CSBB Software Releases
This page describes software releases by the Computational Systems Biology and Bioinformatics group.
Max-margin Conditional Random Field
MMCRF is a structured classification algorithm for output spaces possessing an associative conditional random field structure. It uses kernelized input, and explicit (non-kernelized) output with graph structure. MMCRF uses conditional gradient optimization to and loopy belief propagation for approximate inference, used in gradient computations and prediction.
MMCRF was introduced in:
- J. Rousu, C. Saunders, S. Szedmak, and J. Shawe-Taylor. Efficient algorithms for max-margin structured classification. Predicting Structured Data, pages 105-129, 2007.
The method was applied for drug classification task in papers at PGM-2010 and PRIB-2010:
- Hongyu Su, Markus Heinonen, Juho Rousu. Multilabel Classification of Drug-like Molecules via Max-Margin Conditional Random Fields. Probabilistic Graphical Models, 2010. [Dataset]
- Hongyu Su, Markus Heinonen, Juho Rousu. Structured Output Prediction of Anti-Cancer Drug Activity. Pattern Recognition in Bioinformatics 2010. Lecture notes in bioinformatics, 2010. [Dataset]
ReTrace
ReTrace is a computational tool for finding branching pathways in genome-scale metabolic networks.
ReMatch
ReMatch is a tool for automating the biochemical nomenclature matching problem encountered in construction of metabolic network models.
Positional Isotopomer Distribution Calculator
Positional Isotopomer Distribution Calculator (PIDC) is a software package that computes a positional isotopomer distribution of the selected atom type of the compound when mass spectra of the compound and its fragments are given.
Fragment Identificator
Fragment Identificator (FiD) is an Windows application for identification of molecular fragments from tandem mass spectrometry data when molecule and spectrum are given.
Pathway Assistant
Pathway Assistant offers tools for metabolic modeling.Note: Pathway Assistant is offline for now.
String kernels
Implementations of the gappy string kernel algorithm described in the paper by Rousu and Shawe-Taylor are available here:- A MATLAB code is available from here
- kernlab stringkernel package contains a C++ implementation of the algorithm by Martin Kober
Previous update: 25.10.2010 - Esa Pitkänen