Brain network analysis technology reveals the organizational mechanism and information processing mode by constructing the structural connection network between brain regions. It has achieved satisfactory results in brain disease prediction tasks, promoting the progress of neuroscience. In recent years, graph transformer has become the most mainstream method for brain analysis with its powerful feature extraction ability and attention mechanism. However, these methods face two challenges, i.e., lack of interpretability, and neglect of semantic associations among brain regions. To solve these problems, we proposed a large language model (LLM)-driven causal knowledge brain network transformer framework, termed BrainCKT, which is plug-and-play, and can adapt to most of the existing mainstream graph transformer-based methods. Specifically, we constructed a brain region causal graph and used its adjacency matrix to guide the learning process of the self-attention mechanism. In addition, we constructed a brain science knowledge graph and encoded it through a pre-trained model to enhance the original brain region features. Finally, we integrated BrainCKT into four mainstream graph transformer baselines for verification. Experimental results on two brain imaging datasets proved the effectiveness of BrainCKT.

Spatial transcriptomics has revolutionized the ability to investigate transcriptional patterns within tissue morphology. However, many ST clustering pipelines operate on a single preselected gene set, typically prioritizing either highly variable genes (HVGs) or spatially variable genes (SVGs), and therefore may not directly model how genes with different levels of global variability provide complementary cues for spatial domain identification. Although non-HVG signals can be partially captured through SVG selection and spatial graph modeling, a dedicated two-view formulation that disentangles high-variance and low-variance gene subsets and fuses them under a unified objective remains underexplored. To this end, we propose a Spatial Transcriptomics clustering framework for Cross-view information Fusion, termed STCF, which casts HVGs and low-variability genes (LVGs) as two gene-expression views and integrates them via a plug-and-play cross-view fusion strategy. Specifically, STCF introduces a cross-view fusion mechanism that employs reverse-scaled cosine error loss (R-SCE) to balance alignment and separation of gene embeddings, ensuring robust representation learning while preserving spatial coherence, which enhances the model's ability to resolve fine-grained spatial structures. Extensive experiments on three benchmark datasets (DLPFC, HBC, and MBA) demonstrate the superiority, effectiveness, and transferability of STCF. Case studies further validate its ability to uncover latent spatial patterns and improve clustering precision.

Subgraph Federated Learning (FL) has emerged as a promising paradigm for node classification tasks wherein subgraphs derived from a global graph are distributed across multiple devices to mitigate data leakage risks. Similar to other FL systems, subgraph FL faces significant security challenges, particularly from backdoor attacks, an area that remains extensively underexplored. Existing attacks typically follow a two-phase strategy to implant backdoors. However, in subgraph FL, such attacks often lead toDivergence Amplification, a phenomenon characterized by significant parameter discrepancies between normal and backdoored models, thereby compromising attack stealthiness. To tackle this challenge, we propose BEEF, a Backdoor attack with an End-to-End Framework designed for effectiveness, stealth, and durability. Unlike conventional methods, BEEF incorporates a dedicated trigger generator, which is jointly trained with a backdoored model. To increase its stealthiness, BEEF crafts adversarial perturbations as triggers that provoke misclassification while leaving the model’s parameters entirely untouched. Furthermore, by calibrating a subset of low-salience parameters associated with backdoor activation, BEEF ensures stable performance and sustained effectiveness across FL rounds. Comprehensive evaluations across eight datasets, four models, five state-of-the-art attacks, and six aggregation methods demonstrate BEEF’s effectiveness in deceiving GNNs while maintaining minimal impact on normal data performance. Additionally, we adapt BEEF to federated graph classification tasks, broadening its applicability and practicality.

Reasoning paths are reliable information in knowledge graph completion (KGC) in which algorithms can find strong clues of the actual relation between entities. However, in real-world applications, it is difficult to guarantee that computationally affordable paths exist toward all candidate entities. According to our observation, the prediction accuracy drops significantly when paths are absent. To make the proposed algorithm more stable against the missing path circumstances, we introduce soft reasoning paths. Concretely, a specific learnable latent path embedding is concatenated to each relation to help better model the characteristics of the corresponding paths. The combination of the relation and the corresponding learnable embedding is termed a soft path in our paper. By aligning the soft paths with the reasoning paths, a learnable embedding is guided to learn a generalized path representation of the corresponding relation. In addition, we introduce a hierarchical ranking strategy to make full use of information about the entity, relation, path, and soft path to help improve both the efficiency and accuracy of the model. Extensive experimental results illustrate that our algorithm outperforms the compared state-of-the-art algorithms by a notable margin. Our code will be released at https://github.com/7HHHHH/SRP-KGC.

