Search Results for "markov" - Page 2
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Showing 164 open source projects for "markov"
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DOS R231 sysreq
16 Bit DOS executables
... of labels can be created. Not just only four. LAMBDA.EXE log rote schedule markov four triplets Tested on DOSBox for windows 10, works. Tested on DOSBox Turbo for Android, works well. -
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vbTRACK_2D
Bayesian analysis of 2D(x,y) time series particle tracks using Matlab.
Matlab program analyzes 2D (xy) time-series data (tracks) by variaional Bayes, hidden Markov, Gaussian mixture pattern recognition pattern recognition methods. It finds the number of states, the position of each state, and assigns each time-point to its most probable specific state. -
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gentext genmidi chung is a small text generation / midi piano music gen generator based on SORT dychotomic algorythm (inspired from ai neural networks RNN LSTM and Markov chains but not at all the same) .Trained with an input text file , it can generate random variants text / music stream in response to user input or freely (user enters empty input) or realtime non stop. Written in easy fast compiled freebasic. Generates midi music when load miditext txt files saved with brainpiano3...
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Visual Figaro
System safety, dependability and security analysis
Visual Figaro is an integrated environment to develop component libraries for the dependability modeling tool KB3 used by EDF (http://www.edf.fr/recherche/codes-de-calcul/kb3). KB3 is based on the FIGARO reliability modeling language, suitable for describing CTMC (continuous time Markov chains), DES (discrete event simulation) models, and for automatic generation of fault trees. FIGARO is objet oriented, close to natural language and enables building libraries of reusable components (knowledge... -
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HMMBase.jl
Hidden Markov Models for Julia
HMMBase is not maintained anymore. It will keep being available as a Julia package but we encourage existing and new users to migrate to HiddenMarkovModels.jl which offers a similar interface. For more information see HiddenMarkovModels.jl: when did HMMs get so fast?. HMMBase provides a lightweight and efficient abstraction for hidden Markov models in Julia. Most HMMs libraries only support discrete (e.g. categorical) or Normal distributions. In contrast HMMBase builds upon Distributions.jl... -
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IMMpractical implements various Markov chain model-based methods for analysis of DNA sequences. Please cite: Sparks, M.E., Brendel, V. and Dorman, K.S. (2007) Markov model variants for appraisal of coding potential in plant DNA. LNBI. 4463:394-405.
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Carnatic Music Guru / JRaaga
Carnatic Music Guru - JRaaga
VISIT THIS PAGE AS MORE FEATURES ARE BEING ADDED. If you have downloaded 2.03 or above - Use Help>Check Updates to download latest version. If that does not update: Download CMGUpdater from here: update/CMGUpdater.jar Copy it to the update/ folder of your JRaaga installation path. Try again Help>Check for updates. If it does not work. Delete existing installation. Download the latest version and try. Carnatic Music Guru is a tutor/player/lesson generator. YOU NEED Java Runtime JRE1.6+ TO... -
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JUMBL
J Usage Model Builder Library
JUMBL is a command line app and Java library that supports automation of model-based statistical testing. It supports creation, management, and application of usage models in the form of finite state Markov chains. -
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LIPRAS, Line-Profile Analysis Software
Peak fitting GUI for diffraction data
LIPRAS v466 LIPRAS [LEEP-ruhs], short for Line-Profile Analysis Software, is a graphical user interface for least-squares fitting of Bragg peaks in powder diffraction data. For any region of the inputted data, user can choose which profile functions to apply to the fit, constrain profile functions, and view the resulting fit in terms of the profile functions chosen. If you use LIPRAS for your research, please cite it: Giovanni Esteves, Klarissa Ramos, Chris M. Fancher, and Jacob L. Jones.... -
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Spotlight
Deep recommender models using PyTorch
..., and 20M. It also incorporates utilities for creating synthetic datasets. For example, generate_sequential generates a Markov-chain-derived interaction dataset, where the next item a user chooses is a function of their previous interactions. Recommendations can be seen as a sequence prediction task: given the items a user has interacted with in the past, what will be the next item they will interact with? Spotlight provides a range of models. -
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MetaErg
Metagenome Annotation Pipeline
MetaErg is a stand-alone and fully automated metagenome and metaproteome annotation pipeline published at: https://www.frontiersin.org/articles/10.3389/fgene.2019.00999/full. If you are using this pipeline for your work, please cite: Dong X and Strous M (2019) An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. Front. Genet. 10:999. doi: 10.3389/fgene.2019.00999 The instructions on configuring and running the MetaErg pipeline is available at GitHub repository:... -
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PhyloMCL
PhyloMCL is a method degined to detect orthologous groups accurately.
