Graph Neural Networks (GNNs) have achieved promising results in various tasks such as node classification and graph classification. Recent studies find that GNNs are vulnerable to adversarial attacks. However, effective backdoor attacks on graphs are still an open problem. In particular, backdoor attack poisons the graph by attaching triggers and the target class label to a set of nodes in the training graph. The backdoored GNNs trained on the poisoned graph will then be misled to predict test nodes to target class once attached with triggers. Though there are some initial efforts in graph backdoor attacks, our empirical analysis shows that they may require a large attack budget for effective backdoor attacks and the injected triggers can be easily detected and pruned. Therefore, in this paper, we study a novel problem of unnoticeable graph backdoor attacks with limited attack budget. To fully utilize the attack budget, we propose to deliberately select the nodes to inject triggers and target class labels in the poisoning phase. An adaptive trigger generator is deployed to obtain effective triggers that are difficult to be noticed. Extensive experiments on real-world datasets against various defense strategies demonstrate the effectiveness of our proposed method in conducting effective unnoticeable backdoor attacks.
The dominant paradigm for machine learning on graphs uses Message Passing Graph Neural Networks (MP-GNNs), in which node representations are updated by aggregating information in their local neighborhood. Recently, there have been increasingly more attempts to adapt the Transformer architecture to graphs in an effort to solve some known limitations of MP-GNN. A challenging aspect of designing Graph Transformers is integrating the arbitrary graph structure into the architecture. We propose Graph Diffuser (GD) to address this challenge. GD learns to extract structural and positional relationships between distant nodes in the graph, which it then uses to direct the Transformer's attention and node representation. We demonstrate that existing GNNs and Graph Transformers struggle to capture long-range interactions and how Graph Diffuser does so while admitting intuitive visualizations. Experiments on eight benchmarks show Graph Diffuser to be a highly competitive model, outperforming the state-of-the-art in a diverse set of domains.
Graph convolutional networks (GCNs) have been very effective in addressing the issue of various graph-structured related tasks. However, recent research has shown that GCNs are vulnerable to a new type of threat called a backdoor attack, where the adversary can inject a hidden backdoor into GCNs so that the attacked model performs well on benign samples, but its prediction will be maliciously changed to the attacker-specified target label if the hidden backdoor is activated by the attacker-defined trigger. A semantic backdoor attack is a new type of backdoor attack on deep neural networks (DNNs), where a naturally occurring semantic feature of samples can serve as a backdoor trigger such that the infected DNN models will misclassify testing samples containing the predefined semantic feature even without the requirement of modifying the testing samples. Since the backdoor trigger is a naturally occurring semantic feature of the samples, semantic backdoor attacks are more imperceptible and pose a new and serious threat. In this paper, we investigate whether such semantic backdoor attacks are possible for GCNs and propose a semantic backdoor attack against GCNs (SBAG) under the context of graph classification to reveal the existence of this security vulnerability in GCNs. SBAG uses a certain type of node in the samples as a backdoor trigger and injects a hidden backdoor into GCN models by poisoning training data. The backdoor will be activated, and the GCN models will give malicious classification results specified by the attacker even on unmodified samples as long as the samples contain enough trigger nodes. We evaluate SBAG on four graph datasets and the experimental results indicate that SBAG is effective.
Recently, much exertion has been paid to design graph self-supervised methods to obtain generalized pre-trained models, and adapt pre-trained models onto downstream tasks through fine-tuning. However, there exists an inherent gap between pretext and downstream graph tasks, which insufficiently exerts the ability of pre-trained models and even leads to negative transfer. Meanwhile, prompt tuning has seen emerging success in natural language processing by aligning pre-training and fine-tuning with consistent training objectives. In this paper, we identify the challenges for graph prompt tuning: The first is the lack of a strong and universal pre-training task across sundry pre-training methods in graph domain. The second challenge lies in the difficulty of designing a consistent training objective for both pre-training and downstream tasks. To overcome above obstacles, we propose a novel framework named SGL-PT which follows the learning strategy ``Pre-train, Prompt, and Predict''. Specifically, we raise a strong and universal pre-training task coined as SGL that acquires the complementary merits of generative and contrastive self-supervised graph learning. And aiming for graph classification task, we unify pre-training and fine-tuning by designing a novel verbalizer-free prompting function, which reformulates the downstream task in a similar format as pretext task. Empirical results show that our method surpasses other baselines under unsupervised setting, and our prompt tuning method can greatly facilitate models on biological datasets over fine-tuning methods.