Few-shot knowledge graph reasoning (FS-KGR) try to infer missing facts in a knowledge graphs using limited data (such as only 3/5 samples).Existing strategies have shown good performance by mining more supervised information for few-shot learning through meta-learning and self-supervised learning. However, the problem of insufficient samples has not been fundamentally solved. In this paper, we propose a novel algorithm based on adversarial learning for Enhancing Negative samples in few-shot scenarios of FS-KGR, termed FS-KEN. Specifically, we are the first to use GAN to conduct data augmentation on FS-KGR scenario. FS-KEN uses policy gradient GANs for negative sample augmentation, solving the gradient back-propagation issue in traditional GANs. The generator aims to produce high-quality negative entities. while the objective of the discriminator is to distinguish between generated entities and real entities. Comprehensive experiments conducted on two few-shot knowledge graph completion datasets reveal that FS-KEN surpasses other baseline models, achieving state-of-the-art results.

Spatial transcriptomics technologies enable the integration of gene expression profiles with spatial context, facilitating a deeper understanding of tissue architecture through downstream tasks such as clustering. However, existing approaches predominantly focus on highly variable genes (HVGs), while the informative structural and contextual signals embedded in low variability genes (LVGs) remain largely underutilized. To bridge this gap, we propose SALVG (Spatial Augmentation via Latent Variable Genes), a novel and plug-and-play framework that leverages LVG-derived structural priors to enhance HVG representation learning for spatial clustering. Specifically, SALVG constructs spatial, feature, and combined graphs for both HVGs and LVGs, and introduces two graph-based augmentation strategies to inject LVG information into HVG graphs. The first strategy enhances the HVG combined graph directly using the LVG combined graph, while the other individually augments HVG spatial and feature graphs with their LVG counterparts before fusing them into a new combined representation. These enhanced graph structures are subsequently employed for downstream clustering. To the best of our knowledge, SALVG is the first framework to exploit LVG signals for assisting HVG-centric spatial transcriptomics clustering, effectively capturing complementary structural and contextual cues. Experiments on multiple benchmarks demonstrate its effectiveness, robustness, and transferability. Case studies further confirm that LVG-derived structure enhances biological interpretability by revealing coherent spatial and cellular patterns.

Spatial transcriptomics (ST) technologies provide gene expression measurements with spatial resolution, enabling the dissection of tissue structure and function. A fundamental challenge in ST analysis is clustering spatial spots into coherent functional regions. While existing models effectively integrate expression and spatial signals, they largely overlook sequence-level biological priors encoded in the DNA sequences of expressed genes. To bridge this gap, we propose SAINT (Sequence-Aware Integration for Nucleotide-informed Transcriptomics), a unified framework that augments spatial representation learning with nucleotide-derived features. We construct sequence-augmented datasets across 14 tissue sections from three widely used ST benchmarks (DLPFC, HBC, and MBA), retrieving reference DNA sequences for each expressed gene and encoding them using a pretrained Nucleotide Transformer. For each spot, gene-level embeddings are aggregated via expression-weighted and attention-based pooling, then fused with spatial-expression representations through a late fusion module. Extensive experiments demonstrate that SAINT consistently improves clustering performance across multiple datasets. Experiments validate the superiority, effectiveness, sensitivity, and transferability of our framework, confirming the complementary value of incorporating sequence-level priors into spatial transcriptomics clustering.

Multi-view clustering (MVC) is a fast-growing research direction. However, most existing MVC works focus on concrete objects (e.g., cats, desks) but ignore abstract objects (e.g., knowledge, thoughts), which are also important parts of our daily lives and more correlated to cognition. Relational knowledge, as a typical abstract concept, describes the relationship between entities. For example, "Cats like eating fishes," as relational knowledge, reveals the relationship "eating" between "cats" and "fishes." To fill this gap, we first point out that MVC on relational knowledge is considered an important scenario. Then, we construct 8 new datasets to lay research grounds for them. Moreover, a simple yet effective relational knowledge MVC paradigm (RK-MVC) is proposed by compensating the omitted sample-global correlations from the structural knowledge information. Concretely, the basic consensus features are first learned via adopted MVC backbones, and sample-global correlations are generated in both coarse-grained and fine-grained manners. In particular, the sample-global correlation learning module can be easily extended to various MVC backbones. Finally, both basic consensus features and sample-global correlation features are weighted fused as the target consensus feature. We adopt 9 typical MVC backbones in this paper for comparison from 7 aspects, demonstrating the promising capacity of our RK-MVC.

