Papers for

bioinformatics data scientists

Papers whose findings have a practical use for this group, as judged from the abstract. Open a paper to read what it means in practice.

Graph coarsening improved by geometric flow based edge weighting

Geometric Flow enhanced Graph Coarsening

Abstract: Recently, researchers have proposed a graph pooling operation, akin to the pooling process in conventional convolutional neural networks (CNN), aimed at reducing the computation cost of Graph convolutional neural networks (GCNNs). While most GCNN-based methods treat graph pooling as a node clustering problem and propose learning a cluster assignment matrix, existing clustering-based pooling methods tend to focus solely on the rough topology information of graphs, neglecting the exploitation of higher-order mutual connections among neighbors. In terms of message passing on graph, the ease of information passing on edges reflects the closeness between neighboring nodes, which significantly relies on the interconnectivity among neighbors. In this study, we address this gap by considering such local connection information and introducing a novel graph pooling method named RicciPool. We introduce discrete graph curvature, particularly Ollivier-Ricci curvature, as a measure of higher-order connectivity around an edge. Subsequently, we construct an Ollivier-Ricci flow formula to reweigh edge weights, leveraging the crucial information provided by Ricci curvature, particularly vital for extracting clusters in graphs. Building upon this foundation, we utilize the spectral clustering technique to learn a new cluster assignment matrix. Experimental results on multiple bioinformatics protein datasets and social networks underscore the effectiveness of our proposed method.

Mon 14 SeptArtificial Intelligence
The gist
Graphs are networks made of nodes connected by edges, and analyzing them can be slow for big graphs. The authors found a better way to group nodes by looking not just at direct connections but also at how tightly connected groups of neighbors are. They use a math idea called Ricci curvature to adjust the importance of edges, making it easier to find meaningful clusters. This helps reduce the size of graphs while keeping important structure, speeding up graph-based computations.
Open 2609.14962v1