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About: Kernel-Based Analysis of Biological Sequences Changes:
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About: A Content Anomaly Detector based on n-Grams Changes:A teeny tiny fix to correctly handle input strings shorter than a registers width
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About: A Tool for Measuring String Similarity Changes:This release fixes the incorrect implementation of the bag distance.
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About: A Tool for Embedding Strings in Vector Spaces Changes:Support for explicit selection of granularity added. Several minor bug fixes. We have reached 1.0
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About: Automatic Analysis of Malware Behavior using Machine Learning Changes:Support for new version of libarchive. Minor bug fixes.
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About: MATLAB toolbox for advanced Brain-Computer Interface (BCI) research. Changes:Initial Announcement on mloss.org.
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About: Sequin is an open source sequence mining library written in C#. Changes:Sequin v1.1.0.0 released
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About: This Java software implements Profile Hidden Markov Models (PHMMs) for protein classification for the WEKA workbench. Standard PHMMs and newly introduced binary PHMMs are used. In addition the software allows propositionalisation of PHMMs. Changes:description changed
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About: Implementation of LSTM for biological sequence analysis (classification, regression, motif discovery, remote homology detection). Additionally a LSTM as logistic regression with spectrum kernel is included. Changes:Spectrum LSTM package included
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About: BACKGROUND:Over the last decade several prediction methods have been developed for determining the structural and functional properties of individual protein residues using sequence and sequence-derived information. Most of these methods are based on support vector machines as they provide accurate and generalizable prediction models. RESULTS:We present a general purpose protein residue annotation toolkit (svmPRAT) to allow biologists to formulate residue-wise prediction problems. svmPRAT formulates the annotation problem as a classification or regression problem using support vector machines. One of the key features of svmPRAT is its ease of use in incorporating any user-provided information in the form of feature matrices. For every residue svmPRAT captures local information around the reside to create fixed length feature vectors. svmPRAT implements accurate and fast kernel functions, and also introduces a flexible window-based encoding scheme that accurately captures signals and pattern for training eective predictive models. CONCLUSIONS:In this work we evaluate svmPRAT on several classification and regression problems including disorder prediction, residue-wise contact order estimation, DNA-binding site prediction, and local structure alphabet prediction. svmPRAT has also been used for the development of state-of-the-art transmembrane helix prediction method called TOPTMH, and secondary structure prediction method called YASSPP. This toolkit developed provides practitioners an efficient and easy-to-use tool for a wide variety of annotation problems. Availability: http://www.cs.gmu.edu/~mlbio/svmprat/ Changes:Initial Announcement on mloss.org.
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About: MALLET is a Java-based package for statistical natural language processing, document classification, clustering, topic modeling, information extraction, and other machine learning applications to [...] Changes:MALLET 2.0 RC4 Release Notes July 16, 2009 Major updates: An implementation of generalized expectation criteria training of MaxEnt classifiers and methods for obtaining constraints (c.f. Gregory Druck, Gideon Mann, Andrew McCallum "Learning from Labeled Features using Generalized Expectation Criteria.") PagedInstanceList has been substantially rewritten by Mike Bond. Bug fixes to topic model hyperparameter optimization and topic inference.
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About: FlexCRFs is a conditional random field toolkit for segmenting and labeling sequence data written in C/C++ using STL library. It was implemented based on the theoretic model presented in (Lafferty et [...] Changes:Initial Announcement on mloss.org.
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About: Local alignment kernels measure the similarity between two sequences by summing up scores obtained from local alignments with gaps of the sequences. Changes:Initial Announcement on mloss.org.
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About: PALMA computes the optimal spliced alignment of a mRNA sequence to a genomic sequence. The main python script takes two FASTA files containing the target (e.g. a DNA sequence, part of the genome) [...] Changes:Initial Announcement on mloss.org.
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About: Lush is an object-oriented Lisp dialect with a super-simple way of integrating C/C++ code and libraries. It includes extensive libraries for numerical computing, machine learning, and computer [...] Changes:Initial Announcement on mloss.org.
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