Related papers: Generating heterogeneous data on gene trees
In recent years, several models have improved the capacity to generate synthetic tabular datasets. However, such models focus on synthesizing simple columnar tables and are not useable on real-life data with complex structures. This paper…
We present Glyph - a Python package for genetic programming based symbolic regression. Glyph is designed for usage let by numerical simulations let by real world experiments. For experimentalists, glyph-remote provides a separation of…
Data plays a fundamental role in consolidating markets, services, and products in the digital financial ecosystem. However, the use of real data, especially in the financial context, can lead to privacy risks and access restrictions,…
Genomic language models (gLMs) have shown mostly modest success in identifying evolutionarily constrained elements in mammalian genomes. To address this issue, we introduce a novel framework for training gLMs that explicitly models…
The increasing risk of epidemics and a fast-growing world population has contributed to a great investment in phylogenetic analysis, in order to track numerous diseases and conceive effective medication and treatments. Phylogenetic analysis…
Domains such as manufacturing and medicine crave for continuous monitoring and analysis of their processes, especially in combination with time series as produced by sensors. Time series data can be exploited to, for example, explain and…
Biological phenotypes are products of complex evolutionary processes in which selective forces influence multiple biological trait measurements in unknown ways. Phylogenetic factor analysis disentangles these relationships across the…
GitHub Copilot, an extension for the Visual Studio Code development environment powered by the large-scale language model Codex, makes automatic program synthesis available for software developers. This model has been extensively studied in…
Polygenic risk scores and other genomic analyses require large individual-level genotype datasets, yet strict data access restrictions impede sharing. Synthetic genotype generation offers a privacy-preserving alternative, but most existing…
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…
The field of neuromorphic computing is in a period of active exploration. While many tools have been developed to simulate neuronal dynamics or convert deep networks to spiking models, general software libraries for learning rules remain…
Recent work has proven the existence of extreme inbreeding in a European ancestry sample taken from the contemporary UK population \cite{nature_01}. This result brings our attention again to a math problem related to inbreeding family trees…
Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry relationships among…
GenoML is a Python package automating machine learning workflows for genomics (genetics and multi-omics) with an open science philosophy. Genomics data require significant domain expertise to clean, pre-process, harmonize and perform…
We present a new Markov chain Monte Carlo algorithm, implemented in software Arbores, for inferring the history of a sample of DNA sequences. Our principal innovation is a bridging procedure, previously applied only for simple stochastic…
In recent years, numerical simulations have become indispensable for addressing complex astrophysical problems. The MagnetoHydroDynamics (MHD) framework represents a key tool for investigating the dynamical evolution of astrophysical…
The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a…
PhyloFrame is a Python library for phylogenetic computation targeting the gap between specialist, compiler-optimized operations and flexible, script-based workflows -- with emphasis on fast, memory-efficient operations for very large tree…
The analysis of experimental results with Python often requires writing many code scripts which all need access to the same set of functions. In a common field of research, this set will be nearly the same for many users. The qspec Python…
Applications that require substantial computational resources today cannot avoid the use of heavily parallel machines. Embracing the opportunities of parallel computing and especially the possibilities provided by a new generation of…