Projects that are tagged with bioinformatics.
Showing Items 1-20 of 26 on page 1 of 2: 1 2 Next

Logo KeBABS 1.2.1

by UBod - April 23, 2015, 13:55:32 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 3210 views, 543 downloads, 3 subscriptions

About: Kernel-Based Analysis of Biological Sequences

Changes:
  • correction of error in model selection for processing via dense LIBSVM
  • remove problem in check for loading of SparseM

Logo JMLR SHOGUN 4.0.0

by sonne - February 5, 2015, 09:09:37 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 92456 views, 12905 downloads, 6 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 release features the work of our 8 GSoC 2014 students [student; mentors]:

  • OpenCV Integration and Computer Vision Applications [Abhijeet Kislay; Kevin Hughes]
  • Large-Scale Multi-Label Classification [Abinash Panda; Thoralf Klein]
  • Large-scale structured prediction with approximate inference [Jiaolong Xu; Shell Hu]
  • Essential Deep Learning Modules [Khaled Nasr; Sergey Lisitsyn, Theofanis Karaletsos]
  • Fundamental Machine Learning: decision trees, kernel density estimation [Parijat Mazumdar ; Fernando Iglesias]
  • Shogun Missionary & Shogun in Education [Saurabh Mahindre; Heiko Strathmann]
  • Testing and Measuring Variable Interactions With Kernels [Soumyajit De; Dino Sejdinovic, Heiko Strathmann]
  • Variational Learning for Gaussian Processes [Wu Lin; Heiko Strathmann, Emtiyaz Khan]

It also contains several cleanups and bugfixes:

Features

  • New Shogun project description [Heiko Strathmann]
  • ID3 algorithm for decision tree learning [Parijat Mazumdar]
  • New modes for PCA matrix factorizations: SVD & EVD, in-place or reallocating [Parijat Mazumdar]
  • Add Neural Networks with linear, logistic and softmax neurons [Khaled Nasr]
  • Add kernel multiclass strategy examples in multiclass notebook [Saurabh Mahindre]
  • Add decision trees notebook containing examples for ID3 algorithm [Parijat Mazumdar]
  • Add sudoku recognizer ipython notebook [Alejandro Hernandez]
  • Add in-place subsets on features, labels, and custom kernels [Heiko Strathmann]
  • Add Principal Component Analysis notebook [Abhijeet Kislay]
  • Add Multiple Kernel Learning notebook [Saurabh Mahindre]
  • Add Multi-Label classes to enable Multi-Label classification [Thoralf Klein]
  • Add rectified linear neurons, dropout and max-norm regularization to neural networks [Khaled Nasr]
  • Add C4.5 algorithm for multiclass classification using decision trees [Parijat Mazumdar]
  • Add support for arbitrary acyclic graph-structured neural networks [Khaled Nasr]
  • Add CART algorithm for classification and regression using decision trees [Parijat Mazumdar]
  • Add CHAID algorithm for multiclass classification and regression using decision trees [Parijat Mazumdar]
  • Add Convolutional Neural Networks [Khaled Nasr]
  • Add Random Forests algorithm for ensemble learning using CART [Parijat Mazumdar]
  • Add Restricted Botlzmann Machines [Khaled Nasr]
  • Add Stochastic Gradient Boosting algorithm for ensemble learning [Parijat Mazumdar]
  • Add Deep contractive and denoising autoencoders [Khaled Nasr]
  • Add Deep belief networks [Khaled Nasr]

Bugfixes

  • Fix reference counting bugs in CList when reference counting is on [Heiko Strathmann, Thoralf Klein, lambday]
  • Fix memory problem in PCA::apply_to_feature_matrix [Parijat Mazumdar]
  • Fix crash in LeastAngleRegression for the case D greater than N [Parijat Mazumdar]
  • Fix memory violations in bundle method solvers [Thoralf Klein]
  • Fix fail in library_mldatahdf5.cpp example when http://mldata.org is not working properly [Parijat Mazumdar]
  • Fix memory leaks in Vowpal Wabbit, LibSVMFile and KernelPCA [Thoralf Klein]
  • Fix memory and control flow issues discovered by Coverity [Thoralf Klein]
  • Fix R modular interface SWIG typemap (Requires SWIG >= 2.0.5) [Matt Huska]

Cleanup and API Changes

  • PCA now depends on Eigen3 instead of LAPACK [Parijat Mazumdar]
  • Removing redundant and fixing implicit imports [Thoralf Klein]
  • Hide many methods from SWIG, reducing compile memory by 500MiB [Heiko Strathmann, Fernando Iglesias, Thoralf Klein]

About: Learns dynamic network changes across conditions and visualize the results in Cytoscape.

Changes:

Initial Announcement on mloss.org.


Logo BACOM2 1.0

by fydennis - October 24, 2014, 15:25:38 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 820 views, 168 downloads, 2 subscriptions

About: revised version of BACOM

Changes:

Initial Announcement on mloss.org.


Logo Weight HMM 1.0

by SongTao - May 27, 2014, 15:29:20 CET [ BibTeX Download ] 698 views, 258 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 ] 590 views, 242 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 jackstraw 1.0

by nc - February 1, 2014, 22:53:41 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 1549 views, 329 downloads, 1 subscription

About: Estimates statistical significance of association between variables and their principal components (PCs).

Changes:

Initial Announcement on mloss.org.


Logo hapFabia 1.4.2

by hochreit - December 28, 2013, 17:24:29 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 3332 views, 653 downloads, 1 subscription

About: hapFabia is an R package for identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data. It detects 100 times smaller segments than previous methods.

