\% for an omitted class (zero-shot).

Designing effective positional encodings for graphs is key to building powerful graph transformers and enhancing message-passing graph neural networks. Although widespread, using Laplacian eigenvectors as positional encodings faces two fundamental challenges: (1) *Non-uniqueness*: there are many different eigendecompositions of the same Laplacian, and (2) *Instability*: small perturbations to the Laplacian could result in completely different eigenspaces, leading to unpredictable changes in positional encoding. Despite many attempts to address non-uniqueness, most methods overlook stability, leading to poor generalization on unseen graph structures. We identify the cause of instability to be the use of "hard partition'' of eigenspaces. Hence, we introduce Stable and Expressive Positional Encodings (SPE), an architecture for processing eigenvectors that uses eigenvalues to ``softly partition'' eigenspaces. SPE is the first architecture that is (1) provably stable, and (2) universally expressive for basis invariant functions whilst respecting all symmetries of eigenvectors. Besides guaranteed stability, we prove that SPE is at least as expressive as existing methods, and highly capable of counting graph structures. Finally, we evaluate the effectiveness of our method on molecular property prediction, and out-of-distribution generalization tasks, finding improved generalization compared to existing positional encoding methods. Our code is available at https://github.com/Graph-COM/SPE.

How to conduct teacher training for knowledge distillation is still an open problem. It has been widely observed that a best-performing teacher does not necessarily yield the best-performing student, suggesting a fundamental discrepancy between the current teacher training practice and the ideal teacher training strategy. To fill this gap, we explore the feasibility of training a teacher that is oriented toward student performance with empirical risk minimization (ERM). Our analyses are inspired by the recent findings that the effectiveness of knowledge distillation hinges on the teacher’s capability to approximate the true label distribution of training inputs. We theoretically establish that ERM minimizer can approximate the true label distribution of training data as long as the feature extractor of the learner network is Lipschitz continuous and is robust to feature transformations. In light of our theory, we propose a teacher training method SoTeacher which incorporates Lipschitz regularization and consistency regularization into ERM. Experiments on benchmark datasets using various knowledge distillation algorithms and teacher-student pairs confirm that SoTeacher can improve student accuracy consistently.

We introduce the FRactional-Order graph Neural Dynamical network (FROND), a new continuous graph neural network (GNN) framework. Unlike traditional continuous GNNs that rely on integer-order differential equations, FROND employs the Caputo fractional derivative to leverage the non-local properties of fractional calculus. This approach enables the capture of long-term dependencies in feature updates, moving beyond the Markovian update mechanisms in conventional integer-order models and offering enhanced capabilities in graph representation learning. We offer an interpretation of the node feature updating process in FROND from a non-Markovian random walk perspective when the feature updating is particularly governed by a diffusion process. We demonstrate analytically that oversmoothing can be mitigated in this setting. Experimentally, we validate the FROND framework by comparing the fractional adaptations of various established integer-order continuous GNNs, demonstrating their consistently improved performance and underscoring the framework's potential as an effective extension to enhance traditional continuous GNNs. The code is available at \url{https://github.com/zknus/ICLR2024-FROND}.

Realistic graphs contain both (1) rich self-features of nodes and (2) informative structures of neighborhoods, jointly handled by a Graph Neural Network (GNN) in the typical setup. We propose to decouple the two modalities by **M**ixture **o**f **w**eak and **st**rong experts (**Mowst**), where the weak expert is a light-weight Multi-layer Perceptron (MLP), and the strong expert is an off-the-shelf GNN. To adapt the experts' collaboration to different target nodes, we propose a "confidence" mechanism based on the dispersion of the weak expert's prediction logits. The strong expert is conditionally activated in the low-confidence region when either the node's classification relies on neighborhood information, or the weak expert has low model quality. We reveal interesting training dynamics by analyzing the influence of the confidence function on loss: our training algorithm encourages the specialization of each expert by effectively generating soft splitting of the graph. In addition, our "confidence" design imposes a desirable bias toward the strong expert to benefit from GNN's better generalization capability. Mowst is easy to optimize and achieves strong expressive power, with a computation cost comparable to a single GNN. Empirically, Mowst on 4 backbone GNN architectures show significant accuracy improvement on 6 standard node classification benchmarks, including both homophilous and heterophilous graphs (https://github.com/facebookresearch/mowst-gnn).

