iN2V: Bringing Transductive Node Embeddings to Inductive Graphs

Shallow node embeddings like node2vec (N2V) can be used for nodes without features or to supplement existing features with structure-based information. Embedding methods like N2V are limited in their application on new nodes, which restricts them to the transductive setting where the entire graph, including the test nodes, is available during training. We propose inductive node2vec (iN2V), which combines a post-hoc procedure to compute embeddings for nodes unseen during training and modifications to the original N2V training procedure to prepare the embeddings for this post-hoc procedure. We conduct experiments on several benchmark datasets and demonstrate that iN2V is an effective approach to bringing transductive embeddings to an inductive setting. Using iN2V embeddings improves node classification by 1 point on average, with up to 6 points of improvement depending on the dataset and the number of unseen nodes. Our iN2V is a plug-in approach to create new or enrich existing embeddings. It can also be combined with other embedding methods, making it a versatile approach for inductive node representation learning. Code to reproduce the results is available at https://github.com/Foisunt/iN2V .

Graph-Based Floor Separation Using Node Embeddings and Clustering of WiFi Trajectories

Indoor positioning systems (IPSs) are increasingly vital for location-based services in complex multi-storey environments. This study proposes a novel graph-based approach for floor separation using Wi-Fi fingerprint trajectories, addressing the challenge of vertical localization in indoor settings. We construct a graph where nodes represent Wi-Fi fingerprints, and edges are weighted by signal similarity and contextual transitions. Node2Vec is employed to generate low-dimensional embeddings, which are subsequently clustered using K-means to identify distinct floors. Evaluated on the Huawei University Challenge 2021 dataset, our method outperforms traditional community detection algorithms, achieving an accuracy of 68.97%, an F1- score of 61.99%, and an Adjusted Rand Index of 57.19%. By publicly releasing the preprocessed dataset and implementation code, this work contributes to advancing research in indoor positioning. The proposed approach demonstrates robustness to signal noise and architectural complexities, offering a scalable solution for floor-level localization.

Node2Vec-DGI-EL: A Hierarchical Graph Representation Learning Model for Ingredient-Disease Association Prediction

Traditional Chinese medicine, as an essential component of traditional medicine, contains active ingredients that serve as a crucial source for modern drug development, holding immense therapeutic potential and development value. A multi-layered and complex network is formed from Chinese medicine to diseases and used to predict the potential associations between Chinese medicine ingredients and diseases. This study proposes an ingredient-disease association prediction model (Node2Vec-DGI-EL) based on hierarchical graph representation learning. First, the model uses the Node2Vec algorithm to extract node embedding vectors from the network as the initial features of the nodes. Next, the network nodes are deeply represented and learned using the DGI algorithm to enhance the model's expressive power. To improve prediction accuracy and robustness, an ensemble learning method is incorporated to achieve more accurate ingredient-disease association predictions. The effectiveness of the model is then evaluated through a series of theoretical verifications. The results demonstrated that the proposed model significantly outperformed existing methods, achieving an AUC of 0.9987 and an AUPR of 0.9545, thereby indicating superior predictive capability. Ablation experiments further revealed the contribution and importance of each module. Additionally, case studies explored potential associations, such as triptonide with hypertensive retinopathy and methyl ursolate with colorectal cancer. Molecular docking experiments validated these findings, showing the triptonide-PGR interaction and the methyl ursolate-NFE2L2 interaction can bind stable. In conclusion, the Node2Vec-DGI-EL model focuses on TCM datasets and effectively predicts ingredient-disease associations, overcoming the reliance on node semantic information.

DeepSTA: A Spatial-Temporal Attention Network for Logistics Delivery Timely Rate Prediction in Anomaly Conditions

Prediction of couriers' delivery timely rates in advance is essential to the logistics industry, enabling companies to take preemptive measures to ensure the normal operation of delivery services. This becomes even more critical during anomaly conditions like the epidemic outbreak, during which couriers' delivery timely rate will decline markedly and fluctuates significantly. Existing studies pay less attention to the logistics scenario. Moreover, many works focusing on prediction tasks in anomaly scenarios fail to explicitly model abnormal events, e.g., treating external factors equally with other features, resulting in great information loss. Further, since some anomalous events occur infrequently, traditional data-driven methods perform poorly in these scenarios. To deal with them, we propose a deep spatial-temporal attention model, named DeepSTA. To be specific, to avoid information loss, we design an anomaly spatio-temporal learning module that employs a recurrent neural network to model incident information. Additionally, we utilize Node2vec to model correlations between road districts, and adopt graph neural networks and long short-term memory to capture the spatial-temporal dependencies of couriers. To tackle the issue of insufficient training data in abnormal circumstances, we propose an anomaly pattern attention module that adopts a memory network for couriers' anomaly feature patterns storage via attention mechanisms. The experiments on real-world logistics datasets during the COVID-19 outbreak in 2022 show the model outperforms the best baselines by 12.11% in MAE and 13.71% in MSE, demonstrating its superior performance over multiple competitive baselines.

