Graph Neural Networks for Brain Graph Learning: A Survey

Exploring the complex structure of the human brain is crucial for understanding its functionality and diagnosing brain disorders. Thanks to advancements in neuroimaging technology, a novel approach has emerged that involves modeling the human brain as a graph-structured pattern, with different brain regions represented as nodes and the functional relationships among these regions as edges. Moreover, graph neural networks (GNNs) have demonstrated a significant advantage in mining graph-structured data. Developing GNNs to learn brain graph representations for brain disorder analysis has recently gained increasing attention. However, there is a lack of systematic survey work summarizing current research methods in this domain. In this paper, we aim to bridge this gap by reviewing brain graph learning works that utilize GNNs. We first introduce the process of brain graph modeling based on common neuroimaging data. Subsequently, we systematically categorize current works based on the type of brain graph generated and the targeted research problems. To make this research accessible to a broader range of interested researchers, we provide an overview of representative methods and commonly used datasets, along with their implementation sources. Finally, we present our insights on future research directions. The repository of this survey is available at \url{https://github.com/XuexiongLuoMQ/Awesome-Brain-Graph-Learning-with-GNNs}.

Regressor-free Molecule Generation to Support Drug Response Prediction

Drug response prediction (DRP) is a crucial phase in drug discovery, and the most important metric for its evaluation is the IC50 score. DRP results are heavily dependent on the quality of the generated molecules. Existing molecule generation methods typically employ classifier-based guidance, enabling sampling within the IC50 classification range. However, these methods fail to ensure the sampling space range's effectiveness, generating numerous ineffective molecules. Through experimental and theoretical study, we hypothesize that conditional generation based on the target IC50 score can obtain a more effective sampling space. As a result, we introduce regressor-free guidance molecule generation to ensure sampling within a more effective space and support DRP. Regressor-free guidance combines a diffusion model's score estimation with a regression controller model's gradient based on number labels. To effectively map regression labels between drugs and cell lines, we design a common-sense numerical knowledge graph that constrains the order of text representations. Experimental results on the real-world dataset for the DRP task demonstrate our method's effectiveness in drug discovery. The code is available at:https://anonymous.4open.science/r/RMCD-DBD1.

A Cross-Field Fusion Strategy for Drug-Target Interaction Prediction

Drug-target interaction (DTI) prediction is a critical component of the drug discovery process. In the drug development engineering field, predicting novel drug-target interactions is extremely crucial.However, although existing methods have achieved high accuracy levels in predicting known drugs and drug targets, they fail to utilize global protein information during DTI prediction. This leads to an inability to effectively predict interaction the interactions between novel drugs and their targets. As a result, the cross-field information fusion strategy is employed to acquire local and global protein information. Thus, we propose the siamese drug-target interaction SiamDTI prediction method, which utilizes a double channel network structure for cross-field supervised learning.Experimental results on three benchmark datasets demonstrate that SiamDTI achieves higher accuracy levels than other state-of-the-art (SOTA) methods on novel drugs and targets.Additionally, SiamDTI's performance with known drugs and targets is comparable to that of SOTA approachs. The code is available at https://anonymous.4open.science/r/DDDTI-434D.

Hi-GMAE: Hierarchical Graph Masked Autoencoders

Graph Masked Autoencoders (GMAEs) have emerged as a notable self-supervised learning approach for graph-structured data. Existing GMAE models primarily focus on reconstructing node-level information, categorizing them as single-scale GMAEs. This methodology, while effective in certain contexts, tends to overlook the complex hierarchical structures inherent in many real-world graphs. For instance, molecular graphs exhibit a clear hierarchical organization in the form of the atoms-functional groups-molecules structure. Hence, the inability of single-scale GMAE models to incorporate these hierarchical relationships often leads to their inadequate capture of crucial high-level graph information, resulting in a noticeable decline in performance. To address this limitation, we propose Hierarchical Graph Masked AutoEncoders (Hi-GMAE), a novel multi-scale GMAE framework designed to handle the hierarchical structures within graphs. First, Hi-GMAE constructs a multi-scale graph hierarchy through graph pooling, enabling the exploration of graph structures across different granularity levels. To ensure masking uniformity of subgraphs across these scales, we propose a novel coarse-to-fine strategy that initiates masking at the coarsest scale and progressively back-projects the mask to the finer scales. Furthermore, we integrate a gradual recovery strategy with the masking process to mitigate the learning challenges posed by completely masked subgraphs. Diverging from the standard graph neural network (GNN) used in GMAE models, Hi-GMAE modifies its encoder and decoder into hierarchical structures. This entails using GNN at the finer scales for detailed local graph analysis and employing a graph transformer at coarser scales to capture global information. Our experiments on 15 graph datasets consistently demonstrate that Hi-GMAE outperforms 17 state-of-the-art self-supervised competitors.

