5 papers · ranked by Valyu relevance
Mengzhen Guo, Stefan Grünewald
We present Lpnet, a variant of the widely used Neighbor-net method that approximates pairwise distances between taxa by a circular phylogenetic network. We first apply standard methods to construct a binary phylogenetic tree and then use integer linear programming to compute an optimal circular orderings that agrees…
Frans Zdyb, Julius B. Kirkegaard
Biological image and video analysis is full of discrete decisions: whether an object is present, which multi-hypothesis detections are real, whether two detections are tracking the same object, or whether a cell divides or not. Standard pipelines resolve these locally and in sequence, e.g through non-max suppression…
Virgile Andreani, Eric J. South, Mary J. Dunlop
Dense arrangements of binding sites within nucleotide sequences can collectively influence downstream transcription rates or initiate biomolecular interactions. For example, natural promoter regions can harbor many overlapping transcription factor binding sites that influence the rate of transcription initiation.…
Henri Schmidt, Benjamin J. Raphael
Reconstructing unobserved ancestral states of a phylogenetic tree provides insight into the history of evolving systems and is one of the fundamental problems in phylogenetics. For a fixed phylogenetic tree, the most parsimonious ancestral reconstruction – a solution to the small parsimony problem – can be efficiently…
Pouya Ahadi, Balabhaskar Balasundaram, Juan S. Borrero, Charles Chen
In this study, we address the mate selection problem in the hybridization stage of a breeding pipeline, which constitutes the multi-objective breeding goal key to the performance of a variety development program. The solution framework we formulate seeks to ensure that individuals with the most desirable genomic…