label propagation
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2022 ◽  
Vol 40 (4) ◽  
pp. 1-27
Author(s):  
Hongwei Wang ◽  
Jure Leskovec

Label Propagation Algorithm (LPA) and Graph Convolutional Neural Networks (GCN) are both message passing algorithms on graphs. Both solve the task of node classification, but LPA propagates node label information across the edges of the graph, while GCN propagates and transforms node feature information. However, while conceptually similar, theoretical relationship between LPA and GCN has not yet been systematically investigated. Moreover, it is unclear how LPA and GCN can be combined under a unified framework to improve the performance. Here we study the relationship between LPA and GCN in terms of feature/label influence , in which we characterize how much the initial feature/label of one node influences the final feature/label of another node in GCN/LPA. Based on our theoretical analysis, we propose an end-to-end model that combines GCN and LPA. In our unified model, edge weights are learnable, and the LPA serves as regularization to assist the GCN in learning proper edge weights that lead to improved performance. Our model can also be seen as learning the weights of edges based on node labels, which is more direct and efficient than existing feature-based attention models or topology-based diffusion models. In a number of experiments for semi-supervised node classification and knowledge-graph-aware recommendation, our model shows superiority over state-of-the-art baselines.


Author(s):  
Lionel Alangeh Ngobesing ◽  
Yılmaz Atay

Abstract: In network science and big data, the concept of finding meaningful infrastructures in networks has emerged as a method of finding groups of entities with similar properties within very complex systems. The whole concept is generally based on finding subnetworks which have more properties (links) amongst nodes belonging to the same cluster than nodes in other groups (A concept presented by Girvan and Newman, 2002). Today meaningful infrastructure identification is applied in all types of networks from computer networks, to social networks to biological networks. In this article we will look at how meaningful infrastructure identification is applied in biological networks. This concept is important in biological networks as it helps scientist discover patterns in proteins or drugs which helps in solving many medical mysteries. This article will encompass the different algorithms that are used for meaningful infrastructure identification in biological networks. These include Genetic Algorithm, Differential Evolution, Water Cycle Algorithm (WCA), Walktrap Algorithm, Connect Intensity Iteration Algorithm (CIIA), Firefly algorithms and Overlapping Multiple Label Propagation Algorithm. These al-gorithms are compared with using performance measurement parameters such as the Mod-ularity, Normalized Mutual Information, Functional Enrichment, Recall and Precision, Re-dundancy, Purity and Surprise, which we will also discuss here.


Biomolecules ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 64
Author(s):  
Chen Jin ◽  
Zhuangwei Shi ◽  
Ken Lin ◽  
Han Zhang

Many studies have clarified that microRNAs (miRNAs) are associated with many human diseases. Therefore, it is essential to predict potential miRNA-disease associations for disease pathogenesis and treatment. Numerous machine learning and deep learning approaches have been adopted to this problem. In this paper, we propose a Neural Inductive Matrix completion-based method with Graph Autoencoders (GAE) and Self-Attention mechanism for miRNA-disease associations prediction (NIMGSA). Some of the previous works based on matrix completion ignore the importance of label propagation procedure for inferring miRNA-disease associations, while others cannot integrate matrix completion and label propagation effectively. Varying from previous studies, NIMGSA unifies inductive matrix completion and label propagation via neural network architecture, through the collaborative training of two graph autoencoders. This neural inductive matrix completion-based method is also an implementation of self-attention mechanism for miRNA-disease associations prediction. This end-to-end framework can strengthen the robustness and preciseness of both matrix completion and label propagation. Cross validations indicate that NIMGSA outperforms current miRNA-disease prediction methods. Case studies demonstrate that NIMGSA is competent in detecting potential miRNA-disease associations.


Author(s):  
Kaiyuan Yang ◽  
Junfeng Wang ◽  
Zhiyang Fang ◽  
Peng Wu ◽  
Zihua Song

Animals ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 29
Author(s):  
Somayeh Sharifi ◽  
Maryam Lotfi Shahreza ◽  
Abbas Pakdel ◽  
James M. Reecy ◽  
Nasser Ghadiri ◽  
...  

Mastitis, a disease with high incidence worldwide, is the most prevalent and costly disease in the dairy industry. Gram-negative bacteria such as Escherichia coli (E. coli) are assumed to be among the leading agents causing acute severe infection with clinical signs. E. Coli, environmental mastitis pathogens, are the primary etiological agents of bovine mastitis in well-managed dairy farms. Response to E. Coli infection has a complex pattern affected by genetic and environmental parameters. On the other hand, the efficacy of antibiotics and/or anti-inflammatory treatment in E. coli mastitis is still a topic of scientific debate, and studies on the treatment of clinical cases show conflicting results. Unraveling the bio-signature of mastitis in dairy cattle can open new avenues for drug repurposing. In the current research, a novel, semi-supervised heterogeneous label propagation algorithm named Heter-LP, which applies both local and global network features for data integration, was used to potentially identify novel therapeutic avenues for the treatment of E. coli mastitis. Online data repositories relevant to known diseases, drugs, and gene targets, along with other specialized biological information for E. coli mastitis, including critical genes with robust bio-signatures, drugs, and related disorders, were used as input data for analysis with the Heter-LP algorithm. Our research identified novel drugs such as Glibenclamide, Ipratropium, Salbutamol, and Carbidopa as possible therapeutics that could be used against E. coli mastitis. Predicted relationships can be used by pharmaceutical scientists or veterinarians to find commercially efficacious medicines or a combination of two or more active compounds to treat this infectious disease.


Author(s):  
Paul Burkhardt

The fastest deterministic algorithms for connected components take logarithmic time and perform superlinear work on a Parallel Random Access Machine (PRAM). These algorithms maintain a spanning forest by merging and compressing trees, which requires pointer-chasing operations that increase memory access latency and are limited to shared-memory systems. Many of these PRAM algorithms are also very complicated to implement. Another popular method is “leader-contraction” where the challenge is to select a constant fraction of leaders that are adjacent to a constant fraction of non-leaders with high probability, but this can require adding more edges than were in the original graph. Instead we investigate label propagation because it is deterministic, easy to implement, and does not rely on pointer-chasing. Label propagation exchanges representative labels within a component using simple graph traversal, but it is inherently difficult to complete in a sublinear number of steps. We are able to overcome the problems with label propagation for graph connectivity. We introduce a surprisingly simple framework for deterministic, undirected graph connectivity using label propagation that is easily adaptable to many computational models. It achieves logarithmic convergence independently of the number of processors and without increasing the edge count. We employ a novel method of propagating directed edges in alternating direction while performing minimum reduction on vertex labels. We present new algorithms in PRAM, Stream, and MapReduce. Given a simple, undirected graph [Formula: see text] with [Formula: see text] vertices, [Formula: see text] edges, our approach takes O(m) work each step, but we can only prove logarithmic convergence on a path graph. It was conjectured by Liu and Tarjan (2019) to take [Formula: see text] steps or possibly [Formula: see text] steps. Our experiments on a range of difficult graphs also suggest logarithmic convergence. We leave the proof of convergence as an open problem.


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