Persistent homology, a technique from computational topology, has recently shown strong empirical performance in the context of graph classification. Being able to capture long range graph properties via higher-order topological features, such as cycles of arbitrary length, in combination with multi-scale topological descriptors, has improved predictive performance for data sets with prominent topological structures, such as molecules. At the same time, the theoretical properties of persistent homology have not been formally assessed in this context. This paper intends to bridge the gap between computational topology and graph machine learning by providing a brief introduction to persistent homology in the context of graphs, as well as a theoretical discussion and empirical analysis of its expressivity for graph learning tasks.
In recent years, Graph Neural Networks (GNNs) have been popular in the graph classification task. Currently, shallow GNNs are more common due to the well-known over-smoothing problem facing deeper GNNs. However, they are sub-optimal without utilizing the information from distant nodes, i.e., the long-range dependencies. The mainstream methods in the graph classification task can extract the long-range dependencies either by designing the pooling operations or incorporating the higher-order neighbors, while they have evident drawbacks by modifying the original graph structure, which may result in information loss in graph structure learning. In this paper, by justifying the smaller influence of the over-smoothing problem in the graph classification task, we evoke the importance of stacking-based GNNs and then employ them to capture the long-range dependencies without modifying the original graph structure. To achieve this, two design needs are given for stacking-based GNNs, i.e., sufficient model depth and adaptive skip-connection schemes. By transforming the two design needs into designing data-specific inter-layer connections, we propose a novel approach with the help of neural architecture search (NAS), which is dubbed LRGNN (Long-Range Graph Neural Networks). Extensive experiments on five datasets show that the proposed LRGNN can achieve the best performance, and obtained data-specific GNNs with different depth and skip-connection schemes, which can better capture the long-range dependencies.
Contemporary graph learning algorithms are not well-defined for large molecules since they do not consider the hierarchical interactions among the atoms, which are essential to determine the molecular properties of macromolecules. In this work, we propose Multiresolution Graph Transformers (MGT), the first graph transformer architecture that can learn to represent large molecules at multiple scales. MGT can learn to produce representations for the atoms and group them into meaningful functional groups or repeating units. We also introduce Wavelet Positional Encoding (WavePE), a new positional encoding method that can guarantee localization in both spectral and spatial domains. Our proposed model achieves competitive results on two macromolecule datasets consisting of polymers and peptides, and one drug-like molecule dataset. Importantly, our model outperforms other state-of-the-art methods and achieves chemical accuracy in estimating molecular properties (e.g., GAP, HOMO and LUMO) calculated by Density Functional Theory (DFT) in the polymers dataset. Furthermore, the visualizations, including clustering results on macromolecules and low-dimensional spaces of their representations, demonstrate the capability of our methodology in learning to represent long-range and hierarchical structures. Our PyTorch implementation is publicly available at https://github.com/HySonLab/Multires-Graph-Transformer
This note describes a new approach to classifying graphs that leverages graph generative models (GGM). Assuming a GGM that defines a joint probability distribution over graphs and their class labels, I derive classification formulas for the probability of a class label given a graph. A new conditional ELBO can be used to train a generative graph auto-encoder model for discrimination. While leveraging generative models for classification has been well explored for non-relational i.i.d. data, to our knowledge it is a novel approach to graph classification.
