Related papers: A step towards neural genome assembly

This paper addresses the challenging problem of retrieval and matching of graph structured objects, and makes two key contributions. First, we demonstrate how Graph Neural Networks (GNN), which have emerged as an effective model for various…

Graphs serve as fundamental descriptors for systems composed of interacting elements, capturing a wide array of data types, from molecular interactions to social networks and knowledge graphs. In this paper, we present an exhaustive review…

The decoupled Graph Convolutional Network (GCN), a recent development of GCN that decouples the neighborhood aggregation and feature transformation in each convolutional layer, has shown promising performance for graph representation…

We present GERN, a novel scalable framework for training GNNs in node classification tasks, based on effective resistance, a standard tool in spectral graph theory. Our method progressively refines the GNN weights on a sequence of random…

In this work, we propose to train a graph neural network via resampling from a graphon estimate obtained from the underlying network data. More specifically, the graphon or the link probability matrix of the underlying network is first…

Graph data are pervasive in many real-world applications. Recently, increasing attention has been paid on graph neural networks (GNNs), which aim to model the local graph structures and capture the hierarchical patterns by aggregating the…

As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment, and assembly.…

The advent of Graph Neural Networks (GNNs) has revolutionized the field of machine learning, offering a novel paradigm for learning on graph-structured data. Unlike traditional neural networks, GNNs are capable of capturing complex…

Graphs neural networks (GNNs) learn node features by aggregating and combining neighbor information, which have achieved promising performance on many graph tasks. However, GNNs are mostly treated as black-boxes and lack human intelligible…

In recent years, graph neural networks (GNNs) have become increasingly popular for solving NP-hard combinatorial optimization (CO) problems, such as maximum cut and maximum independent set. The core idea behind these methods is to represent…

Graphs are often used to organize data because of their simple topological structure, and therefore play a key role in machine learning. And it turns out that the low-dimensional embedded representation obtained by graph representation…

Recently, message-passing graph neural networks (MPNNs) have shown potential for solving combinatorial and continuous optimization problems due to their ability to capture variable-constraint interactions. While existing approaches leverage…

Graph Neural Networks (GNNs) are a powerful representational tool for solving problems on graph-structured inputs. In almost all cases so far, however, they have been applied to directly recovering a final solution from raw inputs, without…

Deep convolutional neural networks (CNNs) have shown excellent performance in object recognition tasks and dense classification problems such as semantic segmentation. However, training deep neural networks on large and sparse datasets is…

Many real-world networks exhibit correlations between the node degrees. For instance, in social networks nodes tend to connect to nodes of similar degree. Conversely, in biological and technological networks, high-degree nodes tend to be…

Assortment optimization seeks to select a subset of substitutable products, subject to constraints, to maximize expected revenue. The problem is NP-hard due to its combinatorial and nonlinear nature and arises frequently in industries such…

Graph Convolutional Neural Networks (GCNNs) are generalizations of CNNs to graph-structured data, in which convolution is guided by the graph topology. In many cases where graphs are unavailable, existing methods manually construct graphs…

Graph neural networks (GNNs) are emerging for machine learning research on graph-structured data. GNNs achieve state-of-the-art performance on many tasks, but they face scalability challenges when it comes to real-world applications that…

In network tomography, one goal is to identify a small set of failed links in a network, by sending a few packets through the network and seeing which reach their destination. This problem can be seen as a variant of combinatorial group…

We focus on graph-to-sequence learning, which can be framed as transducing graph structures to sequences for text generation. To capture structural information associated with graphs, we investigate the problem of encoding graphs using…