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Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene duplication, and gene loss/gain complicate accurate genome assembly from metagenomic communities. Detecting repeats is a crucial first step in overcoming these challenges. To address this issue, we propose GraSSRep, a novel approach that leverages the assembly graph's structure through graph neural networks (GNNs) within a self-supervised learning framework to classify DNA sequences into repetitive and non-repetitive categories. Specifically, we frame this problem as a node classification task within a metagenomic assembly graph. In a self-supervised fashion, we rely on a high-precision (but low-recall) heuristic to generate pseudo-labels for a small proportion of the nodes. We then use those pseudo-labels to train a GNN embedding and a random forest classifier to propagate the labels to the remaining nodes. In this way, GraSSRep combines sequencing features with predefined and learned graph features to achieve state-of-the-art performance in repeat detection. We evaluate our method using simulated and synthetic metagenomic datasets. The results on the simulated data highlight our GraSSRep's robustness to repeat attributes, demonstrating its effectiveness in handling the complexity of repeated sequences. Additionally, our experiments with synthetic metagenomic datasets reveal that incorporating the graph structure and the GNN enhances our detection performance. Finally, in comparative analyses, GraSSRep outperforms existing repeat detection tools with respect to precision and recall. 

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$$8\times $$ $8\times$, to SOTA performance on the Amazon2M dataset.