Despite the success of automated machine learning (AutoML), which aims to find the best design, including the architecture of deep networks and hyper-parameters, conventional AutoML methods are computationally expensive and hardly provide insights into the relations of different model design choices. To tackle the challenges, we propose FALCON, an efficient sample-based method to search for the optimal model design. Our key insight is to model the design space of possible model designs as a design graph, where the nodes represent design choices, and the edges denote design similarities. FALCON features 1) a task-agnostic module, which performs message passing on the design graph via a Graph Neural Network (GNN), and 2) a task-specific module, which conducts label propagation of the known model performance information on the design graph. Both modules are combined to predict the design performances in the design space, navigating the search direction. We conduct extensive experiments on 27 node and graph classification tasks from various application domains, and an image classification task on the CIFAR-10 dataset. We empirically show that FALCON can efficiently obtain the well-performing designs for each task using only 30 explored nodes. Specifically, FALCON has a comparable time cost with the one-shot approaches while achieving an average improvement of 3.3% compared with the best baselines.
Graph neural networks (GNNs) are able to leverage the structure of graph data by passing messages along the edges of the graph. While this allows GNNs to learn features depending on the graph structure, for certain graph topologies it leads to inefficient information propagation and a problem known as oversquashing. This has recently been linked with the curvature and spectral gap of the graph. On the other hand, adding edges to the message-passing graph can lead to increasingly similar node representations and a problem known as oversmoothing. We propose a computationally efficient algorithm that prevents oversquashing by systematically adding edges to the graph based on spectral expansion. We combine this with a relational architecture, which lets the GNN preserve the original graph structure and provably prevents oversmoothing. We find experimentally that our algorithm outperforms existing graph rewiring methods in several graph classification tasks.
Graph neural networks (GNNs) find applications in various domains such as computational biology, natural language processing, and computer security. Owing to their popularity, there is an increasing need to explain GNN predictions since GNNs are black-box machine learning models. One way to address this is counterfactual reasoning where the objective is to change the GNN prediction by minimal changes in the input graph. Existing methods for counterfactual explanation of GNNs are limited to instance-specific local reasoning. This approach has two major limitations of not being able to offer global recourse policies and overloading human cognitive ability with too much information. In this work, we study the global explainability of GNNs through global counterfactual reasoning. Specifically, we want to find a small set of representative counterfactual graphs that explains all input graphs. Towards this goal, we propose GCFExplainer, a novel algorithm powered by vertex-reinforced random walks on an edit map of graphs with a greedy summary. Extensive experiments on real graph datasets show that the global explanation from GCFExplainer provides important high-level insights of the model behavior and achieves a 46.9% gain in recourse coverage and a 9.5% reduction in recourse cost compared to the state-of-the-art local counterfactual explainers.
Recently, implicit graph neural networks (GNNs) have been proposed to capture long-range dependencies in underlying graphs. In this paper, we introduce and justify two weaknesses of implicit GNNs: the constrained expressiveness due to their limited effective range for capturing long-range dependencies, and their lack of ability to capture multiscale information on graphs at multiple resolutions. To show the limited effective range of previous implicit GNNs, We first provide a theoretical analysis and point out the intrinsic relationship between the effective range and the convergence of iterative equations used in these models. To mitigate the mentioned weaknesses, we propose a multiscale graph neural network with implicit layers (MGNNI) which is able to model multiscale structures on graphs and has an expanded effective range for capturing long-range dependencies. We conduct comprehensive experiments for both node classification and graph classification to show that MGNNI outperforms representative baselines and has a better ability for multiscale modeling and capturing of long-range dependencies.
The goal of this paper is to introduce pooling strategies for simplicial convolutional neural networks. Inspired by graph pooling methods, we introduce a general formulation for a simplicial pooling layer that performs: i) local aggregation of simplicial signals; ii) principled selection of sampling sets; iii) downsampling and simplicial topology adaptation. The general layer is then customized to design four different pooling strategies (i.e., max, top-k, self-attention, and separated top-k) grounded in the theory of topological signal processing. Also, we leverage the proposed layers in a hierarchical architecture that reduce complexity while representing data at different resolutions. Numerical results on real data benchmarks (i.e., flow and graph classification) illustrate the advantage of the proposed methods with respect to the state of the art.
