Despite the success of Graph Neural Networks (GNNs) in modeling recommender systems as bipartite graphs, their ability to capture diverse user-item relations remains limited by the sparsity of observed interactions, which fails to reveal the underlying latent intents. We propose IACLR (Intention Alignment via Contrastive Learning for bipartite graph Recommendation), a framework that constructs an Intent-Graph by augmenting the bipartite recommendation graphs with an implicit intent layer. Instead of relying solely on observed edges, IACLR introduces a set of intent nodes that bridge users and items through shared semantic and behavioral patterns. These nodes are used to construct an Intent-Graph, where they act as both intermediaries that enrich structural connectivity and global anchors that summarize latent user interests. Within this graph, IACLR performs contrastive alignment across multiple data views and enforces consistency among users, intents, and items, thereby enhancing robustness under data sparsity. Experiments on benchmark datasets (e.g., Amazon-books and Yelp) demonstrate that IACLR consistently outperforms strong graph-based, revealing its effectiveness in capturing fine-grained user–item relationships and integrating multi-faceted signals. The framework is applicable to various recommendation scenarios, including academic paper recommendations, e-commerce, and content platforms.

Graph neural networks (GNNs) are widely used in information retrieval, but they often require large amounts of labeled data. To address this problem, self-supervised methods like graph contrastive learning (GCL) are developed to learn from graph structures without labeled data. However, GCL faces a challenge in practice. Plenty of traditional GCL methods differ fundamentally from GNNs in handling neighboring nodes, hindering effective contrastive learning. To address the above issue, we propose a graph self-supervised learning model based on Contrastive Graph Matching (ConGM). The model effectively mitigates the conflict between GCL methods and the homophily assumption of GNNs by using linear node matching and quadratic edge alignment mechanisms to treat some neighboring nodes as both positive and negative samples, rather than considering all neighboring nodes as negative samples as in traditional GCL methods. Additionally, to tackle the imbalance of positive and negative samples in edge alignment, we design a bi-level negative sample selection strategy to choose appropriate hard negative samples. Extensive experiments conducted on multiple benchmark datasets have validated the effectiveness of our proposed method.

Link sign prediction in signed bipartite graphs, which are extensively utilized across diverse domains such as social networks and recommendation systems, has recently emerged as a pivotal challenge. However, significant space and time complexities associated with the scalability of bipartite graphs pose substantial challenges, particularly in large-scale environments. To address these issues, this paper introduces the SignFlow Bipartite Subgraph Network (SBSN), balancing sublinear training memory growth through a heuristic subgraph extraction method integrated with a novel message passing module, with optimal inference efficiency achieved via the node feature distillation module. Our subgraph sampling approach reduces the graph size by focusing on neighborhoods around target links and employs an optimized directed message passing mechanism to aggregate critical structural patterns. This mechanism allows SBSN to efficiently learn rich local structural patterns essential for accurate sign prediction. Furthermore, to overcome the inefficiency of subgraph sampling-based models during inference, SBSN incorporates a node feature distillation module after the first training stage. This module distills subgraph features into node features, enabling fast inference while retaining the rich structural information of subgraphs. Experiments reveal that SBSN shows superior performance in both medium- and large-scale datasets, efficiently managing memory and computational resources, making it a scalable solution for extensive applications.

Signed bipartite graphs are widely employed in social networks, recommender systems, and other domains, where the nodes represent two different sets, such as users and commodities, and the links have positive and negative signs to reflect the ratings. Link sign prediction is a crucial task, but the link class imbalance when one type of link (e.g., the head class) is significantly more numerous than another (e.g., the tail class) makes this task extremely challenging. To address this challenge, we propose a Line-Graph-Based Dynamic Balancing Prediction (LDBP) method. Specifically, we first convert the links of a signed bipartite graph into nodes of a line graph, and then the link class imbalance problem in the bipartite graph is naturally transformed to the problem of node class imbalance in the line graph. To tackle this problem, we introduce a Centroid Contrastive Learning (CCL) method and design a Dynamic Synthesis & Deletion (DSD) strategy for the tail-class nodes. By dynamically adjusting the quantity of synthesized tail-class nodes, we obtain a Balanced Line Graph (BaLG). Extensive experiments on real-world datasets demonstrate the effectiveness of our method in improving the accuracy of link sign prediction and addressing the issue of link class imbalance.

