Related papers: constNJ: an algorithm to reconstruct sets of phylo…
Rearrangement operations transform a phylogenetic tree into another one and hence induce a metric on the space of phylogenetic trees. Popular operations for unrooted phylogenetic trees are NNI (nearest neighbour interchange), SPR (subtree…
Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…
This study introduces a novel approach to ensure the existence and uniqueness of optimal parameters in neural networks. The paper details how a recurrent neural networks (RNN) can be transformed into a contraction in a domain where its…
Convolutional Neural Networks (CNNs) are hard to deploy on edge devices due to its high computation and storage complexities. As a common practice for model compression, network pruning consists of two major categories: unstructured and…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
A consensus tree is a phylogenetic tree that synthesizes a given collection of phylogenetic trees, all of which share the same leaf labels but may have different topologies, typically obtained through bootstrapping. Our research focuses on…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
We propose a reinforcement-learning algorithm to tackle the challenge of reconstructing phylogenetic trees. The search for the tree that best describes the data is algorithmically challenging, thus all current algorithms for phylogeny…
Suppose N is a phylogenetic network indicating a complicated relationship among individuals and taxa. Often of interest is a much simpler network, for example, a species tree T, that summarizes the most fundamental relationships. The…
Short spanning trees subject to additional constraints are important building blocks in various approximation algorithms. Especially in the context of the Traveling Salesman Problem (TSP), new techniques for finding spanning trees with…
Tree-structured LSTM is promising way to consider long-distance interaction over hierarchies. However, there have been few research efforts on the hyperparameter tuning of the construction and traversal of tree-structured LSTM. To name a…
The Neighbor-Joining algorithm is a popular distance-based phylogenetic method that computes a tree metric from a dissimilarity map arising from biological data. Realizing dissimilarity maps as points in Euclidean space, the algorithm…
Recurrent neural networks (RNNs) have recently achieved remarkable successes in a number of applications. However, the huge sizes and computational burden of these models make it difficult for their deployment on edge devices. A practically…
We describe a kernel of size 9k-8 for the NP-hard problem of computing the Tree Bisection and Reconnect (TBR) distance k between two unrooted binary phylogenetic trees. We achieve this by extending the existing portfolio of reduction rules…
Convolutional neural networks (CNNs) have succeeded in many practical applications. However, their high computation and storage requirements often make them difficult to deploy on resource-constrained devices. In order to tackle this issue,…
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
Given the high computational complexity of decision tree estimation, classical methods construct a tree by adding one node at a time in a recursive way. To facilitate promoting fairness, we propose a fairness criterion local to the tree…
The neighbor-joining algorithm is a popular phylogenetics method for constructing trees from dissimilarity maps. The neighbor-net algorithm is an extension of the neighbor-joining algorithm and is used for constructing split networks. We…
In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations…
Recurrent Neural Network (RNN) and its variations such as Long Short-Term Memory (LSTM) and Gated Recurrent Unit (GRU), have become standard building blocks for learning online data of sequential nature in many research areas, including…