Knowledge graphs (KGs) represent known entities and their relationships using triplets, but this method cannot represent relationships between facts, limiting their expressiveness. Recently, the Bi-level Knowledge Graph (Bi-level KG) has addressed this issue by modeling facts as nodes and establishing relationships between these facts, introducing two new tasks: triplet prediction and conditional link prediction. Existing methods enhance triplets through data augmentation method and represent facts using entity representations. However, these methods do not address the isolated nodes at the structure level, nor do they effectively capture the information of facts at the feature level. To address these two issues, we design a data augmentation method that identifies islanded node by detecting anomalous structures and features in the graph. Subsequently, we perform similar subgraph matching for each isolated node to construct potential facts. To enrich the features of facts, we design a weighted combination initialization method for facts and introduce a new relation $\widetilde {R}$ , to connect facts with related entities. This approach allows for the co-training of fact and entity representations during the training process. Extensive experiments validate the effectiveness of our data augmentation and co-training methods. Our model achieves optimal performance in triplet prediction and conditional link prediction tasks.

Site selection aims to select optimal locations for new stores, which is crucial in business management and urban computing. The early data-driven models heavily relied on feature engineering, which could not effectively model the complex relationships and diverse influences among different data. To alleviate such issues, the knowledge-driven paradigm is proposed based on urban knowledge graphs (KGs). However, the research on them is at an early stage. They omit extra multi-modal information corresponding to brands and stores due to two main challenges, i.e., (1) building available datasets, and (2) designing effective models. It constrains the expressive ability and practical value of previous models. To this end, we first construct new multi-modal urban KGs for site selection with three extra modal (i.e., visual, textual, and acoustic) attributes. Then, we propose a novel multi-modal knowledge-driven model (MGKsite). Concretely, a graph neural network (GNN) based fusion network is designed to fuse the features based on the attribute K-Nearest Neighbor (KNN) graph, which models both intra and inter-modal correlations among the features. The fused embeddings are further injected into the knowledge-driven backbones for learning and inference. Experiments prove promising capacities of MGKsite from five aspects, i.e., superiority, effectiveness, sensitivity, transferability and complexity.

As an emerging task, temporal graph clustering (TGC) is committed to clustering nodes on temporal graphs through interaction sequence-based batch-processing patterns. These patterns allow for more flexibility in finding a balance between time and space requirements than adjacency matrix-based static graph clustering. However, as a new task, TGC still has important unresolved challenges, such as insufficient information. This challenge manifests itself in a variety of problems in real-world datasets, including missing features (eigenvalues are missing or even nonexistent), long-tail nodes (most inactive nodes have little interaction), and noisy data (data is subject to anomalies, errors, and sparsity). These problems occur before training, making it difficult for the model to train well with insufficient information. To solve the challenge, we propose a method that introduces multiview clustering (MVC) into TGC, called MVTGC. Our method aims to perform data augmentation on the temporal graph by constructing multiple views to increase the information richness. In particular, we utilize different techniques to model a certain part of the temporal graph to generate enhanced views focusing on different angles. These views are combined into training through early fusion and late fusion and ultimately enhance the model's receptive field and information richness. Comparative experiments and a case study on real-world datasets demonstrate the significance and effectiveness of MVTGC, which achieves at most 10.48% performance improvement. The code and data are available at https://github.com/MGitHubL/MVTGC.

Few-shot relation reasoning on knowledge graphs (FS-KGR) is an important and practical problem that aims to infer long-tail relations and has drawn increasing attention these years. Among all the proposed methods, self-supervised learning (SSL) methods, which effectively extract the hidden essential inductive patterns relying only on the support sets, have achieved promising performance. However, the existing SSL methods simply cut down connections between high-frequency and long-tail relations, which ignores the fact, i.e., the two kinds of information could be highly related to each other. Specifically, we observe that relations with similar contextual meanings, called aliasing relations (ARs), may have similar attributes. In other words, the ARs of the target long-tail relation could be in high-frequency, and leveraging such attributes can largely improve the reasoning performance. Based on the interesting observation above, we proposed a novel Self-supervised learning model by leveraging Aliasing Relations to assist FS-KGR, termed SARF. Specifically, we propose a graph neural network (GNN)-based AR-assist module to encode the ARs. Besides, we further provide two fusion strategies, i.e., simple summation and learnable fusion, to fuse the generated representations, which contain extra abundant information underlying the ARs, into the self-supervised reasoning backbone for performance enhancement. Extensive experiments on three few-shot benchmarks demonstrate that SARF achieves state-of-the-art (SOTA) performance compared with other methods in most cases.