Personalized news recommendation plays a vital role in mitigating information overload, yet challenges persist in accurately capturing user preferences and fine-grained interests. Leveraging the semantic understanding and extraction capabilities of large language models (LLMs), we propose a Multi-Interest Personalized News Recommendation (MIPNR) model to address these issues. MIPNR separately models user interests at the user, news, and entity levels. Specifically, we introduce a Category-Guided Interest-News Matching (CGIN-Matching) method to identify potential interests, a Local News Entity Graph (LNEG) to model subtle entity relationships, and an entity-wise attention mechanism to extract fine-grained interests. In addition, LLMs are used to generate explicit textual descriptions of user preferences. Extensive experiments on real-world datasets demonstrate the effectiveness of our approach.

In the field of graph representation learning for molecular property prediction, self-supervised learning is highly appreciated for its ability to mine potential connections in unlabeled data. However, existing approaches such as neighborhood prediction or contrastive learning often lack in fusing structural and semantic features of molecular graphs. To address this issue, we propose a Graph Matching Based Graph Self-Supervised Learning (GMSSL) framework, which aims to comprehensively learn the structure and semantics of molecular graphs. Specifically, utilizing intra-graph and inter-graph convolution and graph matching methods, GMSSL is able to encode complex information for efficient training without supervision. After pre-training and fine-tuning, GMSSL demonstrates powerful molecular property prediction on multiple datasets.

To enhance the accuracy and reliability of the response of large language models (LLMs) in professional domain-specific question answering, this paper proposes an approach to enhance the capabilities of LLMs by prompting them to "think twice." This methodology encourages a second-pass processing, allowing for deeper analysis and more refined outputs. We developed a prototype-logic-inspired query optimizer (PQO) to enhance the response of LLM. It refines initial queries using few-shot learning and self-reflection, leading to more insightful questions. Our experimental results show that the proposed approach obtains empirically validated answers.

As a popular similarity measurement, Graph Edit Distance (GED) can be applied to various downstream tasks. Traditional GED solvers have difficulty in generalization and time efficiency, so deep graph similarity learning models have emerged as a promising trend. However, existing methods lack distinguishing embeddings for cross-dependencies between graphs and intra-graph representations. In this paper, we propose a deep network architecture GED-CDA by introducing a graph-graph context dependency attention module to enhance embeddings. Our graph-graph context dependency attention module consists of a cross-attention layer and a self-attention layer, which can both learn the interactions between graph pairs and capture the connections within graphs. In addition, we also introduce a spectral encoding strategy to bring topological information of graphs into node representations. Extensive experimental results on three real-world graph datasets demonstrate the effectiveness of our proposed GED-CDA in the GED task.

Deriving from image matching and understanding, semantic keypoint matching aims at establishing correspondence between keypoint sets in images. As graphs are powerful tools to represent points and their complex relationships, graph matching provides an effective way to find desired semantic keypoint correspondences. Recent deep graph matching methods have shown excellent performance, but there is still a lack of exploration and utilization of spatial information of keypoints as nodes in graphs. More specifically, existing methods are insufficient to capture the relative spatial relations through current graph construction approaches from the locations of semantic keypoints. To address these issues, we introduce a positional reconstruction encoder-decoder (PR-EnDec) to model intrinsic graph spatial structure, and present an end-to-end graph matching network PREGM based on PR-EnDec. Our PR-EnDec consists of a positional encoder that learns effective node spatial embedding with the affine transformation invariance, and a spatial relation decoder that further utilizes the high-order spatial information by reconstructing the locational structure of graphs contained in the node coordinates. Extensive experimental results on three public keypoint matching datasets demonstrate the effectiveness of our proposed PREGM.

