SHOGUN is a machine learning toolbox whose focus is on large scale kernel methods and especially on Support Vector Machines (SVM). It provides a generic SVM object interfacing to several different SVM implementations, all making use of the same underlying, efficient kernel implementations. Apart from SVMs and regression, SHOGUN also features a number of linear methods like Linear Discriminant Analysis (LDA), Linear Programming Machine (LPM), (Kernel) Perceptrons, and algorithms to train hidden Markov models. SHOGUN can be used from within C++, Matlab, R, Octave, and Python.
BioJava aims to provide a comprehensive set of Java components for the rapid development of applications in Bioinformatics. It contains interfaces for representing Sequences, Features, and other important bioinformatics concepts. It can also read and write sequence data in a variety of common formats and communicate with Ensembl databases and with DAS and BioCorba servers.
libagf is a library of variable-bandwidth kernel estimators for statistical classification, PDF estimation, and interpolation/non-linear regression using both Gaussian kernels and k-nearest-neighbours. Statistical classification allows the use of a pre-trained model for considerable speed gains. Also included are clustering algorithms. It includes command line executables as well as easy-to-use libraries.
MLPACK is a C++ machine learning library with an emphasis on scalability, speed, and ease-of-use. Its aim is to make machine learning possible for novice users by means of a simple, consistent API, while simultaneously exploiting C++ language features to provide maximum performance and maximum flexibility for expert users. It contains algorithms such as k-means, Gaussian mixture models, hidden Markov models, density estimation trees, kernel PCA, locality-sensitive hashing, sparse coding, linear regression and least-angle regression.
Daikon is an implementation of dynamic detection of likely invariants. An invariant is a property (such as "x=2*y+5" or "this.next.prev = this" or "myarray is sorted by <") that holds at a certain point or points in a program. Invariants are often seen in assert statements, documentation, and formal specifications. Invariants can be useful in program understanding and a host of other applications. Daikon runs a program, observes the values that the program computes, and then reports properties that were true over the observed executions. It can detect properties in Java, C, C++, Perl, and IOA programs, in spreadsheet files, and in other data sources.
Koalog Constraint Solver is a powerful constraint solver written in Java. It provides cutting-edge technology for solving satisfaction and optimization problems, including scheduling, time-tabling, resource-allocation, puzzles (sudoku.koalog.com is powered by Koalog Constraint Solver), and configuration (Koalog Configurator is powered by Koalog Constraint Solver).
ACL2 is a mathematical logic, programming language, and mechanical theorem prover based on the applicative subset of Common Lisp. It is an "industrial-strength" version of the NQTHM or Boyer/Moore theorem prover, and has been used for the formal verification of commercial microprocessors, the Java Virtual Machine, interesting algorithms, and so forth.