Graph neural network (GNN)-based graph learning has been popular in natural language and programming language processing, particularly in text and source code classification. Typically, GNNs are constructed by incorporating alternating layers which learn transformations of graph node features, along with graph pooling layers that use graph pooling operators (e.g., Max-pooling) to effectively reduce the number of nodes while preserving the semantic information of the graph. Recently, to enhance GNNs in graph learning tasks, Manifold-Mixup, a data augmentation technique that produces synthetic graph data by linearly mixing a pair of graph data and their labels, has been widely adopted. However, the performance of Manifold-Mixup can be highly affected by graph pooling operators, and there have not been many studies that are dedicated to uncovering such affection. To bridge this gap, we take an early step to explore how graph pooling operators affect the performance of Mixup-based graph learning. To that end, we conduct a comprehensive empirical study by applying Manifold-Mixup to a formal characterization of graph pooling based on 11 graph pooling operations (9 hybrid pooling operators, 2 non-hybrid pooling operators). The experimental results on both natural language datasets (Gossipcop, Politifact) and programming language datasets (JAVA250, Python800) demonstrate that hybrid pooling operators are more effective for Manifold-Mixup than the standard Max-pooling and the state-of-the-art graph multiset transformer (GMT) pooling, in terms of producing more accurate and robust GNN models.
Graph Neural Networks (GNNs) have recently been applied to graph learning tasks and achieved state-of-the-art (SOTA) results. However, many competitive methods run GNNs multiple times with subgraph extraction and customized labeling to capture information that is hard for normal GNNs to learn. Such operations are time-consuming and do not scale to large graphs. In this paper, we propose an efficient GNN framework called Geodesic GNN (GDGNN) that requires only one GNN run and injects conditional relationships between nodes into the model without labeling. This strategy effectively reduces the runtime of subgraph methods. Specifically, we view the shortest paths between two nodes as the spatial graph context of the neighborhood around them. The GNN embeddings of nodes on the shortest paths are used to generate geodesic representations. Conditioned on the geodesic representations, GDGNN can generate node, link, and graph representations that carry much richer structural information than plain GNNs. We theoretically prove that GDGNN is more powerful than plain GNNs. We present experimental results to show that GDGNN achieves highly competitive performance with SOTA GNN models on various graph learning tasks while taking significantly less time.
Understanding generalization and robustness of machine learning models fundamentally relies on assuming an appropriate metric on the data space. Identifying such a metric is particularly challenging for non-Euclidean data such as graphs. Here, we propose a pseudometric for attributed graphs, the Tree Mover's Distance (TMD), and study its relation to generalization. Via a hierarchical optimal transport problem, TMD reflects the local distribution of node attributes as well as the distribution of local computation trees, which are known to be decisive for the learning behavior of graph neural networks (GNNs). First, we show that TMD captures properties relevant to graph classification: a simple TMD-SVM performs competitively with standard GNNs. Second, we relate TMD to generalization of GNNs under distribution shifts, and show that it correlates well with performance drop under such shifts.
Most Graph Neural Networks (GNNs) predict the labels of unseen graphs by learning the correlation between the input graphs and labels. However, by presenting a graph classification investigation on the training graphs with severe bias, surprisingly, we discover that GNNs always tend to explore the spurious correlations to make decision, even if the causal correlation always exists. This implies that existing GNNs trained on such biased datasets will suffer from poor generalization capability. By analyzing this problem in a causal view, we find that disentangling and decorrelating the causal and bias latent variables from the biased graphs are both crucial for debiasing. Inspiring by this, we propose a general disentangled GNN framework to learn the causal substructure and bias substructure, respectively. Particularly, we design a parameterized edge mask generator to explicitly split the input graph into causal and bias subgraphs. Then two GNN modules supervised by causal/bias-aware loss functions respectively are trained to encode causal and bias subgraphs into their corresponding representations. With the disentangled representations, we synthesize the counterfactual unbiased training samples to further decorrelate causal and bias variables. Moreover, to better benchmark the severe bias problem, we construct three new graph datasets, which have controllable bias degrees and are easier to visualize and explain. Experimental results well demonstrate that our approach achieves superior generalization performance over existing baselines. Furthermore, owing to the learned edge mask, the proposed model has appealing interpretability and transferability. Code and data are available at: https://github.com/googlebaba/DisC.