SCMPPI: Supervised Contrastive Multimodal Framework for Predicting Protein-Protein Interactions

Protein-Protein Interaction (PPI) prediction is a key task in uncovering cellular functional networks and disease mechanisms. However, traditional experimental methods are time-consuming and costly, and existing computational models face challenges in cross-modal feature fusion, robustness, and false-negative suppression. In this paper, we propose a novel supervised contrastive multimodal framework, SCMPPI, for PPI prediction. By integrating protein sequence features (AAC, DPC, CKSAAP-ESMC) with PPI network topology information (Node2Vec graph embedding), and combining an improved supervised contrastive learning strategy, SCMPPI significantly enhances PPI prediction performance. For the PPI task, SCMPPI introduces a negative sample filtering mechanism and modifies the contrastive loss function, effectively optimizing multimodal features. Experiments on eight benchmark datasets, including yeast, human, and H.pylori, show that SCMPPI outperforms existing state-of-the-art methods (such as DF-PPI and TAGPPI) in key metrics such as accuracy ( 98.01%) and AUC (99.62%), and demonstrates strong generalization in cross-species prediction (AUC > 99% on multi-species datasets). Furthermore, SCMPPI has been successfully applied to CD9 networks, the Wnt pathway, and cancer-specific networks, providing a reliable tool for disease target discovery. This framework also offers a new paradigm for multimodal biological information fusion and contrastive learning in collaborative optimization for various combined predictions.

Node Embeddings via Neighbor Embeddings

Graph layouts and node embeddings are two distinct paradigms for non-parametric graph representation learning. In the former, nodes are embedded into 2D space for visualization purposes. In the latter, nodes are embedded into a high-dimensional vector space for downstream processing. State-of-the-art algorithms for these two paradigms, force-directed layouts and random-walk-based contrastive learning (such as DeepWalk and node2vec), have little in common. In this work, we show that both paradigms can be approached with a single coherent framework based on established neighbor embedding methods. Specifically, we introduce graph t-SNE, a neighbor embedding method for two-dimensional graph layouts, and graph CNE, a contrastive neighbor embedding method that produces high-dimensional node representations by optimizing the InfoNCE objective. We show that both graph t-SNE and graph CNE strongly outperform state-of-the-art algorithms in terms of local structure preservation, while being conceptually simpler.

A quantum annealing approach to graph node embedding

Node embedding is a key technique for representing graph nodes as vectors while preserving structural and relational properties, which enables machine learning tasks like feature extraction, clustering, and classification. While classical methods such as DeepWalk, node2vec, and graph convolutional networks learn node embeddings by capturing structural and relational patterns in graphs, they often require significant computational resources and struggle with scalability on large graphs. Quantum computing provides a promising alternative for graph-based learning by leveraging quantum effects and introducing novel optimization approaches. Variational quantum circuits and quantum kernel methods have been explored for embedding tasks, but their scalability remains limited due to the constraints of noisy intermediate-scale quantum (NISQ) hardware. In this paper, we investigate quantum annealing (QA) as an alternative approach that mitigates key challenges associated with quantum gate-based models. We propose several formulations of the node embedding problem as a quadratic unconstrained binary optimization (QUBO) instance, making it compatible with current quantum annealers such as those developed by D-Wave. We implement our algorithms on a D-Wave quantum annealer and evaluate their performance on graphs with up to 100 nodes and embedding dimensions of up to 5. Our findings indicate that QA is a viable approach for graph-based learning, providing a scalable and efficient alternative to previous quantum embedding techniques.

Stationary distribution of node2vec random walks on household models

The node2vec random walk has proven to be a key tool in network embedding algorithms. These random walks are tuneable, and their transition probabilities depend on the previous visited node and on the triangles containing the current and the previously visited node. Even though these walks are widely used in practice, most mathematical properties of node2vec walks are largely unexplored, including their stationary distribution. We study the node2vec random walk on community-structured household model graphs. We prove an explicit description of the stationary distribution of node2vec walks in terms of the walk parameters. We then show that by tuning the walk parameters, the stationary distribution can interpolate between uniform, size-biased, or the simple random walk stationary distributions, demonstrating the wide range of possible walks. We further explore these effects on some specific graph settings.

Machine Learning-Based Security Policy Analysis

Security-Enhanced Linux (SELinux) is a robust security mechanism that enforces mandatory access controls (MAC), but its policy language's complexity creates challenges for policy analysis and management. This research investigates the automation of SELinux policy analysis using graph-based techniques combined with machine learning approaches to detect policy anomalies. The study addresses two key questions: Can SELinux policy analysis be automated through graph analysis, and how do different anomaly detection models compare in analyzing SELinux policies? We will be comparing different machine learning models by evaluating their effectiveness in detecting policy violations and anomalies. Our approach utilizes Neo4j for graph representation of policies, with Node2vec transforming these graph structures into meaningful vector embeddings that can be processed by our machine learning models. In our results, the MLP Neural Network consistently demonstrated superior performance across different dataset sizes, achieving 95% accuracy with balanced precision and recall metrics, while both Random Forest and SVM models showed competitive but slightly lower performance in detecting policy violations. This combination of graph-based modeling and machine learning provides a more sophisticated and automated approach to understanding and analyzing complex SELinux policies compared to traditional manual analysis methods.

Two Layer Walk: A Community-Aware Graph Embedding

Community structures are critical for understanding the mesoscopic organization of networks, bridging local and global patterns. While methods such as DeepWalk and node2vec capture local positional information through random walks, they fail to preserve community structures. Other approaches like modularized nonnegative matrix factorization and evolutionary algorithms address this gap but are computationally expensive and unsuitable for large-scale networks. To overcome these limitations, we propose Two Layer Walk (TLWalk), a novel graph embedding algorithm that incorporates hierarchical community structures. TLWalk balances intra- and inter-community relationships through a community-aware random walk mechanism without requiring additional parameters. Theoretical analysis demonstrates that TLWalk effectively mitigates locality bias. Experiments on benchmark datasets show that TLWalk outperforms state-of-the-art methods, achieving up to 3.2% accuracy gains for link prediction tasks. By encoding dense local and sparse global structures, TLWalk proves robust and scalable across diverse networks, offering an efficient solution for network analysis.