Changes:

o citation update

o plot function improved


Logo FABIA 2.8.0

by hochreit - October 18, 2013, 10:14:57 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 10492 views, 2199 downloads, 1 subscription

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About: FABIA is a biclustering algorithm that clusters rows and columns of a matrix simultaneously. Consequently, members of a row cluster are similar to each other on a subset of columns and, analogously, members of a column cluster are similar to each other on a subset of rows. Biclusters are found by factor analysis where both the factors and the loading matrix are sparse. FABIA is a multiplicative model that extracts linear dependencies between samples and feature patterns. Applications include detection of transcriptional modules in gene expression data and identification of haplotypes/>identity by descent< consisting of rare variants obtained by next generation sequencing.

Changes:

CHANGES IN VERSION 2.8.0

NEW FEATURES

o rescaling of lapla
o extractPlot does not plot sorted matrices

CHANGES IN VERSION 2.4.0

o spfabia bugfixes

CHANGES IN VERSION 2.3.1

NEW FEATURES

o Getters and setters for class Factorization

2.0.0:

  • spfabia: fabia for a sparse data matrix (in sparse matrix format) and sparse vector/matrix computations in the code to speed up computations. spfabia applications: (a) detecting >identity by descent< in next generation sequencing data with rare variants, (b) detecting >shared haplotypes< in disease studies based on next generation sequencing data with rare variants;
  • fabia for non-negative factorization (parameter: non_negative);
  • changed to C and removed dependencies to Rcpp;
  • improved update for lambda (alpha should be smaller, e.g. 0.03);
  • introduced maximal number of row elements (lL);
  • introduced cycle bL when upper bounds nL or lL are effective;
  • reduced computational complexity;
  • bug fixes: (a) update formula for lambda: tighter approximation, (b) corrected inverse of the conditional covariance matrix of z;

1.4.0:

  • New option nL: maximal number of biclusters per row element;
  • Sort biclusters according to information content;
  • Improved and extended preprocessing;
  • Update to R2.13

Logo JMLR Jstacs 2.1

by keili - June 3, 2013, 07:32:55 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 16051 views, 3865 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 BCILAB 1.0-beta

by chkothe - January 6, 2012, 23:47:55 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 3941 views, 786 downloads, 1 subscription

About: MATLAB toolbox for advanced Brain-Computer Interface (BCI) research.

Changes:

Initial Announcement on mloss.org.


Logo NetPro 1.1.17

by lml - January 25, 2011, 19:02:53 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 3771 views, 892 downloads, 1 subscription

About: Tools for functional network analysis.

Changes:

Initial Announcement on mloss.org.


Logo Epistatic MAP Imputation 1.1

by colm - November 25, 2010, 21:01:10 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 3120 views, 730 downloads, 1 subscription

About: Epistatic miniarray profiles (E-MAPs) are a high-throughput approach capable of quantifying aggravating or alleviating genetic interactions between gene pairs. The datasets resulting from E-MAP experiments typically take the form of a symmetric pairwise matrix of interaction scores. These datasets have a significant number of missing values - up to 35% - that can reduce the effectiveness of some data analysis techniques and prevent the use of others. This project contains nearest neighbor based tools for the imputation and prediction of these missing values. The code is implemented in Python and uses a nearest neighbor based approach. Two variants are used - a simple weighted nearest neighbors, and a local least squares based regression.

Changes:

Initial Announcement on mloss.org.


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 ] 6168 views, 1471 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 ] 8155 views, 1632 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 Dependency modeling toolbox 0.2

by lml - April 30, 2010, 14:38:45 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 7800 views, 1209 downloads, 1 subscription

About: Investigation of dependencies between multiple data sources allows the discovery of regularities and interactions that are not seen in individual data sets. The demand for such methods is increasing with the availability and size of co-occurring observations in computational biology, open data initiatives, and in other domains. We provide practical, open access implementations of general-purpose algorithms that help to realize the full potential of these information sources.

Changes:

Three independent modules (drCCA, pint, MultiWayCCA) have been added.


Logo svmPRAT 1.0

by rangwala - December 28, 2009, 00:27:03 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 4085 views, 1022 downloads, 1 subscription

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.


Logo seqan 1.2

by sonne - November 2, 2009, 14:54:08 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 6714 views, 1286 downloads, 1 subscription

About: SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data.

Changes:
  • 5 more applications, i.e. DFI, MicroRazerS, PairAlign, SeqCons, TreeRecon
  • stable release of RazerS supporting paired-end read mapping and configurable sensitivity
  • new alignment algorithms, e.g. banded, configurable alignments (overlap, semi-global, ...)
  • realignment algorithm
  • NGS data structures and formats, e.g. SAM, Amos, ...
  • new alphabets, e.g. Dna with base call qualities, profile characters
  • auxiliary data structures and algorithms, e.g. double ended queue, command line parser
  • positional scores
  • CMake support

Logo Easysvm 0.3

by gxr - June 25, 2009, 18:33:04 CET [ Project Homepage BibTeX Download ] 8575 views, 1660 downloads, 1 subscription

About: The Easysvm package provides a set of tools based on the Shogun toolbox allowing to train and test SVMs in a simple way.

Changes:

Fixes for shogun 0.7.3.


Logo arts 0.2

by sonne - May 25, 2009, 09:56:31 CET [ Project Homepage BibTeX BibTeX for corresponding Paper Download ] 4851 views, 1021 downloads, 1 subscription

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

Changes:

Initial Announcement on mloss.org.


Showing Items 1-20 of 26 on page 1 of 2: 1 2 Next