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  1. Free, publicly-accessible full text available October 29, 2024
  2. Abstract Motivation

    Model organisms are widely used to better understand the molecular causes of human disease. While sequence similarity greatly aids this cross-species transfer, sequence similarity does not imply functional similarity, and thus, several current approaches incorporate protein–protein interactions to help map findings between species. Existing transfer methods either formulate the alignment problem as a matching problem which pits network features against known orthology, or more recently, as a joint embedding problem.


    We propose a novel state-of-the-art joint embedding solution: Embeddings to Network Alignment (ETNA). ETNA generates individual network embeddings based on network topological structure and then uses a Natural Language Processing-inspired cross-training approach to align the two embeddings using sequence-based orthologs. The final embedding preserves both within and between species gene functional relationships, and we demonstrate that it captures both pairwise and group functional relevance. In addition, ETNA’s embeddings can be used to transfer genetic interactions across species and identify phenotypic alignments, laying the groundwork for potential opportunities for drug repurposing and translational studies.

    Availability and implementation

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  3. Abstract

    The graph convolutional network (GCN) is a go-to solution for machine learning on graphs, but its training is notoriously difficult to scale both in terms of graph size and the number of model parameters. Although some work has explored training on large-scale graphs, we pioneer efficient training of large-scale GCN models with the proposal of a novel, distributed training framework, called . disjointly partitions the parameters of a GCN model into several, smaller sub-GCNs that are trained independently and in parallel. Compatible with all GCN architectures and existing sampling techniques, (i) improves model performance, (ii) scales to training on arbitrarily large graphs, (iii) decreases wall-clock training time, and (iv) enables the training of markedly overparameterized GCN models. Remarkably, with , we train an astonishgly-wide 32–768-dimensional GraphSAGE model, which exceeds the capacity of a single GPU by a factor of$$8\times $$8×, to SOTA performance on the Amazon2M dataset.

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  4. Free, publicly-accessible full text available June 4, 2024
  5. We study p -Laplacians and spectral clustering for a recently proposed hypergraph model that incorporates edge-dependent vertex weights (EDVW). These weights can reflect different importance of vertices within a hyperedge, thus conferring the hypergraph model higher expressivity and flexibility. By constructing submodular EDVW-based splitting functions, we convert hypergraphs with EDVW into submodular hypergraphs for which the spectral theory is better developed. In this way, existing concepts and theorems such as p -Laplacians and Cheeger inequalities proposed under the submodular hypergraph setting can be directly extended to hypergraphs with EDVW. For submodular hypergraphs with EDVW-based splitting functions, we propose an efficient algorithm to compute the eigenvector associated with the second smallest eigenvalue of the hypergraph 1-Laplacian. We then utilize this eigenvector to cluster the vertices, achieving higher clustering accuracy than traditional spectral clustering based on the 2-Laplacian. More broadly, the proposed algorithm works for all submodular hypergraphs that are graph reducible. Numerical experiments using real-world data demonstrate the effectiveness of combining spectral clustering based on the 1-Laplacian and EDVW. 
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  6. Abstract We develop a framework for incorporating edge-dependent vertex weights (EDVWs) into the hypergraph minimum s - t cut problem. These weights are able to reflect different importance of vertices within a hyperedge, thus leading to better characterized cut properties. More precisely, we introduce a new class of hyperedge splitting functions that we call EDVWs-based, where the penalty of splitting a hyperedge depends only on the sum of EDVWs associated with the vertices on each side of the split. Moreover, we provide a way to construct submodular EDVWs-based splitting functions and prove that a hypergraph equipped with such splitting functions can be reduced to a graph sharing the same cut properties. In this case, the hypergraph minimum s - t cut problem can be solved using well-developed solutions to the graph minimum s - t cut problem. In addition, we show that an existing sparsification technique can be easily extended to our case and makes the reduced graph smaller and sparser, thus further accelerating the algorithms applied to the reduced graph. Numerical experiments using real-world data demonstrate the effectiveness of our proposed EDVWs-based splitting functions in comparison with the all-or-nothing splitting function and cardinality-based splitting functions commonly adopted in existing work. 
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