A couple of days ago I changed most of the data files to use XML. I'm using the TinyXML parser to load a save these files. Specifically, the files that are now XML files are 1) the NEAT parameters file, 2) the "controller" files (neural networks), and 3) the "Training Script" file. Here's a quick description of each one:
1.) The NEAT parameters file holds all of the genetic algorithm parameters (population size, probabilities of various mutations, etc.).
2.) A controller file holds info about the neurons and connections that make up a neural network.
3.) The Training Script file is sort of a high level description of a training sequence. The data it contains include: the location of the NEAT parameters file, whether to seed the population with a trained controller, the location of that controller file, whether to save the trained controllers, whether to save statistics, the output directory for all output files, how often to save controller files (in terms of generations), how many generations should elapse before quitting, how many runs/repetitions of the whole training sequence to perform, the number of sensors and effector the trained controller should have, and whether the desired behavior is "oscillatory." This final parameter decides whether the neural nets should initially contain a lot of recurrent connections. Certain oscillatory behaviors (e.g. walking) need a lot of these from the start.
Also, the Training Script contains Training Stages (XML elements) that each describe a different stage in the evolution process (i.e. incremental evolution). Each stage can contain one or more desired behaviors and a fitness goal. For example, to train a controller to walk, the first Training Stage might use a "Oscillate Legs" desired behavior. Once the fitness of a controller reaches the fitness goal for that stage, the training system switches to the next training stage, which could be "Maximize Forward Distance" in the case of walking. Note that each stage can have more than one desired behavior. You could use a "Minimize Energy Expended" desired behavior along with a walking behavior to make the controller learn to walk while minimizing energy used.
One file still type still needs to be switched to XML: the statistics file. This file will contain information about fitness (best and average), neural net complexity (# of neurons and connections), and speciation.
By the way, one of the reasons I chose XML is because a guy named Derek James recently wrote a NeuroEvolution Visualization Toolkit - http://nevt.sourceforge.net This takes XML files (neural nets and statistics files) and converts them to SVG (scalable vector graphics) files. This should come in handy later.