GraIL and its variants have shown their promising capacities for inductive relation reasoning on knowledge graphs. However, the uni-directional message-passing mechanism hinders such models from exploiting hidden mutual relations between entities in directed graphs. Besides, the enclosing subgraph extraction in most GraIL-based models restricts the model from extracting enough discriminative information for reasoning. Consequently, the expressive ability of these models is limited. To address the problems, we propose a novel GraIL-based framework, termed MINES, by introducing a Message Intercommunication mechanism on the Neighbor-Enhanced Subgraph. Concretely, the message intercommunication mechanism is designed to capture the omitted hidden mutual information. It introduces bi-directed information interactions between connected entities by inserting an undirected/bi-directed GCN layer between uni-directed RGCN layers. Moreover, inspired by the success of involving more neighbors in other graph-based tasks, we extend the neighborhood area beyond the enclosing subgraph to enhance the information collection for inductive relation reasoning. Extensive experiments prove the promising capacity of the proposed MINES from various aspects, especially for the superiority, effectiveness, and transfer ability.

Various information in different modalities in an intuitive way in multi-modal knowledge graphs (MKGs), which are utilized in different downstream tasks, like recommendation. However, most MKGs are still far from complete, which motivates the flourishing of MKG reasoning models. Recently, with the development of general artificial intelligence, pre-trained transformers have drawn increasing attention, especially in multi-modal scenarios. However, the research of multi-modal pre-trained transformers (MPT) for knowledge graph reasoning (KGR) is still at an early stage. As the biggest difference between MKG and other multi-modal data, the rich structural information underlying the MKG is still not fully utilized in previous MPT. Most of them only use the graph structure as a retrieval map for matching images and texts connected with the same entity, which hinders their reasoning performances. To this end, the graph Structure Guided Multi-modal Pre-trained Transformer is proposed for knowledge graph reasoning (SGMPT). Specifically, the graph structure encoder is adopted for structural feature encoding. Then, a structure-guided fusion module with two simple yet effective strategies, i.e., weighted summation and alignment constraint, is designed to inject the structural information into both the textual and visual features. To the best of our knowledge, SGMPT is the first MPT for multi-modal KGR, which mines structural information underlying MKGs. Extensive experiments on FB15k-237-IMG and WN18-IMG, demonstrate that our SGMPT outperforms existing state-of-the-art models, and proves the effectiveness of the designed strategies.

Traditional knowledge graph embedding (KGE) models map entities and relations to unique embedding vectors in a shallow lookup manner. As the scale of data becomes larger, this manner will raise unaffordable computational costs. Anchor-based strategies have been treated as effective ways to alleviate such efficiency problems by propagation on representative entities instead of the whole graph. However, most existing anchor-based KGE models select the anchors in a primitive manner, which limits their performance. To this end, we propose a novel anchor-based strategy for KGE, i.e., a relational clustering-based anchor selection strategy (RecPiece), where two characteristics are leveraged, i.e., (1) representative ability of the cluster centroids and (2) descriptive ability of relation types in KGs. Specifically, we first perform clustering over features of factual triplets instead of entities, where cluster number is naturally set as number of relation types since each fact can be characterized by its relation in KGs. Then, representative triplets are selected around the clustering centroids, further mapped into corresponding anchor entities. Extensive experiments on six datasets show that RecPiece achieves higher performances but comparable or even fewer parameters compared to previous anchor-based KGE models, indicating that our model can select better anchors in a more scalable way.

Knowledge graph reasoning (KGR), aiming to deduce new facts from existing facts based on mined logic rules underlying knowledge graphs (KGs), has become a fast-growing research direction. It has been proven to significantly benefit the usage of KGs in many AI applications, such as question answering, recommendation systems, and etc. According to the graph types, existing KGR models can be roughly divided into three categories, i.e., static models, temporal models, and multi-modal models. Early works in this domain mainly focus on static KGR, and recent works try to leverage the temporal and multi-modal information, which are more practical and closer to real-world. However, no survey papers and open-source repositories comprehensively summarize and discuss models in this important direction. To fill the gap, we conduct a first survey for knowledge graph reasoning tracing from static to temporal and then to multi-modal KGs. Concretely, the models are reviewed based on bi-level taxonomy, i.e., top-level (graph types) and base-level (techniques and scenarios). Besides, the performances, as well as datasets, are summarized and presented. Moreover, we point out the challenges and potential opportunities to enlighten the readers.