Since their introduction, graph attention networks achieved outstanding results in graph representation learning tasks. However, these networks consider only pairwise relationships among nodes and then they are not able to fully exploit higher-order interactions present in many real world data-sets. In this paper, we introduce Cell Attention Networks (CANs), a neural architecture operating on data defined over the vertices of a graph, representing the graph as the 1-skeleton of a cell complex introduced to capture higher order interactions. In particular, we exploit the lower and upper neighborhoods, as encoded in the cell complex, to design two independent masked self-attention mechanisms, thus generalizing the conventional graph attention strategy. The approach used in CANs is hierarchical and it incorporates the following steps: i) a lifting algorithm that learns {\it edge features} from {\it node features}; ii) a cell attention mechanism to find the optimal combination of edge features over both lower and upper neighbors; iii) a hierarchical {\it edge pooling} mechanism to extract a compact meaningful set of features. The experimental results show that CAN is a low complexity strategy that compares favorably with state of the art results on graph-based learning tasks.
Recently, subgraphs-enhanced Graph Neural Networks (SGNNs) have been introduced to enhance the expressive power of Graph Neural Networks (GNNs), which was proved to be not higher than the 1-dimensional Weisfeiler-Leman isomorphism test. The new paradigm suggests using subgraphs extracted from the input graph to improve the model's expressiveness, but the additional complexity exacerbates an already challenging problem in GNNs: explaining their predictions. In this work, we adapt PGExplainer, one of the most recent explainers for GNNs, to SGNNs. The proposed explainer accounts for the contribution of all the different subgraphs and can produce a meaningful explanation that humans can interpret. The experiments that we performed both on real and synthetic datasets show that our framework is successful in explaining the decision process of an SGNN on graph classification tasks.
Multimodal machine learning has been widely studied for the development of general intelligence. Recently, the remarkable multimodal algorithms, the Perceiver and Perceiver IO, show competitive results for diverse dataset domains and tasks. However, recent works, Perceiver and Perceiver IO, have focused on heterogeneous modalities, including image, text, and speech, and there are few research works for graph structured datasets. A graph is one of the most generalized dataset structures, and we can represent the other dataset, including images, text, and speech, as graph structured data. A graph has an adjacency matrix different from other dataset domains such as text and image, and it is not trivial to handle the topological information, relational information, and canonical positional information. In this study, we provide a Graph Perceiver IO, the Perceiver IO for the graph structured dataset. We keep the main structure of the Graph Perceiver IO as the Perceiver IO because the Perceiver IO already handles the diverse dataset well, except for the graph structured dataset. The Graph Perceiver IO is a general method, and it can handle diverse datasets such as graph structured data as well as text and images. Comparing the graph neural networks, the Graph Perceiver IO requires a lower complexity, and it can incorporate the local and global information efficiently. We show that Graph Perceiver IO shows competitive results for diverse graph-related tasks, including node classification, graph classification, and link prediction.
Graph Neural Networks achieve state-of-the-art performance on a plethora of graph classification tasks, especially due to pooling operators, which aggregate learned node embeddings hierarchically into a final graph representation. However, they are not only questioned by recent work showing on par performance with random pooling, but also ignore completely higher-order connectivity patterns. To tackle this issue, we propose HoscPool, a clustering-based graph pooling operator that captures higher-order information hierarchically, leading to richer graph representations. In fact, we learn a probabilistic cluster assignment matrix end-to-end by minimising relaxed formulations of motif spectral clustering in our objective function, and we then extend it to a pooling operator. We evaluate HoscPool on graph classification tasks and its clustering component on graphs with ground-truth community structure, achieving best performance. Lastly, we provide a deep empirical analysis of pooling operators' inner functioning.
This paper presents the Persistent Weisfeiler-Lehman Random walk scheme (abbreviated as PWLR) for graph representations, a novel mathematical framework which produces a collection of explainable low-dimensional representations of graphs with discrete and continuous node features. The proposed scheme effectively incorporates normalized Weisfeiler-Lehman procedure, random walks on graphs, and persistent homology. We thereby integrate three distinct properties of graphs, which are local topological features, node degrees, and global topological invariants, while preserving stability from graph perturbations. This generalizes many variants of Weisfeiler-Lehman procedures, which are primarily used to embed graphs with discrete node labels. Empirical results suggest that these representations can be efficiently utilized to produce comparable results to state-of-the-art techniques in classifying graphs with discrete node labels, and enhanced performances in classifying those with continuous node features.
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.
