RUGAN is a form of generative machine learning that can learn to mimic measurements from experiments or computer simulation. In the same way that generative adversarial neural networks can learn to make synthetic images of cats, RUGAN can make synthetic observations that are numerically accurate. For some implementations see https://github.com/CLEANit/RUGAN. For details and an interesting use case, see our publication.
Extensive deep neural networks
EDNN are a form of neural network which can learn from small systems and be used at arbitrary scale. Here are some implimentations. For more info, see our publication.
Leucippus is a plugin for the popular ImageJ project which can extract positional and compositional information from nanoscale microscopy data using computer vision.
HASHKAT (Agent Based Simulation)
HASHKAT is a dynamical network simulation tool designed to model the growth of and information propagation within an online social network. It is an agent-based, kinetic Monte Carlo engine capable of simulating online networks such as Facebook, Twitter, LinkedIn, etc.
HASHKAT incorporates all elements of online social networks including multiple user profiles (e.g. standard users, organizations, celebrities, and bots), user messaging, trending topics, and advertising. Agents within the network make decisions (e.g. follow, unfollow, broadcast, and rebroadcast) based on a variety of user defined factors including geography, political affiliation, musical interests, and humour.
HASHKAT allows for simulation of a realistic online social network, enabling users to test hypotheses for growth mechanisms and scenarios for information propagation. As it solves the forward problem, HASHKAT can be used with Big Data analytics tools to test data collection protocols and ensure inverse model validity.
All of the above are hosted on github.org. They are free for use provided you cite us (see the README file for each repo for a paper reference if there is one, otherwise a weblink here is sufficient). To use them, simply type "git clone git://github.com/itamblyn/XXX.git" into your terminal (assuming you're using Linux or OS X), where XXX is the name of the desired repo. In case you're wondering, from Wikipedia: "Git is a distributed revision control and source code management system with an emphasis on speed".
Codes we use
Here are a list of commercial and FOSS codes which we use in our research.