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

Genetic Programming (GP) is an evolutionary algorithm commonly used for machine learning tasks. In this paper we present a method that allows GP to transform the representation of a large-scale machine learning dataset into a more compact…

Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the…

An exact-match overlap graph of $n$ given strings of length $\ell$ is an edge-weighted graph in which each vertex is associated with a string and there is an edge $(x,y)$ of weight $\omega = \ell - |ov_{max}(x,y)|$ if and only if $\omega…

The prevalence of neutral mutations implies that biological systems typically have many more genotypes than phenotypes. But can the way that genotypes are distributed over phenotypes determine evolutionary outcomes? Answering such questions…

This paper presents Planar Gaussian Splatting (PGS), a novel neural rendering approach to learn the 3D geometry and parse the 3D planes of a scene, directly from multiple RGB images. The PGS leverages Gaussian primitives to model the scene…

Recommender Systems (RSs) are used to provide users with personalized item recommendations and help them overcome the problem of information overload. Currently, recommendation methods based on deep learning are gaining ground over…

Graphs and networks are common ways of depicting biological information. In biology, many different biological processes are represented by graphs, such as regulatory networks, metabolic pathways and protein--protein interaction networks.…

Graphs are naturally used to describe the structures of various real-world systems in biology, society, computer science etc., where subgraphs or motifs as basic blocks play an important role in function expression and information…

Small subgraphs (graphlets) are important features to describe fundamental units of a large network. The calculation of the subgraph frequency distributions has a wide application in multiple domains including biology and engineering.…

Existing genetic programming (GP) methods are typically designed based on a certain representation, such as tree-based or linear representations. These representations show various pros and cons in different domains. However, due to the…

A new framework is proposed to study rank-structured matrices arising from discretizations of 2D and 3D elliptic operators. In particular, we introduce the notion of a graph-induced rank structure (GIRS) which aims to capture the fine low…

Reconstructing the causal network in a complex dynamical system plays a crucial role in many applications, from sub-cellular biology to economic systems. Here we focus on inferring gene regulation networks (GRNs) from perturbation or gene…

While 3D Gaussian splatting (3DGS) offers explicit and efficient scene representations for cone-beam computed tomography reconstruction, conventional photometric optimization inherently suffers from spectral bias under ultra sparse-view…

Overlapping genes exist in all domains of life and are much more abundant than expected at their first discovery in the late 1970s. Assuming that the reference gene is read in frame +0, an overlapping gene can be encoded in two reading…

Predicting the labels of graph-structured data is crucial in scientific applications and is often achieved using graph neural networks (GNNs). However, when data is scarce, GNNs suffer from overfitting, leading to poor performance.…

Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms,…

Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform…

Convolutional neural networks have been widely applied to hyperspectral image classification. However, traditional convolutions can not effectively extract features for objects with irregular distributions. Recent methods attempt to address…

Gene regulation is a series of processes that control gene expression and its extent. The connections among genes and their regulatory molecules, usually transcription factors, and a descriptive model of such connections, are known as gene…

Gene assembly in ciliates is an extremely involved DNA transformation process, which transforms a nucleus, the micronucleus, to another functionally different nucleus, the macronucleus. In this paper we characterize which loop recombination…