Graph Visualization, also known as Graph Drawing, aims to find geometric embeddings of graphs that optimize certain criteria. Stress is a widely used metric; stress is minimized when every pair of nodes is positioned at their shortest path distance. However, stress optimization presents computational challenges due to its inherent complexity and is usually solved using heuristics in practice. We introduce a scalable Graph Neural Network (GNN) based Graph Drawing framework with sub-quadratic runtime that can learn to optimize stress. Inspired by classical stress optimization techniques and force-directed layout algorithms, we create a coarsening hierarchy for the input graph. Beginning at the coarsest level, we iteratively refine and un-coarsen the layout, until we generate an embedding for the original graph. To enhance information propagation within the network, we propose a novel positional rewiring technique based on intermediate node positions. Our empirical evaluation demonstrates that the framework achieves state-of-the-art performance while remaining scalable.

We propose a novel random walk-based algorithm for unbiased estimation of arbitrary functions of a weighted adjacency matrix, coined general graph random features (g-GRFs). This includes many of the most popular examples of kernels defined on the nodes of a graph. Our algorithm enjoys subquadratic time complexity with respect to the number of nodes, overcoming the notoriously prohibitive cubic scaling of exact graph kernel evaluation. It can also be trivially distributed across machines, permitting learning on much larger networks. At the heart of the algorithm is a modulation function which upweights or downweights the contribution from different random walks depending on their lengths. We show that by parameterising it with a neural network we can obtain g-GRFs that give higher-quality kernel estimates or perform efficient, scalable kernel learning. We provide robust theoretical analysis and support our findings with experiments including pointwise estimation of fixed graph kernels, solving non-homogeneous graph ordinary differential equations, node clustering and kernel regression on triangular meshes.

Metagenomics studies genomic material derived from mixed microbial communities in diverse environments, holding considerable significance for both human health and environmental sustainability. Metagenomic binning refers to the clustering of genomic subsequences obtained from high-throughput DNA sequencing into distinct bins, each representing a constituent organism within the community. Mainstream binning methods primarily rely on sequence features such as composition and abundance, making them unable to effectively handle sequences shorter than 1,000 bp and inherent noise within sequences. Several binning tools have emerged, aiming to enhance binning outcomes by using the assembly graph generated by assemblers, which encodes valuable overlapping information among genomic sequences. However, existing assembly graph-based binners mainly focus on simplified contig-level assembly graphs that are recreated from assembler’s original graphs, unitig-level assembly graphs. The simplification reduces the resolution of the connectivity information in original graphs. In this paper, we design a novel binning tool named UnitigBin, which leverages representation learning on unitig-level assembly graphs while adhering to heterophilious constraints imposed by single-copy marker genes, ensuring that constrained contigs cannot be grouped together. Extensive experiments conducted on synthetic and real datasets demonstrate that UnitigBin significantly surpasses state-of-the-art binning tools.

We present the Evolving Graph Fourier Transform (EFT), the first invertible spectral transform that captures evolving representations on temporal graphs. We motivate our work by the inadequacy of existing methods for capturing the evolving graph spectra, which are also computationally expensive due to the temporal aspect along with the graph vertex domain. We view the problem as an optimization over the Laplacian of the continuous time dynamic graph. Additionally, we propose pseudo-spectrum relaxations that decompose the transformation process, making it highly computationally efficient. The EFT method adeptly captures the evolving graph's structural and positional properties, making it effective for downstream tasks on evolving graphs. Hence, as a reference implementation, we develop a simple neural model induced with \eft for capturing evolving graph spectra. We empirically validate our theoretical findings on a number of large-scale and standard temporal graph benchmarks and demonstrate that our model achieves state-of-the-art performance.