Graph Neural Networks (GNNs) have achieved promising performance in semi-supervised node classification in recent years. However, the problem of insufficient supervision, together with representation collapse, largely limits the performance of the GNNs in this field. To alleviate the collapse of node representations in semi-supervised scenario, we propose a novel graph contrastive learning method, termed M ixed G raph C ontrastive N etwork (MGCN). In our method, we improve the discriminative capability of the latent embeddings by an interpolation-based augmentation strategy and a correlation reduction mechanism. Specifically, we first conduct the interpolation-based augmentation in the latent space and then force the prediction model to change linearly between samples. Second, we enable the learned network to tell apart samples across two interpolation-perturbed views through forcing the correlation matrix across views to approximate an identity matrix. By combining the two settings, we extract rich supervision information from both the abundant unlabeled nodes and the rare yet valuable labeled nodes for discriminative representation learning. Extensive experimental results on six datasets demonstrate the effectiveness and the generality of MGCN compared to the existing state-of-the-art methods. The code of MGCN is available at https://github.com/xihongyang1999/MGCN on Github.

Federated knowledge graph reasoning (FedKGR) aims to perform reasoning over different clients while protecting data privacy, drawing increasing attention to its high practical value. Previous works primarily focus on data heterogeneity, ignoring challenges from limited data scale and primitive negative sample strategies, i.e., random entity replacement, which yield low-quality negatives and zero loss issues. Meanwhile, generative adversarial networks (GANs) are widely used in different fields to generate high-quality negative samples, but no work has been developed for FedKGR. To this end, we propose a plug-and-playEntity-awareAdversarialNegative sampling strategy for FedKGR, termed FedEAN. Specifically, we are the first to adopt GANs to generate high-quality negative samples in different clients. It takes the target triplet in each batch as input and outputs high-quality negative samples, which guaranteed by the joint training of the generator and discriminator. Moreover, we design an entity-aware adaptive negative sampling mechanism based on the similarity of entity representations before and after server aggregation, which can persevere the entity global consistency across clients during training. Extensive experiments demonstrate that FedEAN excels with various FedKGR backbones, demonstrating its ability to construct high-quality negative samples and address the zero-loss issue.

Audiovisual data is everywhere in this digital age, which raises higher requirements for the deep learning models developed on them. To well handle the information of the multi-modal data is the key to a better audiovisual modal. We observe that these audiovisual data naturally have temporal attributes, such as the time information for each frame in the video. More concretely, such data is inherently multi-modal according to both audio and visual cues, which proceed in a strict chronological order. It indicates that temporal information is important in multi-modal acoustic event modeling for both intra- and inter-modal. However, existing methods deal with each modal feature independently and simply fuse them together, which neglects the mining of temporal relation and thus leads to sub-optimal performance. With this motivation, we propose a Temporal Multi-modal graph learning method for Acoustic event Classification, called TMac, by modeling such temporal information via graph learning techniques. In particular, we construct a temporal graph for each acoustic event, dividing its audio data and video data into multiple segments. Each segment can be considered as a node, and the temporal relationships between nodes can be considered as timestamps on their edges. In this case, we can smoothly capture the dynamic information in intra-modal and inter-modal. Several experiments are conducted to demonstrate TMac outperforms other SOTA models in performance. Our code is available at https://github.com/MGitHubL/TMac.

Reasoning on temporal knowledge graphs (TKGR), aiming to infer missing events along the timeline, has been widely studied to alleviate incompleteness issues in TKG, which is composed of a series of KG snapshots at different timestamps. Two types of information, i.e., intra-snapshot structural information and inter-snapshot temporal interactions, mainly contribute to the learned representations for reasoning in previous models. However, these models fail to leverage (1) semantic correlations between relationships for the former information and (2) the periodic temporal patterns along the timeline for the latter one. Thus, such insufficient mining manners hinder expressive ability, leading to sub-optimal performances. To address these limitations, we propose a novel reasoning model, termed RPC, which sufficiently mines the information underlying the Relational correlations and Periodic patterns via two novel Correspondence units, i.e., relational correspondence unit (RCU) and periodic correspondence unit (PCU). Concretely, relational graph convolutional network (RGCN) and RCU are used to encode the intra-snapshot graph structural information for entities and relations, respectively. Besides, the gated recurrent units (GRU) and PCU are designed for sequential and periodic inter-snapshot temporal interactions, separately. Moreover, the model-agnostic time vectors are generated by time2vector encoders to guide the time-dependent decoder for fact scoring. Extensive experiments on six benchmark datasets show that RPC outperforms the state-of-the-art TKGR models, and also demonstrate the effectiveness of two novel strategies in our model.