The construction of machine learning models involves many bi-level multi-objective optimization problems (BL-MOPs), where upper level (UL) candidate solutions must be evaluated via training weights of a model in the lower level (LL). Due to the Pareto optimality of sub-problems and the complex dependency across UL solutions and LL weights, an UL solution is feasible if and only if the LL weight is Pareto optimal. It is computationally expensive to determine which LL Pareto weight in the LL Pareto weight set is the most appropriate for each UL solution. This paper proposes a bi-level multi-objective learning framework (BLMOL), coupling the above decision-making process with the optimization process of the UL-MOP by introducing LL preference $r$. Specifically, the UL variable and $r$ are simultaneously searched to minimize multiple UL objectives by evolutionary multi-objective algorithms. The LL weight with respect to $r$ is trained to minimize multiple LL objectives via gradient-based preference multi-objective algorithms. In addition, the preference surrogate model is constructed to replace the expensive evaluation process of the UL-MOP. We consider a novel case study on multi-task graph neural topology search. It aims to find a set of Pareto topologies and their Pareto weights, representing different trade-offs across tasks at UL and LL, respectively. The found graph neural network is employed to solve multiple tasks simultaneously, including graph classification, node classification, and link prediction. Experimental results demonstrate that BLMOL can outperform some state-of-the-art algorithms and generate well-representative UL solutions and LL weights.
Graph neural networks (GNNs) are a type of neural model that tackle graphical tasks in an end-to-end manner. Recently, GNNs have been receiving increased attention in machine learning and data mining communities because of the higher performance they achieve in various tasks, including graph classification, link prediction, and recommendation. However, the complicated dynamics of GNNs make it difficult to understand which parts of the graph features contribute more strongly to the predictions. To handle the interpretability issues, recently, various GNN explanation methods have been proposed. In this study, a flexible model agnostic explanation method is proposed to detect significant structures in graphs using the Hilbert-Schmidt independence criterion (HSIC), which captures the nonlinear dependency between two variables through kernels. More specifically, we extend the GraphLIME method for node explanation with a group lasso and a fused lasso-based node explanation method. The group and fused regularization with GraphLIME enables the interpretation of GNNs in substructure units. Then, we show that the proposed approach can be used for the explanation of sequential graph classification tasks. Through experiments, it is demonstrated that our method can identify crucial structures in a target graph in various settings.
In this work, we study the problem of partitioning a set of graphs into different groups such that the graphs in the same group are similar while the graphs in different groups are dissimilar. This problem was rarely studied previously, although there have been a lot of work on node clustering and graph classification. The problem is challenging because it is difficult to measure the similarity or distance between graphs. One feasible approach is using graph kernels to compute a similarity matrix for the graphs and then performing spectral clustering, but the effectiveness of existing graph kernels in measuring the similarity between graphs is very limited. To solve the problem, we propose a novel method called Deep Graph-Level Clustering (DGLC). DGLC utilizes a graph isomorphism network to learn graph-level representations by maximizing the mutual information between the representations of entire graphs and substructures, under the regularization of a clustering module that ensures discriminative representations via pseudo labels. DGLC achieves graph-level representation learning and graph-level clustering in an end-to-end manner. The experimental results on six benchmark datasets of graphs show that our DGLC has state-of-the-art performance in comparison to many baselines.
Graph Transformer (GT) recently has emerged as a new paradigm of graph learning algorithms, outperforming the previously popular Message Passing Neural Network (MPNN) on multiple benchmarks. Previous work (Kim et al., 2022) shows that with proper position embedding, GT can approximate MPNN arbitrarily well, implying that GT is at least as powerful as MPNN. In this paper, we study the inverse connection and show that MPNN with virtual node (VN), a commonly used heuristic with little theoretical understanding, is powerful enough to arbitrarily approximate the self-attention layer of GT. In particular, we first show that if we consider one type of linear transformer, the so-called Performer/Linear Transformer (Choromanski et al., 2020; Katharopoulos et al., 2020), then MPNN + VN with only O(1) depth and O(1) width can approximate a self-attention layer in Performer/Linear Transformer. Next, via a connection between MPNN + VN and DeepSets, we prove the MPNN + VN with O(n^d) width and O(1) depth can approximate the self-attention layer arbitrarily well, where d is the input feature dimension. Lastly, under some assumptions, we provide an explicit construction of MPNN + VN with O(1) width and O(n) depth approximating the self-attention layer in GT arbitrarily well. On the empirical side, we demonstrate that 1) MPNN + VN is a surprisingly strong baseline, outperforming GT on the recently proposed Long Range Graph Benchmark (LRGB) dataset, 2) our MPNN + VN improves over early implementation on a wide range of OGB datasets and 3) MPNN + VN outperforms Linear Transformer and MPNN on the climate modeling task.
