DA-MoE: Addressing Depth-Sensitivity in Graph-Level Analysis through Mixture of Experts

Graph neural networks (GNNs) are gaining popularity for processing graph-structured data. In real-world scenarios, graph data within the same dataset can vary significantly in scale. This variability leads to depth-sensitivity, where the optimal depth of GNN layers depends on the scale of the graph data. Empirically, fewer layers are sufficient for message passing in smaller graphs, while larger graphs typically require deeper networks to capture long-range dependencies and global features. However, existing methods generally use a fixed number of GNN layers to generate representations for all graphs, overlooking the depth-sensitivity issue in graph structure data. To address this challenge, we propose the depth adaptive mixture of expert (DA-MoE) method, which incorporates two main improvements to GNN backbone: \textbf{1)} DA-MoE employs different GNN layers, each considered an expert with its own parameters. Such a design allows the model to flexibly aggregate information at different scales, effectively addressing the depth-sensitivity issue in graph data. \textbf{2)} DA-MoE utilizes GNN to capture the structural information instead of the linear projections in the gating network. Thus, the gating network enables the model to capture complex patterns and dependencies within the data. By leveraging these improvements, each expert in DA-MoE specifically learns distinct graph patterns at different scales. Furthermore, comprehensive experiments on the TU dataset and open graph benchmark (OGB) have shown that DA-MoE consistently surpasses existing baselines on various tasks, including graph, node, and link-level analyses. The code are available at \url{https://github.com/Celin-Yao/DA-MoE}.

Text-Guided Multi-Property Molecular Optimization with a Diffusion Language Model

Molecular optimization (MO) is a crucial stage in drug discovery in which task-oriented generated molecules are optimized to meet practical industrial requirements. Existing mainstream MO approaches primarily utilize external property predictors to guide iterative property optimization. However, learning all molecular samples in the vast chemical space is unrealistic for predictors. As a result, errors and noise are inevitably introduced during property prediction due to the nature of approximation. This leads to discrepancy accumulation, generalization reduction and suboptimal molecular candidates. In this paper, we propose a text-guided multi-property molecular optimization method utilizing transformer-based diffusion language model (TransDLM). TransDLM leverages standardized chemical nomenclature as semantic representations of molecules and implicitly embeds property requirements into textual descriptions, thereby preventing error propagation during diffusion process. Guided by physically and chemically detailed textual descriptions, TransDLM samples and optimizes encoded source molecules, retaining core scaffolds of source molecules and ensuring structural similarities. Moreover, TransDLM enables simultaneous sampling of multiple molecules, making it ideal for scalable, efficient large-scale optimization through distributed computation on web platforms. Furthermore, our approach surpasses state-of-the-art methods in optimizing molecular structural similarity and enhancing chemical properties on the benchmark dataset. The code is available at: https://anonymous.4open.science/r/TransDLM-A901.

Fragment-Masked Molecular Optimization

Molecular optimization is a crucial aspect of drug discovery, aimed at refining molecular structures to enhance drug efficacy and minimize side effects, ultimately accelerating the overall drug development process. Many target-based molecular optimization methods have been proposed, significantly advancing drug discovery. These methods primarily on understanding the specific drug target structures or their hypothesized roles in combating diseases. However, challenges such as a limited number of available targets and a difficulty capturing clear structures hinder innovative drug development. In contrast, phenotypic drug discovery (PDD) does not depend on clear target structures and can identify hits with novel and unbiased polypharmacology signatures. As a result, PDD-based molecular optimization can reduce potential safety risks while optimizing phenotypic activity, thereby increasing the likelihood of clinical success. Therefore, we propose a fragment-masked molecular optimization method based on PDD (FMOP). FMOP employs a regression-free diffusion model to conditionally optimize the molecular masked regions without training, effectively generating new molecules with similar scaffolds. On the large-scale drug response dataset GDSCv2, we optimize the potential molecules across all 945 cell lines. The overall experiments demonstrate that the in-silico optimization success rate reaches 94.4%, with an average efficacy increase of 5.3%. Additionally, we conduct extensive ablation and visualization experiments, confirming that FMOP is an effective and robust molecular optimization method. The code is available at:https://anonymous.4open.science/r/FMOP-98C2.

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}.

Dual-perspective Cross Contrastive Learning in Graph Transformers

Graph contrastive learning (GCL) is a popular method for leaning graph representations by maximizing the consistency of features across augmented views. Traditional GCL methods utilize single-perspective i.e. data or model-perspective) augmentation to generate positive samples, restraining the diversity of positive samples. In addition, these positive samples may be unreliable due to uncontrollable augmentation strategies that potentially alter the semantic information. To address these challenges, this paper proposed a innovative framework termed dual-perspective cross graph contrastive learning (DC-GCL), which incorporates three modifications designed to enhance positive sample diversity and reliability: 1) We propose dual-perspective augmentation strategy that provide the model with more diverse training data, enabling the model effective learning of feature consistency across different views. 2) From the data perspective, we slightly perturb the original graphs using controllable data augmentation, effectively preserving their semantic information. 3) From the model perspective, we enhance the encoder by utilizing more powerful graph transformers instead of graph neural networks. Based on the model's architecture, we propose three pruning-based strategies to slightly perturb the encoder, providing more reliable positive samples. These modifications collectively form the DC-GCL's foundation and provide more diverse and reliable training inputs, offering significant improvements over traditional GCL methods. Extensive experiments on various benchmarks demonstrate that DC-GCL consistently outperforms different baselines on various datasets and tasks.

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.

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.

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.