Clinical predictive models often rely on patients’ electronic health records (EHR), but integrating medical knowledge to enhance predictions and decision-making is challenging. This is because personalized predictions require personalized knowledge graphs (KGs), which are difficult to generate from patient EHR data. To address this, we propose GraphCare, an open-world framework that uses external KGs to improve EHR-based predictions. Our method extracts knowledge from large language models (LLMs) and external biomedical KGs to build patient-specific KGs, which are then used to train our proposed Bi-attention AugmenTed (BAT) graph neural network (GNN) for healthcare predictions. On two public datasets, MIMIC-III and MIMIC-IV, GraphCare surpasses baselines in four vital healthcare prediction tasks: mortality, readmission, length of stay (LOS), and drug recommendation. On MIMIC-III, it boosts AUROC by 17.6% and 6.6% for mortality and readmission, and F1-score by 7.9% and 10.8% for LOS and drug recommendation, respectively. Notably, GraphCare demonstrates a substantial edge in scenarios with limited data availability. Our findings highlight the potential of using external KGs in healthcare prediction tasks and demonstrate the promise of GraphCare in generating personalized KGs for promoting personalized medicine.

Label imbalance and homophily-heterophily mixture are the fundamental problems encountered when applying Graph Neural Networks (GNNs) to Graph Fraud Detection (GFD) tasks. Existing GNN-based GFD models are designed to augment graph structure to accommodate the inductive bias of GNNs towards homophily, by excluding heterophilic neighbors during message passing. In our work, we argue that the key to applying GNNs for GFD is not to exclude but to {\em distinguish} neighbors with different labels. Grounded in this perspective, we introduce Partitioning Message Passing (PMP), an intuitive yet effective message passing paradigm expressly crafted for GFD. Specifically, in the neighbor aggregation stage of PMP, neighbors with different classes are aggregated with distinct node-specific aggregation functions. By this means, the center node can adaptively adjust the information aggregated from its heterophilic and homophilic neighbors, thus avoiding the model gradient being dominated by benign nodes which occupy the majority of the population. We theoretically establish a connection between the spatial formulation of PMP and spectral analysis to characterize that PMP operates an adaptive node-specific spectral graph filter, which demonstrates the capability of PMP to handle heterophily-homophily mixed graphs. Extensive experimental results show that PMP can significantly boost the performance on GFD tasks.

In this work, we propose a novel link prediction model and further boost it by studying graph incompleteness. First, We introduce MPNN-then-SF, an innovative architecture leveraging structural feature (SF) to guide MPNN's representation pooling, with its implementation, namely Neural Common Neighbor (NCN). NCN exhibits superior expressiveness and scalability compared with existing models, which can be classified into two categories: SF-then-MPNN, augmenting MPNN's input with SF, and SF-and-MPNN, decoupling SF and MPNN. Second, we investigate the impact of graph incompleteness---the phenomenon that some links are unobserved in the input graph---on SF, like the common neighbor. Through dataset visualization, we observe that incompleteness reduces common neighbors and induces distribution shifts, significantly affecting model performance. To address this issue, we propose to use a link prediction model to complete the common neighbor structure. Combining this method with NCN, we propose Neural Common Neighbor with Completion (NCNC). NCN and NCNC outperform recent strong baselines by large margins, and NCNC further surpasses state-of-the-art models in standard link prediction benchmarks.

Speculative decoding~(SD) accelerates large language model inference by employing a faster {\em draft} model for generating multiple tokens, which are then verified in parallel by the larger {\em target} model, resulting in the text generated according to the target model distribution. However, identifying a compact draft model that is well-aligned with the target model is challenging. To tackle this issue, we propose {\em DistillSpec} that uses knowledge distillation to better align the draft model with the target model, before applying SD. DistillSpec makes two key design choices, which we demonstrate via systematic study to be crucial to improve the draft and target alignment: utilizing \emph{on-policy} data generation from the draft model, and \emph{tailoring the divergence function} to the task and decoding strategy. Notably, DistillSpec yields impressive $10 - 45\%$ speedups over standard SD on a range of standard benchmarks, using both greedy and non-greedy sampling. Furthermore, we combine DistillSpec with lossy SD to achieve fine-grained control over the latency vs. task performance trade-off. Finally, in practical scenarios with models of varying sizes, first using distillation to boost the performance of the target model and then applying DistillSpec to train a well-aligned draft model can reduce decoding latency by $6 - 10\times$ with minimal performance drop, compared to standard decoding without distillation.

