Related papers: PhyloFrame: A DataFrame-based Library for Fast, Fl…
Probabilistic programming frameworks are powerful tools for statistical modelling and inference. They are not immediately generalisable to phylogenetic problems due to the particular computational properties of the phylogenetic tree object.…
Phylogenetic profiles - presence-absence patterns of genes across taxa - are rich information sources for inferring the evolutionary history of genes and gene families. When aggregated across many genes, these profiles can reveal…
In the last few years, the field of data science has been growing rapidly as various businesses have adopted statistical and machine learning techniques to empower their decision making and applications. Scaling data analysis, possibly…
In silico evolution instantiates the processes of heredity, variation, and differential reproductive success (the three "ingredients" for evolution by natural selection) within digital populations of computational agents. Consequently,…
Phylogenetics is a fundamental component of evolutionary analysis frameworks in biology and linguistics. Recently, the advent of large-scale genomics and the SARS-CoV-2 pandemic has highlighted the necessity for phylogenetic software to…
Phylogenetic trees are pervasively used to depict evolutionary relationships. Increasingly, researchers need to visualize large trees and compare multiple large trees inferred for the same set of taxa (reflecting uncertainty in the tree…
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…
Contemporary bioinformatics has seen in profound new visibility into the composition, structure, and history of the natural world around us. Arguably, the central pillar of bioinformatics is phylogenetics -- the study of hereditary…
PaPy, which stands for parallel pipelines in Python, is a highly flexible framework that enables the construction of robust, scalable workflows for either generating or processing voluminous datasets. A workflow is created from user-written…
phyloDB is a modular and extensible framework for large-scale phylogenetic analyses, which are essential for understanding epidemics evolution. It relies on the Neo4j graph database for data storage and processing, providing a schema and an…
Linear operators and optimisation are at the core of many algorithms used in signal and image processing, remote sensing, and inverse problems. For small to medium-scale problems, existing software packages (e.g., MATLAB, Python numpy and…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, like recombination between genes, hybridization between lineages, and lateral gene…
Mojo is an emerging programming language built on MLIR (Multi-Level Intermediate Representation) and supports JIT (Just-in-Time) compilation. It enables transparent hardware-specific optimizations (e.g., for CPUs and GPUs), while allowing…
Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art…
Evolutionary relationships between species are usually inferred through phylogenetic analysis, which provides phylogenetic trees computed from allelic profiles built by sequencing specific regions of the sequences and abstracting them to…
Optimizing scientific computing algorithms for modern GPUs is a labor-intensive and iterative process involving repeated code modification, benchmarking, and tuning across complex hardware and software stacks. Recent work has explored large…
In this paper, we present PARTIME, a software library written in Python and based on PyTorch, designed specifically to speed up neural networks whenever data is continuously streamed over time, for both learning and inference. Existing…
This paper introduces PhyloLM, a method adapting phylogenetic algorithms to Large Language Models (LLMs) to explore whether and how they relate to each other and to predict their performance characteristics. Our method calculates a…
Collapse Lineage Tree (CLTree) is a software tool that annotates, roots, and evaluates phylogenetic trees by using lineages. A recursive algorithm was designed to annotate the branches by the common taxonomic lineage of its descendants in a…
Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded…