Graffe: Graph Representation Learning via Diffusion Probabilistic Models

Diffusion probabilistic models (DPMs), widely recognized for their potential to generate high-quality samples, tend to go unnoticed in representation learning. While recent progress has highlighted their potential for capturing visual semantics, adapting DPMs to graph representation learning remains in its infancy. In this paper, we introduce Graffe, a self-supervised diffusion model proposed for graph representation learning. It features a graph encoder that distills a source graph into a compact representation, which, in turn, serves as the condition to guide the denoising process of the diffusion decoder. To evaluate the effectiveness of our model, we first explore the theoretical foundations of applying diffusion models to representation learning, proving that the denoising objective implicitly maximizes the conditional mutual information between data and its representation. Specifically, we prove that the negative logarithm of the denoising score matching loss is a tractable lower bound for the conditional mutual information. Empirically, we conduct a series of case studies to validate our theoretical insights. In addition, Graffe delivers competitive results under the linear probing setting on node and graph classification tasks, achieving state-of-the-art performance on 9 of the 11 real-world datasets. These findings indicate that powerful generative models, especially diffusion models, serve as an effective tool for graph representation learning.

A Conjoint Graph Representation Learning Framework for Hypertension Comorbidity Risk Prediction

The comorbidities of hypertension impose a heavy burden on patients and society. Early identification is necessary to prompt intervention, but it remains a challenging task. This study aims to address this challenge by combining joint graph learning with network analysis. Motivated by this discovery, we develop a Conjoint Graph Representation Learning (CGRL) framework that: a) constructs two networks based on disease coding, including the patient network and the disease difference network. Three comorbidity network features were generated based on the basic difference network to capture the potential relationship between comorbidities and risk diseases; b) incorporates computational structure intervention and learning feature representation, CGRL was developed to predict the risks of diabetes and coronary heart disease in patients; and c) analysis the comorbidity patterns and exploring the pathways of disease progression, the pathological pathogenesis of diabetes and coronary heart disease may be revealed. The results show that the network features extracted based on the difference network are important, and the framework we proposed provides more accurate predictions than other strong models in terms of accuracy.

PyTDC: A multimodal machine learning training, evaluation, and inference platform for biomedical foundation models

Existing biomedical benchmarks do not provide end-to-end infrastructure for training, evaluation, and inference of models that integrate multimodal biological data and a broad range of machine learning tasks in therapeutics. We present PyTDC, an open-source machine-learning platform providing streamlined training, evaluation, and inference software for multimodal biological AI models. PyTDC unifies distributed, heterogeneous, continuously updated data sources and model weights and standardizes benchmarking and inference endpoints. This paper discusses the components of PyTDC's architecture and, to our knowledge, the first-of-its-kind case study on the introduced single-cell drug-target nomination ML task. We find state-of-the-art methods in graph representation learning and domain-specific methods from graph theory perform poorly on this task. Though we find a context-aware geometric deep learning method that outperforms the evaluated SoTA and domain-specific baseline methods, the model is unable to generalize to unseen cell types or incorporate additional modalities, highlighting PyTDC's capacity to facilitate an exciting avenue of research developing multimodal, context-aware, foundation models for open problems in biomedical AI.

A Survey on Temporal Interaction Graph Representation Learning: Progress, Challenges, and Opportunities

Temporal interaction graphs (TIGs), defined by sequences of timestamped interaction events, have become ubiquitous in real-world applications due to their capability to model complex dynamic system behaviors. As a result, temporal interaction graph representation learning (TIGRL) has garnered significant attention in recent years. TIGRL aims to embed nodes in TIGs into low-dimensional representations that effectively preserve both structural and temporal information, thereby enhancing the performance of downstream tasks such as classification, prediction, and clustering within constantly evolving data environments. In this paper, we begin by introducing the foundational concepts of TIGs and emphasize the critical role of temporal dependencies. We then propose a comprehensive taxonomy of state-of-the-art TIGRL methods, systematically categorizing them based on the types of information utilized during the learning process to address the unique challenges inherent to TIGs. To facilitate further research and practical applications, we curate the source of datasets and benchmarks, providing valuable resources for empirical investigations. Finally, we examine key open challenges and explore promising research directions in TIGRL, laying the groundwork for future advancements that have the potential to shape the evolution of this field.

A Noise-Resilient Semi-Supervised Graph Autoencoder for Overlapping Semantic Community Detection

Community detection in networks with overlapping structures remains a significant challenge, particularly in noisy real-world environments where integrating topology, node attributes, and prior information is critical. To address this, we propose a semi-supervised graph autoencoder that combines graph multi-head attention and modularity maximization to robustly detect overlapping communities. The model learns semantic representations by fusing structural, attribute, and prior knowledge while explicitly addressing noise in node features. Key innovations include a noise-resistant architecture and a semantic semi-supervised design optimized for community quality through modularity constraints. Experiments demonstrate superior performance the model outperforms state-of-the-art methods in overlapping community detection (improvements in NMI and F1-score) and exhibits exceptional robustness to attribute noise, maintaining stable performance under 60\% feature corruption. These results highlight the importance of integrating attribute semantics and structural patterns for accurate community discovery in complex networks.

Multi-Modal Molecular Representation Learning via Structure Awareness

Accurate extraction of molecular representations is a critical step in the drug discovery process. In recent years, significant progress has been made in molecular representation learning methods, among which multi-modal molecular representation methods based on images, and 2D/3D topologies have become increasingly mainstream. However, existing these multi-modal approaches often directly fuse information from different modalities, overlooking the potential of intermodal interactions and failing to adequately capture the complex higher-order relationships and invariant features between molecules. To overcome these challenges, we propose a structure-awareness-based multi-modal self-supervised molecular representation pre-training framework (MMSA) designed to enhance molecular graph representations by leveraging invariant knowledge between molecules. The framework consists of two main modules: the multi-modal molecular representation learning module and the structure-awareness module. The multi-modal molecular representation learning module collaboratively processes information from different modalities of the same molecule to overcome intermodal differences and generate a unified molecular embedding. Subsequently, the structure-awareness module enhances the molecular representation by constructing a hypergraph structure to model higher-order correlations between molecules. This module also introduces a memory mechanism for storing typical molecular representations, aligning them with memory anchors in the memory bank to integrate invariant knowledge, thereby improving the model generalization ability. Extensive experiments have demonstrated the effectiveness of MMSA, which achieves state-of-the-art performance on the MoleculeNet benchmark, with average ROC-AUC improvements ranging from 1.8% to 9.6% over baseline methods.

Multi-Granular Attention based Heterogeneous Hypergraph Neural Network

Heterogeneous graph neural networks (HeteGNNs) have demonstrated strong abilities to learn node representations by effectively extracting complex structural and semantic information in heterogeneous graphs. Most of the prevailing HeteGNNs follow the neighborhood aggregation paradigm, leveraging meta-path based message passing to learn latent node representations. However, due to the pairwise nature of meta-paths, these models fail to capture high-order relations among nodes, resulting in suboptimal performance. Additionally, the challenge of ``over-squashing'', where long-range message passing in HeteGNNs leads to severe information distortion, further limits the efficacy of these models. To address these limitations, this paper proposes MGA-HHN, a Multi-Granular Attention based Heterogeneous Hypergraph Neural Network for heterogeneous graph representation learning. MGA-HHN introduces two key innovations: (1) a novel approach for constructing meta-path based heterogeneous hypergraphs that explicitly models higher-order semantic information in heterogeneous graphs through multiple views, and (2) a multi-granular attention mechanism that operates at both the node and hyperedge levels. This mechanism enables the model to capture fine-grained interactions among nodes sharing the same semantic context within a hyperedge type, while preserving the diversity of semantics across different hyperedge types. As such, MGA-HHN effectively mitigates long-range message distortion and generates more expressive node representations. Extensive experiments on real-world benchmark datasets demonstrate that MGA-HHN outperforms state-of-the-art models, showcasing its effectiveness in node classification, node clustering and visualization tasks.

GRAPE: Heterogeneous Graph Representation Learning for Genetic Perturbation with Coding and Non-Coding Biotype

Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene regulatory networks (GRN) is essential to understand and predict the effects of genetic perturbations. However, current methods fail to fully leverage gene-related information, and solely rely on simple evaluation metrics to construct coarse-grained GRN. More importantly, they ignore functional differences between biotypes, limiting the ability to capture potential gene interactions. In this work, we leverage pre-trained large language model and DNA sequence model to extract features from gene descriptions and DNA sequence data, respectively, which serve as the initialization for gene representations. Additionally, we introduce gene biotype information for the first time in genetic perturbation, simulating the distinct roles of genes with different biotypes in regulating cellular processes, while capturing implicit gene relationships through graph structure learning (GSL). We propose GRAPE, a heterogeneous graph neural network (HGNN) that leverages gene representations initialized with features from descriptions and sequences, models the distinct roles of genes with different biotypes, and dynamically refines the GRN through GSL. The results on publicly available datasets show that our method achieves state-of-the-art performance.

Concept Factorization via Self-Representation and Adaptive Graph Structure Learning

Concept Factorization (CF) models have attracted widespread attention due to their excellent performance in data clustering. In recent years, many variant models based on CF have achieved great success in clustering by taking into account the internal geometric manifold structure of the dataset and using graph regularization techniques. However, their clustering performance depends greatly on the construction of the initial graph structure. In order to enable adaptive learning of the graph structure of the data, we propose a Concept Factorization Based on Self-Representation and Adaptive Graph Structure Learning (CFSRAG) Model. CFSRAG learns the affinity relationship between data through a self-representation method, and uses the learned affinity matrix to implement dynamic graph regularization constraints, thereby ensuring dynamic learning of the internal geometric structure of the data. Finally, we give the CFSRAG update rule and convergence analysis, and conduct comparative experiments on four real datasets. The results show that our model outperforms other state-of-the-art models.

Federated Deconfounding and Debiasing Learning for Out-of-Distribution Generalization

Attribute bias in federated learning (FL) typically leads local models to optimize inconsistently due to the learning of non-causal associations, resulting degraded performance. Existing methods either use data augmentation for increasing sample diversity or knowledge distillation for learning invariant representations to address this problem. However, they lack a comprehensive analysis of the inference paths, and the interference from confounding factors limits their performance. To address these limitations, we propose the \underline{Fed}erated \underline{D}econfounding and \underline{D}ebiasing \underline{L}earning (FedDDL) method. It constructs a structured causal graph to analyze the model inference process, and performs backdoor adjustment to eliminate confounding paths. Specifically, we design an intra-client deconfounding learning module for computer vision tasks to decouple background and objects, generating counterfactual samples that establish a connection between the background and any label, which stops the model from using the background to infer the label. Moreover, we design an inter-client debiasing learning module to construct causal prototypes to reduce the proportion of the background in prototype components. Notably, it bridges the gap between heterogeneous representations via causal prototypical regularization. Extensive experiments on 2 benchmarking datasets demonstrate that \methodname{} significantly enhances the model capability to focus on main objects in unseen data, leading to 4.5\% higher Top-1 Accuracy on average over 9 state-of-the-art existing methods.