Projects supporting the fasta data format.


Logo JMLR Sally 0.9.0

by konrad - July 1, 2014, 22:43:51 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 18094 views, 3666 downloads, 2 subscriptions

About: A Tool for Embedding Strings in Vector Spaces

Changes:

Support for hash-based dimension reduction: simhash, minhash and Bloom filter. Support for several n-gram variants: regular, sorted, positional and blended n-grams. Simplified configuration.


Logo Weight HMM 1.0

by SongTao - May 27, 2014, 15:29:20 CET [ BibTeX Download ] 279 views, 66 downloads, 1 subscription

About: Discovering short linear protein motif based on selective training of profile hidden Markov models

Changes:

Initial Announcement on mloss.org.


Logo Mr. 1.0

by SongTao - May 27, 2014, 15:20:40 CET [ BibTeX Download ] 196 views, 64 downloads, 1 subscription

About: Discovering short linear protein motif based on selective training of profile hidden Markov models

Changes:

Initial Announcement on mloss.org.


Logo JMLR SHOGUN 3.2.0

by sonne - February 17, 2014, 20:31:36 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 81212 views, 11198 downloads, 5 subscriptions

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About: The SHOGUN machine learning toolbox's focus is on large scale learning methods with focus on Support Vector Machines (SVM), providing interfaces to python, octave, matlab, r and the command line.

Changes:

This is mostly a bugfix release:

Features

  • Fully support python3 now
  • Add mini-batch k-means [Parijat Mazumdar]
  • Add k-means++ [Parijat Mazumdar]
  • Add sub-sequence string kernel [lambday]

Bugfixes

  • Compile fixes for upcoming swig3.0
  • Speedup for gaussian process' apply()
  • Improve unit / integration test checks
  • libbmrm uninitialized memory reads
  • libocas uninitialized memory reads
  • Octave 3.8 compile fixes [Orion Poplawski]
  • Fix java modular compile error [Bjoern Esser]

Logo JMLR Jstacs 2.1

by keili - June 3, 2013, 07:32:55 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 13213 views, 3098 downloads, 2 subscriptions

About: A Java framework for statistical analysis and classification of biological sequences

Changes:

New classes:

  • MultipleIterationsCondition: Requires another TerminationCondition to fail a contiguous, specified number of times
  • ClassifierFactory: Allows for creating standard classifiers
  • SeqLogoPlotter: Plot PNG sequence logos from within Jstacs
  • MultivariateGaussianEmission: Multivariate Gaussian emission density for a Hidden Markov Model
  • MEManager: Maximum entropy model

New features and improvements:

  • Alignment: Added free shift alignment
  • PerformanceMeasure and sub-classes: Extension to weighted test data
  • AbstractClassifier, ClassifierAssessment and sub-classes: Adaption to weighted PerformanceMeasures
  • DNAAlphabet: Parser speed-up
  • PFMComparator: Extension to PFM from other sources/databases
  • ToolBox: New convenience methods for computing several statistics (e.g., median, correlation)
  • SignificantMotifOccurrencesFinder: New methods for computing PWMs and statistics from predictions
  • SequenceScore and sub-classes: New method toString(NumberFormat)
  • DataSet: Adaption to weighted data, e.g., partitioning
  • REnvironment: Changed several methods from String to CharSequence

Restructuring:

  • changed MultiDimensionalSequenceWrapperDiffSM to MultiDimensionalSequenceWrapperDiffSS

Several minor new features, bug fixes, and code cleanups


Logo LSTM for biological sequence analysis 1.0

by mhex - July 28, 2010, 16:32:29 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 5117 views, 1192 downloads, 1 subscription

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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


Logo asp 0.3

by sonne - May 7, 2010, 10:25:39 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 7141 views, 1412 downloads, 1 subscription

About: Accurate splice site predictor for a variety of genomes.

Changes:

Asp now supports three formats:

-g fname for gff format

-s fname for spf format

-b dir for a binary format compatible with mGene.

And a new switch

-t which switches on a sigmoid-based transformation of the svm scores to get scores between 0 and 1.


Logo arts 0.2

by sonne - May 25, 2009, 09:56:31 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 4211 views, 877 downloads, 1 subscription

About: ARTS is an accurate predictor for Transcription Start Sites (TSS).

Changes:

Initial Announcement on mloss.org.