Wenbin Hu

Ge Zhang, Jia Wu, Jian Yang et al. · allen-ai

Graph-structured data consisting of objects (i.e., nodes) and relationships among objects (i.e., edges) are ubiquitous. Graph-level learning is a matter of studying a collection of graphs instead of a single graph. Traditional graph-level learning methods used to be the mainstream. However, with the increasing scale and complexity of graphs, Graph-level Neural Networks (GLNNs, deep learning-based graph-level learning methods) have been attractive due to their superiority in modeling high-dimensional data. Thus, a survey on GLNNs is necessary. To frame this survey, we propose a systematic taxonomy covering GLNNs upon deep neural networks, graph neural networks, and graph pooling. The representative and state-of-the-art models in each category are focused on this survey. We also investigate the reproducibility, benchmarks, and new graph datasets of GLNNs. Finally, we conclude future directions to further push forward GLNNs. The repository of this survey is available at https://github.com/GeZhangMQ/Awesome-Graph-level-Neural-Networks.

Chiaming Hsu, Changtong Zan, Liang Ding et al.

Relation Extraction (RE) is a crucial task in Information Extraction, which entails predicting relationships between entities within a given sentence. However, extending pre-trained RE models to other languages is challenging, particularly in real-world scenarios where Cross-Lingual Relation Extraction (XRE) is required. Despite recent advancements in Prompt-Learning, which involves transferring knowledge from Multilingual Pre-trained Language Models (PLMs) to diverse downstream tasks, there is limited research on the effective use of multilingual PLMs with prompts to improve XRE. In this paper, we present a novel XRE algorithm based on Prompt-Tuning, referred to as Prompt-XRE. To evaluate its effectiveness, we design and implement several prompt templates, including hard, soft, and hybrid prompts, and empirically test their performance on competitive multilingual PLMs, specifically mBART. Our extensive experiments, conducted on the low-resource ACE05 benchmark across multiple languages, demonstrate that our Prompt-XRE algorithm significantly outperforms both vanilla multilingual PLMs and other existing models, achieving state-of-the-art performance in XRE. To further show the generalization of our Prompt-XRE on larger data scales, we construct and release a new XRE dataset- WMT17-EnZh XRE, containing 0.9M English-Chinese pairs extracted from WMT 2017 parallel corpus. Experiments on WMT17-EnZh XRE also show the effectiveness of our Prompt-XRE against other competitive baselines. The code and newly constructed dataset are freely available at \url{https://github.com/HSU-CHIA-MING/Prompt-XRE}.

Zhenyu Yang, Ge Zhang, Jia Wu et al.

Graphs have a superior ability to represent relational data, like chemical compounds, proteins, and social networks. Hence, graph-level learning, which takes a set of graphs as input, has been applied to many tasks including comparison, regression, classification, and more. Traditional approaches to learning a set of graphs heavily rely on hand-crafted features, such as substructures. But while these methods benefit from good interpretability, they often suffer from computational bottlenecks as they cannot skirt the graph isomorphism problem. Conversely, deep learning has helped graph-level learning adapt to the growing scale of graphs by extracting features automatically and encoding graphs into low-dimensional representations. As a result, these deep graph learning methods have been responsible for many successes. Yet, there is no comprehensive survey that reviews graph-level learning starting with traditional learning and moving through to the deep learning approaches. This article fills this gap and frames the representative algorithms into a systematic taxonomy covering traditional learning, graph-level deep neural networks, graph-level graph neural networks, and graph pooling. To ensure a thoroughly comprehensive survey, the evolutions, interactions, and communications between methods from four different branches of development are also examined. This is followed by a brief review of the benchmark data sets, evaluation metrics, and common downstream applications. The survey concludes with a broad overview of 12 current and future directions in this booming field.

Chuang Liu, Xueqi Ma, Yibing Zhan et al.

Graph Neural Networks (GNNs) tend to suffer from high computation costs due to the exponentially increasing scale of graph data and the number of model parameters, which restricts their utility in practical applications. To this end, some recent works focus on sparsifying GNNs with the lottery ticket hypothesis (LTH) to reduce inference costs while maintaining performance levels. However, the LTH-based methods suffer from two major drawbacks: 1) they require exhaustive and iterative training of dense models, resulting in an extremely large training computation cost, and 2) they only trim graph structures and model parameters but ignore the node feature dimension, where significant redundancy exists. To overcome the above limitations, we propose a comprehensive graph gradual pruning framework termed CGP. This is achieved by designing a during-training graph pruning paradigm to dynamically prune GNNs within one training process. Unlike LTH-based methods, the proposed CGP approach requires no re-training, which significantly reduces the computation costs. Furthermore, we design a co-sparsifying strategy to comprehensively trim all three core elements of GNNs: graph structures, node features, and model parameters. Meanwhile, aiming at refining the pruning operation, we introduce a regrowth process into our CGP framework, in order to re-establish the pruned but important connections. The proposed CGP is evaluated by using a node classification task across 6 GNN architectures, including shallow models (GCN and GAT), shallow-but-deep-propagation models (SGC and APPNP), and deep models (GCNII and ResGCN), on a total of 14 real-world graph datasets, including large-scale graph datasets from the challenging Open Graph Benchmark. Experiments reveal that our proposed strategy greatly improves both training and inference efficiency while matching or even exceeding the accuracy of existing methods.