Continual graph learning (CGL) aims to mitigate the topological-feature-induced catastrophic forgetting problem (TCF) in graph neural networks, which plays an essential role in the field of information retrieval. The TCF is mainly caused by the forgetting of node features of old tasks and the forgetting of topological features shared by old and new tasks. Existing CGL methods do not pay enough attention to the forgetting of topological features shared between different tasks. In this paper, we propose a transformer-based CGL method (Trans-CGL), thereby taking full advantage of the transformer's properties to mitigate the TCF problem. Specifically, to alleviate forgetting of node features, we introduce a gated attention mechanism for Trans-CGL based on parameter isolation that allows the model to be independent of each other when learning old and new tasks. Furthermore, to address the forgetting of shared parameters that store topological information between different tasks, we propose an asymmetric mask attention regularization module to constrain the shared attention parameters ensuring that the shared topological information is preserved. Comparative experiments show that the method achieves competitive performance on four real-world datasets.

The increasing demand for molecular formula image data leads to formidable pressure for researchers. Most existing image segmentation approaches can not be directly utilized for molecules, and how to improve the coverage fineness and generate a large amount of labeled training data is worthy of further exploration. To this end, we establish a deep learning based molecular formula image segmentation model (DL-MFS). Specifically, we design a shape constraint loss (SCL) function to refine the detection frame position and propose a rule-based molecular formula image data augmentation method for solving the bottleneck problem that the lack of training data. Experimental results demonstrate the effectiveness of the proposed segmentation model.

Molecular image retrieval is one of the crucial steps in automatic mining and utilization of biochemistry-related literatures, which is also a relatively open and challenging task in cross fields of biochemistry and artificial intelligence. The challenges come from two aspects: 1) there is a lack of open datasets and evaluation criteria for molecular image retrieval. 2) Common retrieval methods always ignore that molecular image retrieval has cross-modal information of both images and SMILES texts. To address the first challenge, we firstly construct a new molecular image retrieval benchmark, named MIR, including 130770 molecular images, labeled structural similarity, and reasonable evaluation metrics. Faced with the second challenge, we propose an effective cross-modal pre-training framework for molecular image retrieval following CLIP. Experimental results reflect the effectiveness of our proposed benchmark MIR and cross-modal pre-training framework.

Chinese Grammatical Error Diagnosis (CGED) suffers the problems of numerous types of grammatical errors and insufficiency of training data. In this paper, we propose a string editing based CGED model that requires less training data by using a unified workflow to handle various types of grammatical errors. Two measures are proposed in our model to enhance the performance of CGED. First, the detection and correction of grammatical errors are divided into different stages. In the stage of error detection, the model only outputs the types of grammatical errors so that the tag vocabulary size is significantly reduced compared with other string editing based models. Secondly, the correction of some grammatical errors is converted to the task of masked character inference, which has plenty of training data and mature solutions. Experiments on datasets of NLPTEA-CGED demonstrate that our model outperforms other CGED models in many aspects.

The binding affinity between drugs and proteins is a substantial part of the drug discovery process. Graph neural networks (GNNs) have shown great promise in graph-related structure by learning the representations of graphs, which are suitable for tasks such as binding affinity prediction. However, most of the existing GNN architectures only pay attention to the information flow on a single graph, while the interaction between two graphs is unconcerned. In this paper, we propose an attention-enhanced graph cross-convolution network (GCAT) to explore binding affinity on pure 3D atomistic geometry. It consists of two components: cross-convolution and self-attention pooling. Specifically, cross-convolution performs an aggregate-update mechanism to simulate the interaction between the protein and the drug, then self-attention pooling is adopted to capture global interactions and get graph-level representations. Extensive experiments conducted on the PDB-Bind dataset demonstrate the effectiveness of our GCAT.

Drug repurposing aims at identifying new indications for approved drugs that are outside the scope of the original indications. Understanding the acting mechanism among drugs, protein targets, and diseases, especially the interdependent and indecomposable relationships, is a critical step. However, most existing methods rely on pairwise relationships. To model the biological interactions between the three types of entities, which are likely ignored by the pairwise paradigm, we propose an end-to-end Event-Graph Neural Network (EGNN) to predict multivariate relationships of drugs, targets, and diseases for drug repurposing. Specifically, we introduce the event to describe the interdependence of drug-target-disease as a complete semantic unit and design the Event-Graph to model the multivariate relationships. To predict the potential relationships, we perform the representation learning on the Event-Graph by a bidirectional aggregating operation and an event-level attention mechanism. Experimental results on real-world datasets demonstrate the effectiveness and promising performance of EGNN compared with several competitive methods.