Link prediction on graphs is a fundamental problem. Subgraph representation learning approaches (SGRLs), by transforming link prediction to graph classification on the subgraphs around the links, have achieved state-of-the-art performance in link prediction. However, SGRLs are computationally expensive, and not scalable to large-scale graphs due to expensive subgraph-level operations. To unlock the scalability of SGRLs, we propose a new class of SGRLs, that we call Scalable Simplified SGRL (S3GRL). Aimed at faster training and inference, S3GRL simplifies the message passing and aggregation operations in each link's subgraph. S3GRL, as a scalability framework, accommodates various subgraph sampling strategies and diffusion operators to emulate computationally-expensive SGRLs. We propose multiple instances of S3GRL and empirically study them on small to large-scale graphs. Our extensive experiments demonstrate that the proposed S3GRL models scale up SGRLs without significant performance compromise (even with considerable gains in some cases), while offering substantially lower computational footprints (e.g., multi-fold inference and training speedup).
Graph-structured data can be found in numerous domains, yet the scarcity of labeled instances hinders its effective utilization of deep learning in many scenarios. Traditional unsupervised domain adaptation (UDA) strategies for graphs primarily hinge on adversarial learning and pseudo-labeling. These approaches fail to effectively leverage graph discriminative features, leading to class mismatching and unreliable label quality. To navigate these obstacles, we develop the Denoising and Nuclear-Norm Wasserstein Adaptation Network (DNAN). DNAN employs the Nuclear-norm Wasserstein discrepancy (NWD), which can simultaneously achieve domain alignment and class distinguishment. DANA also integrates a denoising mechanism via a variational graph autoencoder that mitigates data noise. This denoising mechanism helps capture essential features of both source and target domains, improving the robustness of the domain adaptation process. Our comprehensive experiments demonstrate that DNAN outperforms state-of-the-art methods on standard UDA benchmarks for graph classification.
This work develops a flexible and mathematically sound framework for the design and analysis of graph scattering networks with variable branching ratios and generic functional calculus filters. Spectrally-agnostic stability guarantees for node- and graph-level perturbations are derived; the vertex-set non-preserving case is treated by utilizing recently developed mathematical-physics based tools. Energy propagation through the network layers is investigated and related to truncation stability. New methods of graph-level feature aggregation are introduced and stability of the resulting composite scattering architectures is established. Finally, scattering transforms are extended to edge- and higher order tensorial input. Theoretical results are complemented by numerical investigations: Suitably chosen cattering networks conforming to the developed theory perform better than traditional graph-wavelet based scattering approaches in social network graph classification tasks and significantly outperform other graph-based learning approaches to regression of quantum-chemical energies on QM7.
Identifying a small molecule from its mass spectrum is the primary open problem in computational metabolomics. This is typically cast as information retrieval: an unknown spectrum is matched against spectra predicted computationally from a large database of chemical structures. However, current approaches to spectrum prediction model the output space in ways that force a tradeoff between capturing high resolution mass information and tractable learning. We resolve this tradeoff by casting spectrum prediction as a mapping from an input molecular graph to a probability distribution over molecular formulas. We discover that a large corpus of mass spectra can be closely approximated using a fixed vocabulary constituting only 2% of all observed formulas. This enables efficient spectrum prediction using an architecture similar to graph classification - GrAFF-MS - achieving significantly lower prediction error and orders-of-magnitude faster runtime than state-of-the-art methods.
