AIMC Topic: Phylogeny

Clear Filters Showing 191 to 200 of 212 articles

Predicting Host Association for Shiga Toxin-Producing E. coli Serogroups by Machine Learning.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2021
Escherichia coli is a species of bacteria that can be present in a wide variety of mammalian hosts and potentially soil environments. E. coli has an open genome and can show considerable diversity in gene content between isolates. It is a reasonable ...
Cattle Escherichia coli Infections Animals Phylogeny Serogroup Genome, Bacterial Whole Genome Sequencing Shiga-Toxigenic Escherichia coli Humans Machine Learning
View on PubMed DOI

Supervised learning on phylogenetically distributed data.

Bioinformatics (Oxford, England) Dec 30, 2020
MOTIVATION: The ability to develop robust machine-learning (ML) models is considered imperative to the adoption of ML techniques in biology and medicine fields. This challenge is particularly acute when data available for training is not independent ...
Phylogeny Supervised Machine Learning Neural Networks, Computer Machine Learning
View on PubMed DOI

Distinguishing Felsenstein Zone from Farris Zone Using Neural Networks.

Molecular biology and evolution Dec 16, 2020
Maximum likelihood and maximum parsimony are two key methods for phylogenetic tree reconstruction. Under certain conditions, each of these two methods can perform more or less efficiently, resulting in unresolved or disputed phylogenies. We show that...
Coleoptera Genetic Techniques Animals Phylogeny Neural Networks, Computer
View on PubMed DOI

ModelTeller: Model Selection for Optimal Phylogenetic Reconstruction Using Machine Learning.

Molecular biology and evolution Nov 1, 2020
Statistical criteria have long been the standard for selecting the best model for phylogenetic reconstruction and downstream statistical inference. Although model selection is regarded as a fundamental step in phylogenetics, existing methods for this...
Phylogeny Models, Genetic Machine Learning
View on PubMed DOI

Searching for Models for Psychological Science: A Possible Contribution of Simulation.

Integrative psychological & behavioral science Sep 1, 2020
The problem of the theoretical precariousness of psychology requires defining, at an epistemological level, its concepts and languages and the use of models for finding core concepts and building more or less 'hard' theories. After reviewing some mai...
Biological Evolution Artificial Intelligence Phylogeny Clay Knowledge Humans
View on PubMed DOI

EvoLSTM: context-dependent models of sequence evolution using a sequence-to-sequence LSTM.

Bioinformatics (Oxford, England) Jul 1, 2020
MOTIVATION: Accurate probabilistic models of sequence evolution are essential for a wide variety of bioinformatics tasks, including sequence alignment and phylogenetic inference. The ability to realistically simulate sequence evolution is also at the...
Sequence Alignment Phylogeny Neural Networks, Computer Machine Learning Software
View on PubMed DOI

Deep Residual Neural Networks Resolve Quartet Molecular Phylogenies.

Molecular biology and evolution May 1, 2020
Phylogenetic inference is of fundamental importance to evolutionary as well as other fields of biology, and molecular sequences have emerged as the primary data for this task. Although many phylogenetic methods have been developed to explicitly take ...
Software Animals Phylogeny Red Fluorescent Protein Mammals Deep Learning Luminescent Proteins Plants
View on PubMed DOI

Accurate Inference of Tree Topologies from Multiple Sequence Alignments Using Deep Learning.

Systematic biology Mar 1, 2020
Reconstructing the phylogenetic relationships between species is one of the most formidable tasks in evolutionary biology. Multiple methods exist to reconstruct phylogenetic trees, each with their own strengths and weaknesses. Both simulation and emp...
Sequence Alignment Neural Networks, Computer Deep Learning Phylogeny Computer Simulation Classification
View on PubMed DOI

BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree.

Nucleic acids research Jan 8, 2020
The BiGG Models knowledge base (http://bigg.ucsd.edu) is a centralized repository for high-quality genome-scale metabolic models. For the past 12 years, the website has allowed users to browse and search metabolic models. Within this update, we detai...
User-Computer Interface Models, Biological Reproducibility of Results Knowledge Bases Phylogeny Software Genome
View on PubMed DOI

Automated Taxonomic Identification of Insects with Expert-Level Accuracy Using Effective Feature Transfer from Convolutional Networks.

Systematic biology Nov 1, 2019
Rapid and reliable identification of insects is important in many contexts, from the detection of disease vectors and invasive species to the sorting of material from biodiversity inventories. Because of the shortage of adequate expertise, there has ...
Reproducibility of Results Phylogeny Neural Networks, Computer Classification Insecta Animals
View on PubMed DOI
Popular Topics
Recent Journals