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Textual graphs are ubiquitous in real-world applications, featuring rich text information with complex relationships, which enables advanced research across various fields. Textual graph representation learning aims to generate low-dimensional feature embeddings from textual graphs that can improve the performance of downstream tasks. A high-quality feature embedding should effectively capture both the structural and the textual information in a textual graph. However, most textual graph dataset benchmarks rely on word2vec techniques to generate feature embeddings, which inherently limits their capabilities. Recent works on textual graph representation learning can be categorized into two folds: supervised and unsupervised methods. Supervised methods finetune a language model on labeled nodes, which have limited capabilities when labeled data is scarce. Unsupervised methods, on the other hand, extract feature embeddings by developing complex training pipelines. To address these limitations, we propose a novel unified unsupervised learning autoencoder framework, named Node Level Graph AutoEncoder (NodeGAE). We employ language models as the backbone of the autoencoder, with pretraining on text reconstruction. Additionally, we add an auxiliary loss term to make the feature embeddings aware of the local graph structure. Our method maintains simplicity in the training process and demonstrates generalizability across diverse textual graphs and downstream tasks. We evaluate our method on two core graph representation learning downstream tasks: node classification and link prediction. Comprehensive experiments demonstrate that our approach substantially enhances the performance of diverse graph neural networks (GNNs) across multiple textual graph datasets.

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., Comment: 12 pages, 5 figures, submitted to IEEE TKDE

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.

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., Comment: 22 pages, 7 figures, 9 tables

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., Comment: 10 pages, 6 figures, 3 tables

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., Comment: 9 pages, 3 Figures. Accepted by IJCAI 2024

Graph Transformers (GTs) have demonstrated their advantages across a wide range of tasks. However, the self-attention mechanism in GTs overlooks the graph's inductive biases, particularly biases related to structure, which are crucial for the graph tasks. Although some methods utilize positional encoding and attention bias to model inductive biases, their effectiveness is still suboptimal analytically. Therefore, this paper presents Gradformer, a method innovatively integrating GT with the intrinsic inductive bias by applying an exponential decay mask to the attention matrix. Specifically, the values in the decay mask matrix diminish exponentially, correlating with the decreasing node proximities within the graph structure. This design enables Gradformer to retain its ability to capture information from distant nodes while focusing on the graph's local details. Furthermore, Gradformer introduces a learnable constraint into the decay mask, allowing different attention heads to learn distinct decay masks. Such an design diversifies the attention heads, enabling a more effective assimilation of diverse structural information within the graph. Extensive experiments on various benchmarks demonstrate that Gradformer consistently outperforms the Graph Neural Network and GT baseline models in various graph classification and regression tasks. Additionally, Gradformer has proven to be an effective method for training deep GT models, maintaining or even enhancing accuracy compared to shallow models as the network deepens, in contrast to the significant accuracy drop observed in other GT models.Codes are available at \url{https://github.com/LiuChuang0059/Gradformer}., Comment: 9 pages, 7 figures. Accepted by IJCAI 2024

Lack of nonreciprocity is one of the major drawbacks of solid-state acoustic devices, which has hindered the development of microwave-frequency acoustic isolators and circulators. Here we report giant nonreciprocal transmission of shear-horizontal surface acoustic waves (SH-SAWs) on a LiTaO3 substrate coated with a negative-positive magnetostrictive bilayer structure of Ni/Ti/FeCoSiB. Although the static magnetic moments of two layers are parallel, SH-SAWs can excite optical-mode spin waves much stronger than acoustic-mode ones at relatively low frequencies via magnetoelastic coupling. The measured magnitude nonreciprocity exceeds 40 dB (or 80 dB/mm) at 2.333 GHz. In addition, maximum nonreciprocal phase accumulation reaches 188{\deg} (376{\deg}/mm), which is desired for an effective SAW circulator. Our theoretical model and calculations provide an insight into the observed phenomena and demonstrate a pathway for further improvement of nonreciprocal acoustic devices.