Where to Mask: Structure-Guided Masking for Graph Masked Autoencoders

Graph masked autoencoders (GMAE) have emerged as a significant advancement in self-supervised pre-training for graph-structured data. Previous GMAE models primarily utilize a straightforward random masking strategy for nodes or edges during training. However, this strategy fails to consider the varying significance of different nodes within the graph structure. In this paper, we investigate the potential of leveraging the graph's structural composition as a fundamental and unique prior in the masked pre-training process. To this end, we introduce a novel structure-guided masking strategy (i.e., StructMAE), designed to refine the existing GMAE models. StructMAE involves two steps: 1) Structure-based Scoring: Each node is evaluated and assigned a score reflecting its structural significance. Two distinct types of scoring manners are proposed: predefined and learnable scoring. 2) Structure-guided Masking: With the obtained assessment scores, we develop an easy-to-hard masking strategy that gradually increases the structural awareness of the self-supervised reconstruction task. Specifically, the strategy begins with random masking and progresses to masking structure-informative nodes based on the assessment scores. This design gradually and effectively guides the model in learning graph structural information. Furthermore, extensive experiments consistently demonstrate that our StructMAE method outperforms existing state-of-the-art GMAE models in both unsupervised and transfer learning tasks. Codes are available at https://github.com/LiuChuang0059/StructMAE.

Heterogeneous Subgraph Transformer for Fake News Detection

Fake news is pervasive on social media, inflicting substantial harm on public discourse and societal well-being. We investigate the explicit structural information and textual features of news pieces by constructing a heterogeneous graph concerning the relations among news topics, entities, and content. Through our study, we reveal that fake news can be effectively detected in terms of the atypical heterogeneous subgraphs centered on them, which encapsulate the essential semantics and intricate relations between news elements. However, suffering from the heterogeneity, exploring such heterogeneous subgraphs remains an open problem. To bridge the gap, this work proposes a heterogeneous subgraph transformer (HeteroSGT) to exploit subgraphs in our constructed heterogeneous graph. In HeteroSGT, we first employ a pre-trained language model to derive both word-level and sentence-level semantics. Then the random walk with restart (RWR) is applied to extract subgraphs centered on each news, which are further fed to our proposed subgraph Transformer to quantify the authenticity. Extensive experiments on five real-world datasets demonstrate the superior performance of HeteroSGT over five baselines. Further case and ablation studies validate our motivation and demonstrate that performance improvement stems from our specially designed components.

MoCha-Stereo: Motif Channel Attention Network for Stereo Matching

Learning-based stereo matching techniques have made significant progress. However, existing methods inevitably lose geometrical structure information during the feature channel generation process, resulting in edge detail mismatches. In this paper, the Motif Cha}nnel Attention Stereo Matching Network (MoCha-Stereo) is designed to address this problem. We provide the Motif Channel Correlation Volume (MCCV) to determine more accurate edge matching costs. MCCV is achieved by projecting motif channels, which capture common geometric structures in feature channels, onto feature maps and cost volumes. In addition, edge variations in %potential feature channels of the reconstruction error map also affect details matching, we propose the Reconstruction Error Motif Penalty (REMP) module to further refine the full-resolution disparity estimation. REMP integrates the frequency information of typical channel features from the reconstruction error. MoCha-Stereo ranks 1st on the KITTI-2015 and KITTI-2012 Reflective leaderboards. Our structure also shows excellent performance in Multi-View Stereo. Code is avaliable at https://github.com/ZYangChen/MoCha-Stereo.

