The graph retrieval problem is to search in a large corpus of graphs for ones that are most similar to a query graph. A common consideration for scoring similarity is the maximum common subgraph (MCS) between the query and corpus graphs, usually counting the number of common edges (i.e., MCES). In some applications, it is also desirable that the common subgraph be connected, i.e., the maximum common connected subgraph (MCCS). Finding exact MCES and MCCS is intractable, but may be unnecessary if ranking corpus graphs by relevance is the goal. We design fast and trainable neural functions that approximate MCES and MCCS well. Late interaction methods compute dense representations for the query and corpus graph separately, and compare these representations using simple similarity functions at the last stage, leading to highly scalable systems. Early interaction methods combine information from both graphs right from the input stages, are usually considerably more accurate, but slower. We propose both late and early interaction neural MCES and MCCS formulations. They are both based on a continuous relaxation of a node alignment matrix between query and corpus nodes. For MCCS, we propose a novel differentiable network for estimating the size of the largest connected common subgraph. Extensive experiments with seven data sets show that our proposals are superior among late interaction models in terms of both accuracy and speed. Our early interaction models provide accuracy competitive with the state of the art, at substantially greater speeds.
Graph Neural Networks~(GNNs) are effective tools for graph representation learning. Most GNNs rely on a recursive neighborhood aggregation scheme, named message passing, thereby their theoretical expressive power is limited to the first order Weisfeiler-Lehman test (1-WL). Motivated by the success of retrieval-based models and off-the-shelf high-performance retrieval systems, we propose a non-parametric and model-agnostic scheme called GraphRetrieval to boost existing GNN models. In GraphRetrieval, similar training graphs associated with their ground-truth labels are retrieved as an enhancement to be jointly utilized with the input graph representation to complete various graph property predictive tasks. In particular, to effectively "absorb" useful information from retrieved graphs and "ignore" possible noise, we introduce an adapter based on self-attention to explicitly learn the interaction between an input graph and its retrieved similar graphs. By experimenting with three classic GNN models on 12 different datasets, we have demonstrated GraphRetrieval is able to bring substantial improvements to existing GNN models without comprising the model size and the prediction efficiency. Our work also firstly validates the feasibility and effectiveness of retrieved-enhanced graph neural networks.
Downsampling produces coarsened, multi-resolution representations of data and it is used, for example, to produce lossy compression and visualization of large images, reduce computational costs, and boost deep neural representation learning. Unfortunately, due to their lack of a regular structure, there is still no consensus on how downsampling should apply to graphs and linked data. Indeed reductions in graph data are still needed for the goals described above, but reduction mechanisms do not have the same focus on preserving topological structures and properties, while allowing for resolution-tuning, as is the case in regular data downsampling. In this paper, we take a step in this direction, introducing a unifying interpretation of downsampling in regular and graph data. In particular, we define a graph coarsening mechanism which is a graph-structured counterpart of controllable equispaced coarsening mechanisms in regular data. We prove theoretical guarantees for distortion bounds on path lengths, as well as the ability to preserve key topological properties in the coarsened graphs. We leverage these concepts to define a graph pooling mechanism that we empirically assess in graph classification tasks, providing a greedy algorithm that allows efficient parallel implementation on GPUs, and showing that it compares favorably against pooling methods in literature.
Surrogate models have shown to be an extremely efficient aid in solving engineering problems that require repeated evaluations of an expensive computational model. They are built by sparsely evaluating the costly original model and have provided a way to solve otherwise intractable problems. A crucial aspect in surrogate modelling is the assumption of smoothness and regularity of the model to approximate. This assumption is however not always met in reality. For instance in civil or mechanical engineering, some models may present discontinuities or non-smoothness, e.g., in case of instability patterns such as buckling or snap-through. Building a single surrogate model capable of accounting for these fundamentally different behaviors or discontinuities is not an easy task. In this paper, we propose a three-stage approach for the approximation of non-smooth functions which combines clustering, classification and regression. The idea is to split the space following the localized behaviors or regimes of the system and build local surrogates that are eventually assembled. A sequence of well-known machine learning techniques are used: Dirichlet process mixtures models (DPMM), support vector machines and Gaussian process modelling. The approach is tested and validated on two analytical functions and a finite element model of a tensile membrane structure.
The adaptive processing of structured data is a long-standing research topic in machine learning that investigates how to automatically learn a mapping from a structured input to outputs of various nature. Recently, there has been an increasing interest in the adaptive processing of graphs, which led to the development of different neural network-based methodologies. In this thesis, we take a different route and develop a Bayesian Deep Learning framework for graph learning. The dissertation begins with a review of the principles over which most of the methods in the field are built, followed by a study on graph classification reproducibility issues. We then proceed to bridge the basic ideas of deep learning for graphs with the Bayesian world, by building our deep architectures in an incremental fashion. This framework allows us to consider graphs with discrete and continuous edge features, producing unsupervised embeddings rich enough to reach the state of the art on several classification tasks. Our approach is also amenable to a Bayesian nonparametric extension that automatizes the choice of almost all model's hyper-parameters. Two real-world applications demonstrate the efficacy of deep learning for graphs. The first concerns the prediction of information-theoretic quantities for molecular simulations with supervised neural models. After that, we exploit our Bayesian models to solve a malware-classification task while being robust to intra-procedural code obfuscation techniques. We conclude the dissertation with an attempt to blend the best of the neural and Bayesian worlds together. The resulting hybrid model is able to predict multimodal distributions conditioned on input graphs, with the consequent ability to model stochasticity and uncertainty better than most works. Overall, we aim to provide a Bayesian perspective into the articulated research field of deep learning for graphs.