Graph matching aims at establishing correspondence between node sets of given graphs while keeping the consistency between their edge sets. However, outliers in practical scenarios and equivalent learning of edge representations in deep learning methods are still challenging. To address these issues, we present an Edge Attention-adaptive Graph Matching (EAGM) network and a novel description of edge features. EAGM transforms the matching relation between two graphs into a node and edge classification problem over their assignment graph. To explore the potential of edges, EAGM learns edge attention on the assignment graph to 1) reveal the impact of each edge on graph matching, as well as 2) adjust the learning of edge representations adaptively. To alleviate issues caused by the outliers, we describe an edge by aggregating the semantic information over the space spanned by the edge. Such rich information provides clear distinctions between different edges (e.g., inlier-inlier edges vs. inlier-outlier edges), which further distinguishes outliers in the view of their associated edges. Extensive experiments demonstrate that EAGM achieves promising matching quality compared with state-of-the-arts, on cases both with and without outliers. Our source code along with the experiments is available at https://github.com/bestwei/EAGM.

Drug repositioning has received ever-increasing attention in the field of drug discovery over the last few years. However, the high efficient prediction methods taking full advantage of heterogeneous information networks (HINs) still deserves further research. To this end, this paper proposes an approach for drug repositioning via integrating HINs embedding and link prediction for more potential drug-target interactions. To utilize multiple side information, we introduce a graph convolutional network (GCN) based embedding method for HINs. The obtained drug-related and target-related information is adopted to improve the low-rank matrix completion (LRMC) model. Moreover, a regulation for alleviating the noise of negative samples is designed to enhance the optimization of LRMC. The experiments conducted on the comparative database demonstrate that the proposed method is more effective than the existing approaches in the prediction of drug repositioning.

Cold-start is a long-standing and challenging problem in recommendation systems. To tackle this issue, many cross-domain recommendation approaches are proposed. However, most of them follow a two-stage embedding-and-mapping paradigm, which is hard to be optimized. Besides, they ignore the structure information of the user-item interaction graph, resulting in that the embedding is insufficient to capture the latent collaborative filtering effect. In this paper, we propose a Dual Autoencoder Network (DAN), which implements cross-domain recommendations to cold-start users in an end-to-end manner. The graph convolutional network (GCN) based encoder in DAN explicitly captures high-order collaborative information in user-item interaction graphs. The two-branched decoder is proposed for fully exploiting the data across domains, and therefore the elaborate reconstruction constraints are obtained under a domain swapping strategy. Experiments on two pairs of real-world cross-domain datasets demonstrate that DAN outperforms existing state-of-the-art methods.

As a vital component of graph neural networks, graph pooling remains largely an open problem. Most existing methods are induced by empirical insights, while ignore the effect of topology information for graph coarsening guidance. In this paper, we propose a Topology Discriminative Pooling (TD-Pool) approach, which derives graph pooling architectures from graph kernels for semantic and structural feature co-embedding. Concretely, TD-Pool contains two graph modules, namely recurrent edge module and convolutional node module, for respectively learning topological/semantic embeddings on edges/nodes. The edge module combines Weisfeiler-Lehman graph kernel with neural networks, which captures topology features in a data-driven manner. It is deployed on the line graphs, whose nodes correspond to the original graph edges for semantic-topology decoupling. The node module learns semantic features with graph convolution in the spectral domain, which acts on the original graphs nodes. Extensive experiments demonstrate the effectiveness of our TD-Pool in graph-level tasks.

Quantifying the similarity of compounds is a particularly important problem, as it is able to give rise to many new possibilities for understanding the relationship between molecules. Here we develop a novel algorithm for computing the Molecular similarity. Experimental results on a broad range of real world graphs and tasks show that the proposed similarity measure is very effective.

Potential drug-disease association prediction is important to facilitate drug discovery. However, most of existing drug-disease association prediction approaches rely on assembling multiple drug (disease)-related biological information, which is usually not comprehensively available, and they always fail to explore the latent information in drug-disease network. To tackle these challenges, we propose a graph neural network-based method for drug-disease association prediction, dubbed GNDD, with capturing the complex information between drugs and diseases dispense with any side information. Specifically, GNDD introduces the idea of collaborative filtering in recommendation system to avoid the dependency on multi-data. Furthermore, an embedding propagation strategy is exploited to model the high-order relationships in drug-disease network. We conduct experiments on the Comparative Toxicogenomics Database, demonstrating the effectiveness of our method in drug-disease association prediction.