In the past few years, graph neural networks (GNNs) have become the de facto model of choice for graph classification. While, from the theoretical viewpoint, most GNNs can operate on graphs of any size, it is empirically observed that their classification performance degrades when they are applied on graphs with sizes that differ from those in the training data. Previous works have tried to tackle this issue in graph classification by providing the model with inductive biases derived from assumptions on the generative process of the graphs, or by requiring access to graphs from the test domain. The first strategy is tied to the quality of the assumptions made for the generative process, and requires the use of specific models designed after the explicit definition of the generative process of the data, leaving open the question of how to improve the performance of generic GNN models in general settings. On the other hand, the second strategy can be applied to any GNN, but requires access to information that is not always easy to obtain. In this work we consider the scenario in which we only have access to the training data, and we propose a regularization strategy that can be applied to any GNN to improve its generalization capabilities from smaller to larger graphs without requiring access to the test data. Our regularization is based on the idea of simulating a shift in the size of the training graphs using coarsening techniques, and enforcing the model to be robust to such a shift. Experimental results on standard datasets show that popular GNN models, trained on the 50% smallest graphs in the dataset and tested on the 10% largest graphs, obtain performance improvements of up to 30% when trained with our regularization strategy.
Aiming at two molecular graph datasets and one protein association subgraph dataset in OGB graph classification task, we design a graph neural network framework for graph classification task by introducing PAS(Pooling Architecture Search). At the same time, we improve it based on the GNN topology design method F2GNN to further design the feature selection and fusion strategies, so as to further improve the performance of the model in the graph property prediction task while overcoming the over smoothing problem of deep GNN training. Finally, a performance breakthrough is achieved on these three datasets, which is significantly better than other methods with fixed aggregate function. It is proved that the NAS method has high generalization ability for multiple tasks and the advantage of our method in processing graph property prediction tasks.
The Weisfeiler-Lehman (WL) test is a widely used algorithm in graph machine learning, including graph kernels, graph metrics, and graph neural networks. However, it focuses only on the consistency of the graph, which means that it is unable to detect slight structural differences. Consequently, this limits its ability to capture structural information, which also limits the performance of existing models that rely on the WL test. This limitation is particularly severe for traditional metrics defined by the WL test, which cannot precisely capture slight structural differences. In this paper, we propose a novel graph metric called the Wasserstein WL Subtree (WWLS) distance to address this problem. Our approach leverages the WL subtree as structural information for node neighborhoods and defines node metrics using the $L_1$-approximated tree edit distance ($L_1$-TED) between WL subtrees of nodes. Subsequently, we combine the Wasserstein distance and the $L_1$-TED to define the WWLS distance, which can capture slight structural differences that may be difficult to detect using conventional metrics. We demonstrate that the proposed WWLS distance outperforms baselines in both metric validation and graph classification experiments.
When dealing with tabular data, models based on decision trees are a popular choice due to their high accuracy on these data types, their ease of application, and explainability properties. However, when it comes to graph-structured data, it is not clear how to apply them effectively, in a way that incorporates the topological information with the tabular data available on the vertices of the graph. To address this challenge, we introduce TREE-G. TREE-G modifies standard decision trees, by introducing a novel split function that is specialized for graph data. Not only does this split function incorporate the node features and the topological information, but it also uses a novel pointer mechanism that allows split nodes to use information computed in previous splits. Therefore, the split function adapts to the predictive task and the graph at hand. We analyze the theoretical properties of TREE-G and demonstrate its benefits empirically on multiple graph and vertex prediction benchmarks. In these experiments, TREE-G consistently outperforms other tree-based models and often outperforms other graph-learning algorithms such as Graph Neural Networks (GNNs) and Graph Kernels, sometimes by large margins. Moreover, TREE-Gs models and their predictions can be explained and visualized
We show that standard Transformers without graph-specific modifications can lead to promising results in graph learning both in theory and practice. Given a graph, we simply treat all nodes and edges as independent tokens, augment them with token embeddings, and feed them to a Transformer. With an appropriate choice of token embeddings, we prove that this approach is theoretically at least as expressive as an invariant graph network (2-IGN) composed of equivariant linear layers, which is already more expressive than all message-passing Graph Neural Networks (GNN). When trained on a large-scale graph dataset (PCQM4Mv2), our method coined Tokenized Graph Transformer (TokenGT) achieves significantly better results compared to GNN baselines and competitive results compared to Transformer variants with sophisticated graph-specific inductive bias. Our implementation is available at https://github.com/jw9730/tokengt.