Graphs are a natural representation of brain activity derived from functional magnetic imaging (fMRI) data. It is well known that clusters of anatomical brain regions, known as functional connectivity networks (FCNs), encode temporal relationships which can serve as useful biomarkers for understanding brain function and dysfunction. Previous works, however, ignore the temporal dynamics of the brain and focus on static graphs. In this paper, we propose a dynamic brain graph deep generative model (DBGDGM) which simultaneously clusters brain regions into temporally evolving communities and learns dynamic unsupervised node embeddings. Specifically, DBGDGM represents brain graph nodes as embeddings sampled from a distribution over communities that evolve over time. We parameterise this community distribution using neural networks that learn from subject and node embeddings as well as past community assignments. Experiments demonstrate DBGDGM outperforms baselines in graph generation, dynamic link prediction, and is comparable for graph classification. Finally, an analysis of the learnt community distributions reveals overlap with known FCNs reported in neuroscience literature.
It has been increasingly demanding to develop reliable methods to evaluate the progress of Graph Neural Network (GNN) research for molecular representation learning. Existing GNN benchmarking methods for molecular representation learning focus on comparing the GNNs' performances on some node/graph classification/regression tasks on certain datasets. However, there lacks a principled, task-agnostic method to directly compare two GNNs. Additionally, most of the existing self-supervised learning works incorporate handcrafted augmentations to the data, which has several severe difficulties to be applied on graphs due to their unique characteristics. To address the aforementioned issues, we propose GraphAC (Graph Adversarial Collaboration) -- a conceptually novel, principled, task-agnostic, and stable framework for evaluating GNNs through contrastive self-supervision. We introduce a novel objective function: the Competitive Barlow Twins, that allow two GNNs to jointly update themselves from direct competitions against each other. GraphAC succeeds in distinguishing GNNs of different expressiveness across various aspects, and has demonstrated to be a principled and reliable GNN evaluation method, without necessitating any augmentations.
The segmentation and automatic identification of histological regions of diagnostic interest offer a valuable aid to pathologists. However, segmentation methods are hampered by the difficulty of obtaining pixel-level annotations, which are tedious and expensive to obtain for Whole-Slide images (WSI). To remedy this, weakly supervised methods have been developed to exploit the annotations directly available at the image level. However, to our knowledge, none of these techniques is adapted to deal with WSIs. In this paper, we propose WholeSIGHT, a weakly-supervised method, to simultaneously segment and classify WSIs of arbitrary shapes and sizes. Formally, WholeSIGHT first constructs a tissue-graph representation of the WSI, where the nodes and edges depict tissue regions and their interactions, respectively. During training, a graph classification head classifies the WSI and produces node-level pseudo labels via post-hoc feature attribution. These pseudo labels are then used to train a node classification head for WSI segmentation. During testing, both heads simultaneously render class prediction and segmentation for an input WSI. We evaluated WholeSIGHT on three public prostate cancer WSI datasets. Our method achieved state-of-the-art weakly-supervised segmentation performance on all datasets while resulting in better or comparable classification with respect to state-of-the-art weakly-supervised WSI classification methods. Additionally, we quantify the generalization capability of our method in terms of segmentation and classification performance, uncertainty estimation, and model calibration.
With the rapid deployment of graph neural networks (GNNs) based techniques into a wide range of applications such as link prediction, node classification, and graph classification the explainability of GNNs has become an indispensable component for predictive and trustworthy decision-making. Thus, it is critical to explain why graph neural network (GNN) makes particular predictions for them to be believed in many applications. Some GNNs explainers have been proposed recently. However, they lack to generate accurate and real explanations. To mitigate these limitations, we propose GANExplainer, based on Generative Adversarial Network (GAN) architecture. GANExplainer is composed of a generator to create explanations and a discriminator to assist with the Generator development. We investigate the explanation accuracy of our models by comparing the performance of GANExplainer with other state-of-the-art methods. Our empirical results on synthetic datasets indicate that GANExplainer improves explanation accuracy by up to 35\% compared to its alternatives.