Exploring Sparsity in Graph Transformers

Graph Transformers (GTs) have achieved impressive results on various graph-related tasks. However, the huge computational cost of GTs hinders their deployment and application, especially in resource-constrained environments. Therefore, in this paper, we explore the feasibility of sparsifying GTs, a significant yet under-explored topic. We first discuss the redundancy of GTs based on the characteristics of existing GT models, and then propose a comprehensive \textbf{G}raph \textbf{T}ransformer \textbf{SP}arsification (GTSP) framework that helps to reduce the computational complexity of GTs from four dimensions: the input graph data, attention heads, model layers, and model weights. Specifically, GTSP designs differentiable masks for each individual compressible component, enabling effective end-to-end pruning. We examine our GTSP through extensive experiments on prominent GTs, including GraphTrans, Graphormer, and GraphGPS. The experimental results substantiate that GTSP effectively cuts computational costs, accompanied by only marginal decreases in accuracy or, in some cases, even improvements. For instance, GTSP yields a reduction of 30\% in Floating Point Operations while contributing to a 1.8\% increase in Area Under the Curve accuracy on OGBG-HIV dataset. Furthermore, we provide several insights on the characteristics of attention heads and the behavior of attention mechanisms, all of which have immense potential to inspire future research endeavors in this domain.

Careful Selection and Thoughtful Discarding: Graph Explicit Pooling Utilizing Discarded Nodes

Graph pooling has been increasingly recognized as crucial for Graph Neural Networks (GNNs) to facilitate hierarchical graph representation learning. Existing graph pooling methods commonly consist of two stages: selecting top-ranked nodes and discarding the remaining to construct coarsened graph representations. However, this paper highlights two key issues with these methods: 1) The process of selecting nodes to discard frequently employs additional Graph Convolutional Networks or Multilayer Perceptrons, lacking a thorough evaluation of each node's impact on the final graph representation and subsequent prediction tasks. 2) Current graph pooling methods tend to directly discard the noise segment (dropped) of the graph without accounting for the latent information contained within these elements. To address the first issue, we introduce a novel Graph Explicit Pooling (GrePool) method, which selects nodes by explicitly leveraging the relationships between the nodes and final representation vectors crucial for classification. The second issue is addressed using an extended version of GrePool (i.e., GrePool+), which applies a uniform loss on the discarded nodes. This addition is designed to augment the training process and improve classification accuracy. Furthermore, we conduct comprehensive experiments across 12 widely used datasets to validate our proposed method's effectiveness, including the Open Graph Benchmark datasets. Our experimental results uniformly demonstrate that GrePool outperforms 14 baseline methods for most datasets. Likewise, implementing GrePool+ enhances GrePool's performance without incurring additional computational costs.

Uncertainty-guided Boundary Learning for Imbalanced Social Event Detection

Real-world social events typically exhibit a severe class-imbalance distribution, which makes the trained detection model encounter a serious generalization challenge. Most studies solve this problem from the frequency perspective and emphasize the representation or classifier learning for tail classes. While in our observation, compared to the rarity of classes, the calibrated uncertainty estimated from well-trained evidential deep learning networks better reflects model performance. To this end, we propose a novel uncertainty-guided class imbalance learning framework - UCL$_{SED}$, and its variant - UCL-EC$_{SED}$, for imbalanced social event detection tasks. We aim to improve the overall model performance by enhancing model generalization to those uncertain classes. Considering performance degradation usually comes from misclassifying samples as their confusing neighboring classes, we focus on boundary learning in latent space and classifier learning with high-quality uncertainty estimation. First, we design a novel uncertainty-guided contrastive learning loss, namely UCL and its variant - UCL-EC, to manipulate distinguishable representation distribution for imbalanced data. During training, they force all classes, especially uncertain ones, to adaptively adjust a clear separable boundary in the feature space. Second, to obtain more robust and accurate class uncertainty, we combine the results of multi-view evidential classifiers via the Dempster-Shafer theory under the supervision of an additional calibration method. We conduct experiments on three severely imbalanced social event datasets including Events2012\_100, Events2018\_100, and CrisisLexT\_7. Our model significantly improves social event representation and classification tasks in almost all classes, especially those uncertain ones.