Related papers: Phylotrack: C++ and Python libraries for in silico…
Fast, incremental evolution of physics instrumentation raises the question of efficient software abstraction and transferability of algorithms across similar technologies. This contribution aims to provide an answer by introducing Track…
EC-KitY is a comprehensive Python library for doing evolutionary computation (EC), licensed under the BSD 3-Clause License, and compatible with scikit-learn. Designed with modern software engineering and machine learning integration in…
Representing scientific data sets efficiently on external storage usually involves converting them to a byte string representation using specialized reader/writer routines. The resulting storage files are frequently difficult to interpret…
Scipp is heavily inspired by the Python library xarray. It enriches raw NumPy-like multi-dimensional arrays of data by adding named dimensions and associated coordinates. Multiple arrays are combined into datasets. On top of this, scipp…
Recently, it has been proven that evolutionary algorithms produce good results for a wide range of combinatorial optimization problems. Some of the considered problems are tackled by evolutionary algorithms that use a representation which…
We introduce cilantro, an open-source C++ library for geometric and general-purpose point cloud data processing. The library provides functionality that covers low-level point cloud operations, spatial reasoning, various methods for point…
I present a preliminary version of {\tt APFEL++}, a C++ rewriting of the Fortran 77 evolution code {\tt APFEL}. In this contribution I discuss the new philosophy adopted for the numerical computation of the convolutions, demonstrate the…
Tick is a statistical learning library for Python~3, with a particular emphasis on time-dependent models, such as point processes, and tools for generalized linear models and survival analysis. The core of the library is an optimization…
The automatic generation of computer programs is one of the main applications with practical relevance in the field of evolutionary computation. With program synthesis techniques not only software developers could be supported in their…
The drive for reproducibility in the computational sciences has provoked discussion and effort across a broad range of perspectives: technological, legislative/policy, education, and publishing. Discussion on these topics is not new, but…
Evolutionary Computation is a group of biologically inspired algorithms used to solve complex optimisation problems. It can be split into Evolutionary Algorithms, which take inspiration from genetic inheritance, and Swarm Intelligence…
The application of phylogenetic techniques to the documentation of cultural history can present a distorted picture due to horizontal transmission and blending. Moreover, the units of cultural transmission must be communicable concepts,…
The emergence of multicellularity and developmental programs are among the major problems of evolutionary biology. Traditionally, research in this area has been based on the combination of data analysis and experimental work on one hand and…
Gene innovation is a key mechanism on the evolution and phenotypic diversity of life forms. There is a need for tools able to study gene innovation across an increasingly large number of genomic sequences to maximally capitalise our…
Reconstructing the evolutionary history of a set of species is a central task in computational biology. In real data, it is often the case that some information is missing: the Incomplete Directed Perfect Phylogeny (IDPP) problem asks,…
The Kassiopeia particle tracking framework is an object-oriented software package using modern C++ techniques, written originally to meet the needs of the KATRIN collaboration. Kassiopeia features a new algorithmic paradigm for particle…
This paper introduces PolyDiM, an open-source C++ library tailored for the development and implementation of polytopal discretization methods for partial differential equations. The library provides robust and modular tools to support…
We use a combination of analytic models and computer simulations to gain insight into the dynamics of evolution. Our results suggest that certain interesting phenomena should eventually emerge from the fossil record. For example, there…
With the increasing emphasis on how mobile technologies are experienced in everyday life, researchers are increasingly emphasizing the use of in-situ methods such as Experience Sampling and Day Reconstruction. In our line of research we…
Phylogenetics is a widely used concept in evolutionary biology. It is the reconstruction of evolutionary history by building trees that represent branching patterns and sequences. These trees represent shared history, and it is our…