相关论文: How Overlap Determines the Macronuclear Genes in C…

Statistical phylogenetic inference methods use tree rearrangement operations to perform either hill-climbing local search or Markov chain Monte Carlo across tree topologies. The canonical class of such moves are the subtree-prune-regraft…

With recent advances in high-throughput cell biology the amount of cellular biological data has grown drastically. Such data is often modeled as graphs (also called networks) and studying them can lead to new insights into molecule-level…

We present techniques for effective Gaussian process (GP) modelling of multiple short time series. These problems are common when applying GP models independently to each gene in a gene expression time series data set. Such sets typically…

Self supervised learning (SSL) is a machine learning paradigm where models learn to understand the underlying structure of data without explicit supervision from labeled samples. The acquired representations from SSL have demonstrated…

Representing a graph as a vector is a challenging task; ideally, the representation should be easily computable and conducive to efficient comparisons among graphs, tailored to the particular data and analytical task at hand. Unfortunately,…

The overlap graphs of subtrees in a tree (SOGs) generalise many other graphs classes with set representation characterisations. The complexity of recognising SOGs in open. The complexities of recognising many subclasses of SOGs are known.…

Single-cell RNA sequencing (scRNA-seq) profiles large numbers of cells but loses spatial context, whereas spatial transcriptomics (ST) preserves partial spatial structure at lower resolution. Most existing integration methods either…

Extracting a small subset of representative tuples from a large database is an important task in multi-criteria decision making. The regret-minimizing set (RMS) problem is recently proposed for representative discovery from databases.…

One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies…

Ranked set sampling (RSS) is a stratified sampling method that improves efficiency over simple random sampling (SRS) by utilizing auxiliary information for ranking and stratification. While balanced RSS (BRSS) assumes equal allocation…

Subgraph-based graph representation learning (SGRL) has been recently proposed to deal with some fundamental challenges encountered by canonical graph neural networks (GNNs), and has demonstrated advantages in many important data science…

Gene regulatory networks (GRNs) are increasingly used for explaining biological processes with complex transcriptional regulation. A GRN links the expression levels of a set of genes via regulatory controls that gene products exert on one…

We present a theoretically grounded Gaussian process framework that leverages neural feature maps to construct expressive kernels. We show that the learned feature map can be interpreted as an optimal low-rank approximation to a Gram matrix…

Graph neural networks (GNNs) learn to represent nodes by aggregating information from their neighbors. As GNNs increase in depth, their receptive field grows exponentially, leading to high memory costs. Several existing methods address this…

Next-generation sequencing (NGS) technologies allow new methodologies for alternative splicing (AS) analysis. Current computational methods for AS from NGS data are mainly focused on predicting splice site junctions or de novo assembly of…

Polymers are large macromolecules composed of repeating structural units known as monomers and are widely applied in fields such as energy storage, construction, medicine, and aerospace. However, existing graph neural network methods,…

Shape graphs are complex geometrical structures commonly found in biological and anatomical systems. A shape graph is a collection of nodes, some connected by curvilinear edges with arbitrary shapes. Their high complexity stems from the…

Convolutional neural networks (CNNs) have achieved remarkable performance in hyperspectral image (HSI) classification over the last few years. Despite the progress that has been made, rich and informative spectral information of HSI has…

This paper presents a new approach for assembling graph neural networks based on framelet transforms. The latter provides a multi-scale representation for graph-structured data. We decompose an input graph into low-pass and high-pass…

Graph Neural Networks (GNNs) typically operate by message-passing, where the state of a node is updated based on the information received from its neighbours. Most message-passing models act as graph convolutions, where features are mixed…