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Open Source Java platform for Optimization, DoE, and Learning.
...It provides a graphical user interface (GUI) and a platform which simplifies integration of new algorithms as "Modules".
Implemented Modules
Evolutionary Algorithms:
- CMA-ES
- (1+1)-ES
- Differential Evolution
Deterministic optimization algorithm:
- SIMPLEX
Learning:
- a simple Artificial Neural Net
Optimization problems:
- test functions
- interface for executing other programs (solvers)
- parallel execution of problems
- distributed execution of problems via socket connection between computers
Others:
- data storage
- data analyser and viewer
This project includes the implementation of a neural network MLP, RBF, SOM and Hopfield networks in several popular programming languages. The project also includes examples of the use of neural networks as function approximation and time series prediction. Includes a special program makes it easy to test neural network based on training data and the optimization of the network.
Bioluminescence is a java library for facilitating de novo genome assembly in the context of reads sampled from a single highly-polymorphic diploid individual. Bioluminescence implements a novel algorithm which uses an artificial neural network to classify contigs in a genome assembly as haplotype-specific or not-haplotype-specific. It then uses this information to partition the original input read set into two subsets, each of which has been enriched for one of the haplotypes. Initial results using this technique have dramatically improved de novo asseblies of such data. ...