Jiejun Tan, Wenbin Hu, WeiWei Liu

Relation classification (RC) aims to predict the relationship between a pair of subject and object in a given context. Recently, prompt tuning approaches have achieved high performance in RC. However, existing prompt tuning approaches have the following issues: (1) numerous categories decrease RC performance; (2) manually designed prompts require intensive labor. To address these issues, a novel paradigm, Entity Pre-typing Relation Classification with Prompt Answer Centralizing(EPPAC) is proposed in this paper. The entity pre-tying in EPPAC is presented to address the first issue using a double-level framework that pre-types entities before RC and prompt answer centralizing is proposed to address the second issue. Extensive experiments show that our proposed EPPAC outperformed state-of-the-art approaches on TACRED and TACREV by 14.4% and 11.1%, respectively. The code is provided in the Supplementary Materials.

Hongzhi Zhang, Xiuwen Gong, Shirui Pan et al.

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.

Zelin Yao, Chuang Liu, Xianke Meng et al.

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}.

Chuang Liu, Wenhang Yu, Kuang Gao et al.

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.

Kun Li, Wenbin Hu

Deep learning-based drug response prediction (DRP) methods can accelerate the drug discovery process and reduce R\&D costs. Although the mainstream methods achieve high accuracy in predicting response regression values, the regression-aware representations of these methods are fragmented and fail to capture the continuity of the sample order. This phenomenon leads to models optimized to sub-optimal solution spaces, reducing generalization ability and may result in significant wasted costs in the drug discovery phase. In this paper, we propose \MN, a contrastive learning framework with natural language supervision for the DRP. The \MN~converts regression labels into text, which is merged with the captions text of the drug response as a second modality of the samples compared to the traditional modalities (graph, sequence). In each batch, two modalities of one sample are considered positive pairs and the other pairs are considered negative pairs. At the same time, in order to enhance the continuous representation capability of the numerical text, a common-sense numerical knowledge graph is introduced. We validated several hundred thousand samples from the Genomics of Drug Sensitivity in Cancer dataset, observing the average improvement of the DRP method ranges from 7.8\% to 31.4\% with the application of our framework. The experiments prove that the \MN~effectively constrains the samples to a continuous distribution in the representation space, and achieves impressive prediction performance with only a few epochs of fine-tuning after pre-training. The code is available at: \url{https://gitee.com/xiaoyibang/clipdrug.git}.

Mukun Chen, Jia Wu, Shirui Pan et al.

Molecular representation learning is pivotal in predicting molecular properties and advancing drug design. Traditional methodologies, which predominantly rely on homogeneous graph encoding, are limited by their inability to integrate external knowledge and represent molecular structures across different levels of granularity. To address these limitations, we propose a paradigm shift by encoding molecular graphs into heterogeneous structures, introducing a novel framework: Knowledge-aware Contrastive Heterogeneous Molecular Graph Learning (KCHML). This approach leverages contrastive learning to enrich molecular representations with embedded external knowledge. KCHML conceptualizes molecules through three distinct graph views-molecular, elemental, and pharmacological-enhanced by heterogeneous molecular graphs and a dual message-passing mechanism. This design offers a comprehensive representation for property prediction, as well as for downstream tasks such as drug-drug interaction (DDI) prediction. Extensive benchmarking demonstrates KCHML's superiority over state-of-the-art molecular property prediction models, underscoring its ability to capture intricate molecular features.

Wenbin Hu, Iordanis Chatzinikolaidis, Kai Yuan et al.

This paper studies bipedal locomotion as a nonlinear optimization problem based on continuous and discrete dynamics, by simultaneously optimizing the remaining step duration, the next step duration and the foot location to achieve robustness. The linear inverted pendulum as the motion model captures the center of mass dynamics and its low-dimensionality makes the problem more tractable. We first formulate a holistic approach to search for optimality in the three-dimensional parametric space and use these results as baseline. To further improve computational efficiency, our study investigates a sequential approach with two stages of customized optimization that first optimizes the current step duration, and subsequently the duration and location of the next step. The effectiveness of both approaches is successfully demonstrated in simulation by applying different perturbations. The comparison study shows that these two approaches find mostly the same optimal solutions, but the latter requires considerably less computational time, which suggests that the proposed sequential approach is well suited for real-time implementation with a minor trade-off in optimality.