In computer science and operations research, a genetic algorithm (GA) is a metaheuristic inspired by the process of natural selection that belongs to the larger class of evolutionary algorithms (EA). Genetic algorithms are commonly used to generate high-quality solutions to optimization and search problems via biologically inspired operators such as selection, crossover, and mutation. Some examples of GA applications include optimizing decision trees for better performance, solving sudoku puzzles, hyperparameter optimization, and causal inference.
BioJava is an open-source software project dedicated to provide Java tools to process biological data. BioJava is a set of library functions written in the programming language Java for manipulating sequences, protein structures, file parsers, Common Object Request Broker Architecture (CORBA) interoperability, Distributed Annotation System (DAS), access to AceDB, dynamic programming, and simple statistical routines. BioJava supports a range of data, starting from DNA and protein sequences to the level of 3D protein structures. The BioJava libraries are useful for automating many daily and mundane bioinformatics tasks such as to parsing a Protein Data Bank (PDB) file, interacting with Jmol and many more. This application programming interface (API) provides various file parsers, data models and algorithms to facilitate working with the standard data formats and enables rapid application development and analysis.
Swarm intelligence (SI) is the collective behavior of decentralized, self-organized systems, natural or artificial. The concept is employed in work on artificial intelligence. The expression was introduced by Gerardo Beni and Jing Wang in 1989, in the context of cellular robotic systems.
In computer science and mathematical optimization, a metaheuristic is a higher-level procedure or heuristic designed to find, generate, tune, or select a heuristic that may provide a sufficiently good solution to an optimization problem or a machine learning problem, especially with incomplete or imperfect information or limited computation capacity. Metaheuristics sample a subset of solutions which is otherwise too large to be completely enumerated or otherwise explored. Metaheuristics may make relatively few assumptions about the optimization problem being solved and so may be usable for a variety of problems. Their use is always of interest when exact or other (approximate) methods are not available or are not expedient, either because the calculation time is too long or because, for example, the solution provided is too imprecise.
The Visualization Toolkit (VTK) is a free software system for 3D computer graphics, image processing and scientific visualization.
ITK is a cross-platform, open-source application development framework widely used for the development of image segmentation and image registration programs. Segmentation is the process of identifying and classifying data found in a digitally sampled representation. Typically the sampled representation is an image acquired from such medical instrumentation as CT or MRI scanners. Registration is the task of aligning or developing correspondences between data. For example, in the medical environment, a CT scan may be aligned with an MRI scan in order to combine the information contained in both.
jQuery is a JavaScript library designed to simplify HTML DOM tree traversal and manipulation, as well as event handling, CSS animations, and Ajax. It is free, open-source software using the permissive MIT License. As of August 2022, jQuery is used by 77% of the 10 million most popular websites. Web analysis indicates that it is the most widely deployed JavaScript library by a large margin, having at least three to four times more usage than any other JavaScript library.
ECJ is a freeware evolutionary computation research system written in Java. It is a framework that supports a variety of evolutionary computation techniques, such as genetic algorithms, genetic programming, evolution strategies, coevolution, particle swarm optimization, and differential evolution. The framework models iterative evolutionary processes using a series of pipelines arranged to connect one or more subpopulations of individuals with selection, breeding (such as crossover, and mutation operators that produce new individuals. The framework is open source and is distributed under the Academic Free License. ECJ was created by Sean Luke, a computer science professor at George Mason University, and is maintained by Sean Luke and a variety of contributors.
Cultural algorithms (CA) are a branch of evolutionary computation where there is a knowledge component that is called the belief space in addition to the population component. In this sense, cultural algorithms can be seen as an extension to a conventional genetic algorithm. Cultural algorithms were introduced by Reynolds (see references).
Parallel metaheuristic is a class of techniques that are capable of reducing both the numerical effort and the run time of a metaheuristic. To this end, concepts and technologies from the field of parallelism in computer science are used to enhance and even completely modify the behavior of existing metaheuristics. Just as it exists a long list of metaheuristics like evolutionary algorithms, particle swarm, ant colony optimization, simulated annealing, etc. it also exists a large set of different techniques strongly or loosely based in these ones, whose behavior encompasses the multiple parallel execution of algorithm components that cooperate in some way to solve a problem on a given parallel hardware platform.
A hyper-heuristic is a heuristic search method that seeks to automate, often by the incorporation of machine learning techniques, the process of selecting, combining, generating or adapting several simpler heuristics to efficiently solve computational search problems. One of the motivations for studying hyper-heuristics is to build systems which can handle classes of problems rather than solving just one problem.
In computer science, Java Grammatical Evolution is an implementation of grammatical evolution in the Java programming language. Two examples include the jGE library and GEVA.
MCACEA is a general framework that uses a single evolutionary algorithm (EA) per agent sharing their optimal solutions to coordinate the evolutions of the EAs populations using cooperation objectives. This framework can be used to optimize some characteristics of multiple cooperating agents in mathematical optimization problems. More specifically, due to its nature in which both individual and cooperation objectives are optimize, MCACEA is used in multi-objective optimization problems.
HeuristicLab is a software environment for heuristic and evolutionary algorithms, developed by members of the Heuristic and Evolutionary Algorithm Laboratory (HEAL) at the University of Applied Sciences Upper Austria, in Hagenberg im Mühlkreis. HeuristicLab has a strong focus on providing a graphical user interface so that users are not required to have comprehensive programming skills to adjust and extend the algorithms for a particular problem. In HeuristicLab algorithms are represented as operator graphs and changing or rearranging operators can be done by drag-and-drop without actually writing code. The software thereby tries to shift algorithm development capability from the software engineer to the user and practitioner. Developers can still extend the functionality on code level and can use HeuristicLab's plug-in mechanism that allows them to integrate custom algorithms, solution representations or optimization problems.
The MOEA Framework is an open-source evolutionary computation library for Java that specializes in multi-objective optimization. It supports a variety of multiobjective evolutionary algorithms (MOEAs), including genetic algorithms, genetic programming, grammatical evolution, differential evolution, and particle swarm optimization. As a result, it has been used to conduct numerous comparative studies to assess the efficiency, reliability, and controllability of state-of-the-art MOEAs.
Eclipse Deeplearning4j is a programming library written in Java for the Java virtual machine (JVM). It is a framework with wide support for deep learning algorithms. Deeplearning4j includes implementations of the restricted Boltzmann machine, deep belief net, deep autoencoder, stacked denoising autoencoder and recursive neural tensor network, word2vec, doc2vec, and GloVe. These algorithms all include distributed parallel versions that integrate with Apache Hadoop and Spark.