We present a framework to define a large class of neural networks for which, by construction, training by gradient flow provably reaches arbitrarily low loss when the number of parameters grows. Distinct from the fixed-space global optimality of non-convex optimization, this new form of convergence, and the techniques introduced to prove such convergence, pave the way for a usable deep learning convergence theory in the near future, without overparameterization assumptions relating the number of parameters and training samples. We define these architectures from a simple computation graph and a mechanism to lift it, thus increasing the number of parameters, generalizing the idea of increasing the widths of multi-layer perceptrons. We show that architectures similar to most common deep learning models are present in this class, obtained by sparsifying the weight tensors of usual architectures at initialization. Leveraging tools of algebraic topology and random graph theory, we use the computation graph’s geometry to propagate properties guaranteeing convergence to any precision for these large sparse models.

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

Graph Neural Networks (GNNs) are powerful representation learning tools that have achieved remarkable performance in various downstream tasks. However, there are still open questions regarding their ability to count and list substructures, which play a crucial role in biological and social networks. In this work, we fill this gap and characterize the representation {and generalization} power of GNNs in terms of their ability to produce powerful representations that count substructures. In particular, we study the message-passing operations of GNNs with random node input in a novel fashion, and show how they can produce equivariant representations that are associated with high-order statistical moments. Using these representations, we prove that GNNs can learn how to count cycles, {cliques}, quasi-cliques, and the number of connected components in a graph. We also provide new insights into the generalization capacity of GNNs. Our analysis is constructive and enables the design of a generic GNN architecture that shows remarkable performance in four distinct tasks: cycle detection, cycle counting, graph classification, and molecular property prediction.

Nature performs complex computations constantly at clearly lower cost and higher performance than digital computers. It is crucial to understand how to harness the unique computational power of nature in Machine Learning (ML). In the past decade, besides the development of Neural Networks (NNs), the community has also relentlessly explored nature-powered ML paradigms. Although most of them are still predominantly theoretical, a new practical paradigm enabled by the recent advent of CMOS-compatible room-temperature nature-based computers has emerged. By harnessing a dynamical system's intrinsic behavior of chasing the lowest energy state, this paradigm can solve some simple binary problems delivering considerable speedup and energy savings compared with NNs, while maintaining comparable accuracy. Regrettably, its values to the real world are highly constrained by its binary nature. A clear pathway to its extension to real-valued problems remains elusive. This paper aims to unleash this pathway by proposing a novel end-to-end Nature-Powered Graph Learning (NP-GL) framework. Specifically, through a three-dimensional co-design, NP-GL can leverage the spontaneous energy decrease in nature to efficiently solve real-valued graph learning problems. Experimental results across 4 real-world applications with 6 datasets demonstrate that NP-GL delivers, on average, $6.97\times 10^3$ speedup and $10^5$ energy consumption reduction with comparable or even higher accuracy than Graph Neural Networks (GNNs).

Transductive node prediction has been a popular learning setting in Graph Neural Networks (GNNs). It has been widely observed that the shortage of information flow between the distant nodes and intra-batch nodes (for large-scale graphs) often hurt the generalization of GNNs which overwhelmingly adopt message-passing. Yet there is still no formal and direct theoretical results to quantitatively capture the underlying mechanism, despite the recent advance in both theoretical and empirical studies for GNN's generalization ability. In this paper, the $L$-hop interplay (i.e., message passing capability with training nodes) for a $L$-layer GNN is successfully incorporated in our derived PAC-Bayesian bound for GNNs in the semi-supervised transductive setting. In other words, we quantitatively show how the interplay between training and testing sets influence the generalization ability which also partly explains the effectiveness of some existing empirical methods for enhancing generalization. Based on this result, we further design a plug-and-play ***Graph** **G**lobal **W**orkspace* module for GNNs (InterpGNN-GW) to enhance the interplay, utilizing the key-value attention mechanism to summarize crucial nodes' embeddings into memory and broadcast the memory to all nodes, in contrast to the pairwise attention scheme in previous graph transformers. Extensive experiments on both small-scale and large-scale graph datasets validate the effectiveness of our theory and approaches.

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