Many research tasks in the bioinformatics area, such as bioactivity prediction, de novo molecular design, and synthesis prediction, increasingly utilize graph-similarity-based analysis, which relies on selecting graph representation methods. However, most studies focus on the improvement of the final results of the tasks, and less attention has been paid on the differences of the distribution of the result of graph representation, (e.g. the embedded vectors) and how to evaluate them. In this paper, we propose a metric, mean degree of consistency (MDC), to evaluate the different approaches of graph representation with the help of retrieval results. To implement MDC, we introduce a serialized matching matrix and an optimization method based on partial sequence matching. We evaluate the efficiency and reliability of MDC with a series of experiments on graph-similarity-based retrievals for molecule graphs (MGs). Our result is helpful to the graph researchers for selecting graph representation methods.

Molecular graph generation aims to design molecules with desired biochemical properties, which is promising in drug discovery. Existing methods typically combine deep reinforcement models with adversarial training. However, the reinforced rewards in molecule generation are delayed and sparse while adversarial training suffers mode collapse issue. Moreover, they optimize multiple properties with a linear combination manner, where the models get distracted by potentially conflicting objectives. To tackle the above challenges, we propose a Deep Reinforced framework with Adversarial Imitation and Multitask learning (DR-AIM). First, the reinforced agent generates discrete molecular graphs via deep Q-learning, where the trajectories of high rewards are cached as experts. Then policies are extracted directly from expert trajectories by adversarial imitation learning, in which the discriminator delivers behavior distribution signals to the agent as dense rewards. Second, we propose to realize multi-goal molecule generation as a multitask learning process, where different property optimizations are treated as different tasks to be trained jointly. Extensive experiments demonstrate the effectiveness of DR-AIM in molecule generation.

Zero-shot and few-shot learning aim to improve generalization to unseen concepts, which are promising in many realistic scenarios. Due to the lack of data in unseen domain, relation modeling between seen and unseen domains is vital for knowledge transfer in these tasks. Most existing methods capture seen-unseen relationimplicitly via semantic embedding or feature generation, resulting in inadequate use of relation and some issues remain (e.g. domain shift). To tackle these challenges, we propose a Transferable Graph Generation (TGG ) approach, in which the relation is modeled and utilizedexplicitly via graph generation. Specifically, our proposed TGG contains two main components: (1) Graph generation for relation modeling. Anattention-based aggregate network and arelation kernel are proposed, which generate instance-level graph based on a class-level prototype graph and visual features. Proximity information aggregating is guided by a multi-head graph attention mechanism, where seen and unseen features synthesized by GAN are revised as node embeddings. The relation kernel further generates edges with GCN and graph kernel method, to capture instance-level topological structure while tackling data imbalance and noise. (2) Relation propagation for relation utilization. Adual relation propagation approach is proposed, where relations captured by the generated graph are separately propagated from the seen and unseen subgraphs. The two propagations learn from each other in a dual learning fashion, which performs as an adaptation way for mitigating domain shift. All components are jointly optimized with a meta-learning strategy, and our TGG acts as an end-to-end framework unifying conventional zero-shot, generalized zero-shot and few-shot learning. Extensive experiments demonstrate that it consistently surpasses existing methods of the above three fields by a significant margin.

Chemical Structural Formula(CSF) recognition plays an important role in the molecular design and component retrieval. However, sketch-based CSF recognition remains an obstacle in current retrieval systems. This paper introduces a system for sketch CSF recognition on smart mobile devices. A dual-mode-based method is proposed to distinguish the gestures for character inputs and non-character inputs instead of the ordinary segmentation approaches. An attribute graph model is established to describe effectively all necessary information of a sketched CSF. Chemical knowledge is adopted to refine the candidates of structure relationship among elements. The experiments results demonstrate that the proposed method outperforms the existing methods for free-sketch CSFs on effectiveness and flexibility.