Related papers: C Library for Simulated Evolution of Biological Ne…
An important part of the analysis of bio-molecular networks is to detect different functional units. Different functions are reflected in a different evolutionary dynamics, and hence in different statistical characteristics of network…
We investigate fundamental decisions in the design of instruction set architectures for linear genetic programs that are used as both model systems in evolutionary biology and underlying solution representations in evolutionary computation.…
Constraints placed upon the phenotypes of organisms result from their interactions with the environment. Over evolutionary timescales, these constraints feed back onto smaller molecular subnetworks comprising the organism. The evolution of…
Following in the footsteps of the success of Mathlib - the centralised library of formalised mathematics in Lean - CSLib is a rapidly-growing centralised library of formalised computer science and software. In this paper, we present its…
Inspired by natural evolutionary processes, Evolutionary Computation (EC) has established itself as a cornerstone of Artificial Intelligence. Recently, with the surge in data-intensive applications and large-scale complex systems, the…
A computing environment is proposed, based on batch spreadsheet processing, which produces a spreadsheet display from plain text input files of commands, similar to the way documents are created using LaTeX. In this environment, besides the…
There are a number of ways to procedurally generate interesting three-dimensional shapes, and a method where a cellular neural network is combined with a mesh growth algorithm is presented here. The aim is to create a shape from a genetic…
We present ensmallen, a fast and flexible C++ library for mathematical optimization of arbitrary user-supplied functions, which can be applied to many machine learning problems. Several types of optimizations are supported, including…
The evolution processes of complex systems carry key information in the systems' functional properties. Applying machine learning algorithms, we demonstrate that the historical formation process of various networked complex systems can be…
Web-based applications are highly accessible to users, providing rich, interactive content while eliminating the need to install software locally. However, evolutionary robotics (ER) has faced challenges in this domain as web-based…
This paper presents a real-time simulation involving ''protozoan-like'' cells that evolve by natural selection in a physical 2D ecosystem. Selection pressure is exerted via the requirements to collect mass and energy from the surroundings…
Nowadays the analysis of dynamics of and on networks represents a hot topic in the Social Network Analysis playground. To support students, teachers, developers and researchers in this work we introduce a novel framework, namely NDlib, an…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
Recently, computational modelling became a very important research tool that enables us to study problems that for decades evaded scientific analysis. Evolutionary systems are certainly examples of such problems: they are composed of many…
A powerful experimental approach for investigating computation in networks of biological neurons is the use of cultured dissociated cortical cells grown into networks on a multi-electrode array. Such preparations allow investigation of…
Image translators have been successfully applied to many important low level image processing tasks. However, classical network architecture of image translator like U-Net, is borrowed from other vision tasks like biomedical image…
Generic programming is an effective methodology for developing reusable software libraries. Many programming languages provide generics and have features for describing interfaces, but none completely support the idioms used in generic…
Recent genomic and bioinformatic advances have motivated the development of numerous random network models purporting to describe graphs of biological, technological, and sociological origin. The success of a model has been evaluated by how…
Those seeking to reproduce a computational experiment often need to manually look at the code to see how to build necessary libraries, configure parameters, find data, and invoke the experiment; it is not automatic. Automatic…
The engineered control of cellular function through the design of synthetic genetic networks is becoming plausible. Here we show how a naturally occurring network can be used as a parts list for artificial network design, and how model…