Graph Neural Networks (GNNs) have received considerable attention on graph-structured data learning for a wide variety of tasks. The well-designed propagation mechanism which has been demonstrated effective is the most fundamental part of GNNs. Although most of GNNs basically follow a message passing manner, litter effort has been made to discover and analyze their essential relations. In this paper, we establish a surprising connection between different propagation mechanisms with a unified optimization problem, showing that despite the proliferation of various GNNs, in fact, their proposed propagation mechanisms are the optimal solution optimizing a feature fitting function over a wide class of graph kernels with a graph regularization term. Our proposed unified optimization framework, summarizing the commonalities between several of the most representative GNNs, not only provides a macroscopic view on surveying the relations between different GNNs, but also further opens up new opportunities for flexibly designing new GNNs. With the proposed framework, we discover that existing works usually utilize naive graph convolutional kernels for feature fitting function, and we further develop two novel objective functions considering adjustable graph kernels showing low-pass or high-pass filtering capabilities respectively. Moreover, we provide the convergence proofs and expressive power comparisons for the proposed models. Extensive experiments on benchmark datasets clearly show that the proposed GNNs not only outperform the state-of-the-art methods but also have good ability to alleviate over-smoothing, and further verify the feasibility for designing GNNs with our unified optimization framework.
As a scene graph compactly summarizes the high-level content of an image in a structured and symbolic manner, the similarity between scene graphs of two images reflects the relevance of their contents. Based on this idea, we propose a novel approach for image-to-image retrieval using scene graph similarity measured by graph neural networks. In our approach, graph neural networks are trained to predict the proxy image relevance measure, computed from human-annotated captions using a pre-trained sentence similarity model. We collect and publish the dataset for image relevance measured by human annotators to evaluate retrieval algorithms. The collected dataset shows that our method agrees well with the human perception of image similarity than other competitive baselines.
Deep learning methods for graphs achieve remarkable performance on many node-level and graph-level prediction tasks. However, despite the proliferation of the methods and their success, prevailing Graph Neural Networks (GNNs) neglect subgraphs, rendering subgraph prediction tasks challenging to tackle in many impactful applications. Further, subgraph prediction tasks present several unique challenges, because subgraphs can have non-trivial internal topology, but also carry a notion of position and external connectivity information relative to the underlying graph in which they exist. Here, we introduce SUB-GNN, a subgraph neural network to learn disentangled subgraph representations. In particular, we propose a novel subgraph routing mechanism that propagates neural messages between the subgraph's components and randomly sampled anchor patches from the underlying graph, yielding highly accurate subgraph representations. SUB-GNN specifies three channels, each designed to capture a distinct aspect of subgraph structure, and we provide empirical evidence that the channels encode their intended properties. We design a series of new synthetic and real-world subgraph datasets. Empirical results for subgraph classification on eight datasets show that SUB-GNN achieves considerable performance gains, outperforming strong baseline methods, including node-level and graph-level GNNs, by 12.4% over the strongest baseline. SUB-GNN performs exceptionally well on challenging biomedical datasets when subgraphs have complex topology and even comprise multiple disconnected components.
Spectral clustering (SC) is a popular clustering technique to find strongly connected communities on a graph. SC can be used in Graph Neural Networks (GNNs) to implement pooling operations that aggregate nodes belonging to the same cluster. However, the eigendecomposition of the Laplacian is expensive and, since clustering results are graph-specific, pooling methods based on SC must perform a new optimization for each new sample. In this paper, we propose a graph clustering approach that addresses these limitations of SC. We formulate a continuous relaxation of the normalized minCUT problem and train a GNN to compute cluster assignments that minimize this objective. Our GNN-based implementation is differentiable, does not require to compute the spectral decomposition, and learns a clustering function that can be quickly evaluated on out-of-sample graphs. From the proposed clustering method, we design a graph pooling operator that overcomes some important limitations of state-of-the-art graph pooling techniques and achieves the best performance in several supervised and unsupervised tasks.
Graph neural networks (GNNs) are a popular class of machine learning models whose major advantage is their ability to incorporate a sparse and discrete dependency structure between data points. Unfortunately, GNNs can only be used when such a graph-structure is available. In practice, however, real-world graphs are often noisy and incomplete or might not be available at all. With this work, we propose to jointly learn the graph structure and the parameters of graph convolutional networks (GCNs) by approximately solving a bilevel program that learns a discrete probability distribution on the edges of the graph. This allows one to apply GCNs not only in scenarios where the given graph is incomplete or corrupted but also in those where a graph is not available. We conduct a series of experiments that analyze the behavior of the proposed method and demonstrate that it outperforms related methods by a significant margin.
Text Classification is an important and classical problem in natural language processing. There have been a number of studies that applied convolutional neural networks (convolution on regular grid, e.g., sequence) to classification. However, only a limited number of studies have explored the more flexible graph convolutional neural networks (convolution on non-grid, e.g., arbitrary graph) for the task. In this work, we propose to use graph convolutional networks for text classification. We build a single text graph for a corpus based on word co-occurrence and document word relations, then learn a Text Graph Convolutional Network (Text GCN) for the corpus. Our Text GCN is initialized with one-hot representation for word and document, it then jointly learns the embeddings for both words and documents, as supervised by the known class labels for documents. Our experimental results on multiple benchmark datasets demonstrate that a vanilla Text GCN without any external word embeddings or knowledge outperforms state-of-the-art methods for text classification. On the other hand, Text GCN also learns predictive word and document embeddings. In addition, experimental results show that the improvement of Text GCN over state-of-the-art comparison methods become more prominent as we lower the percentage of training data, suggesting the robustness of Text GCN to less training data in text classification.