相关论文: Global Alignment of Molecular Sequences via Ancest…

Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from…

Genome rearrangement distances are an established method in genome comparison. Works in this area may include various rearrangement operations representing large-scale mutations, gene orientation information, the number of nucleotides in…

A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest…

Horizontal gene transfer (HGT) is an important process in bacterial evolution. Current phylogeny-based approaches to capture it cannot however appropriately account for the fact that HGT can occur between bacteria living in different…

As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…

The sequence reconstruction problem for insertion/deletion channels has attracted significant attention owing to their applications recently in some emerging data storage systems, such as racetrack memories, DNA-based data storage. Our goal…

Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…

Accurate identification of synergistic treatment combinations and their underlying biological mechanisms is critical across many disease domains, especially cancer. In translational oncology research, preclinical systems such as…

Trees are fundamental data structure for many areas of computer science and system engineering. In this report, we show how to ensure eventual consistency of optimistically replicated trees. In optimistic replication, the different replicas…

Phylogenetic networks are rooted directed acyclic graphs that represent evolutionary relationships between species whose past includes reticulation events such as hybridisation and horizontal gene transfer. To search the space of…

Galled trees are studied as a recombination model in theoretic population genetics. This class of phylogenetic networks has been generalized to tree-child networks, normal networks and tree-based networks by relaxing a structural condition.…

We derive tractable criteria for the consistency of Bayesian tree reconstruction procedures, which constitute a central class of algorithms for inferring common ancestry among DNA sequence samples in phylogenetics. Our results encompass…

Until recently, transcriptomics was limited to bulk RNA sequencing, obscuring the underlying expression patterns of individual cells in favor of a global average. Thanks to technological advances, we can now profile gene expression across…

We propose an approach to 3D reconstruction via inverse procedural modeling and investigate two variants of this approach. The first option consists in the fitting set of input parameters using a genetic algorithm. We demonstrate the…

Learning vector representations for programs is a critical step in applying deep learning techniques for program understanding tasks. Various neural network models are proposed to learn from tree-structured program representations, e.g.,…

Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…

A method based on mapping a symbolic sequence into a set of patterns (strings resulting from the sequence parsing) is proposed as a tool for the reconstruction of ancestral sequences. The set union of patterns comprises all the patterns…

How can we identify the training examples that contribute most to the prediction of a tree ensemble? In this paper, we introduce TREX, an explanation system that provides instance-attribution explanations for tree ensembles, such as random…

Latent tree learning(LTL) methods learn to parse sentences using only indirect supervision from a downstream task. Recent advances in latent tree learning have made it possible to recover moderately high quality tree structures by training…

Phylogenetic networks generalize evolutionary trees, and are commonly used to represent evolutionary histories of species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer.…