PhyloMCL is a Markov clustering based method designed to detect ortholog groups effectively and efficiently. It employs two rounds of clustering aiming to recover the complex nature of gene duplications generated by polyploidization and single gene duplication events. PhyloMCL is implemented in C++ to promote computing speed for ortholog inference in genome scale. -
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hiddenDomains
hiddenDomains: a modern HMM to identify ChIP-seq enrichment
hiddenDomains uses a Hidden Markov Model to identify enriched domains in ChIP-seq data. It accepts BAM files for input and can perform an analysis with or without control data. The output is a BED file, ready for the UCSC genome browser, that contains the domains and is color coded according to their posterior probabilities. -
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GPRED-GC
a Gene PREDiction model accounting for 5'-3' GC gradient
A new hidden Markov model (HMM)-based ab initio gene prediction tool for finding genes with highly variable GC contents such as the genes with negative GC gradients in grass genomes. -
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OMEN
OMEN: Ordered Markov ENumerator - Password Guesser
OMEN is a Markov model-based password guesser written in C. It generates password candidates according to their occurrence probabilities, i.e., it outputs most likely passwords first. OMEN significantly improves guessing speed over existing proposals. If you are interested in the details on how OMEN improves on existing Markov model-based password guessing approaches, please refer to OMEN: Faster Password Guessing Using an Ordered Markov Enumerator. OMEN consists of two separate program modules... -
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Accord.NET Framework
Scientific computing, machine learning and computer vision for .NET
The Accord.NET Framework provides machine learning, mathematics, statistics, computer vision, computer audition, and several scientific computing related methods and techniques to .NET. The project is compatible with the .NET Framework. NET Standard, .NET Core, and Mono. -
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The KReator project is a collection of software systems, tools, algorithms and data structures for logic-based knowledge representation. Currently, it includes the software systems KReator and MECore and the library Log4KR: - KReator is an integrated development environment (IDE) for relational probabilistic knowledge representation languages such as Bayesian Logic Programs (BLPs), Markov Logic Networks (MLNs), Relational Maximum Entropy (RME), First-Order Probabilistic Conditional Logic...
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Kinetic Model Builder
GUI for building, simulating and optimizing kinetic models.
A 3D graphical interface for building, simulating and optimizing Markov kinetic models in response to user defined time dependent stimuli. Models can be represented as either states and connecting transitions or interacting allosteric elements (see http://dx.doi.org/10.1085/jgp.201411183). Model parameters can be optimized by fitting model responses to user data. Optional user defined constraint equations for model parameters are parsed with EigenLab (https://github.com/marcel-goldschen-ohm... -
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SnowyOwl
RNA-Seq based gene prediction pipeline for fungal genomes
SnowyOwl is a gene prediction pipeline that uses RNA-Seq data to train and provide hints for the generation of Hidden Markov Model (HMM)-based gene predictions, and to evaluate the resulting models. The pipeline has been validated and streamlined by comparing its predictions to manually curated gene models in three fungal genomes, and its results show substantial increases in sensitivity and selectivity over previous gene predictions. Sensitivity is gained by repeatedly running the HMM gene... -
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vbSPT
variational Bayes single particle tracking
vbSPT is an acronym for variational Bayes single particle tracking, a software package for hidden Markov Model analysis of single particle tracking data, primarily for biophysical applications. Journal reference: Extracting intracellular diffusive states and transition rates from single-molecule tracking data. Fredrik Persson, Martin Lindén, Cecilia Unoson & Johan Elf. Nature Methods (2013). doi:10.1038/nmeth.2367 http://www.nature.com/nmeth/journal/vaop/ncurrent/abs/nmeth.2367.html -
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Hamstr
A tool for directed ortholog search in ESTs and proteins
HaMStR has moved to https://github.com/bionf/hamstr where it is now part of the HaMStR-OneSeq package. HaMStR is a profile hidden Markov model based tool for a directed ortholog search in EST or protein sequence data. The program takes a pre-defined core group of orthologous sequences (core orthologs) and a set of sequences from a search taxon as input. HaMStR then combines in a two-step strategy a pHMM based search and a reverse search via BLAST to extend the core ortholog group with novel... -
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PALM
Probabilistic natural mapping for gene based association study.
PALM is a software that conducts gene-based association analysis. PALM exploits Hidden Markov Models (HMM) to capture the inner genomic structures. Then, unique gene features (termed "palm prints") are extracted for each gene set by calculating the natural gradient. Then palm-prints are tested with chi-square significance test. -
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Frame-Pro
HMM and directed graph consensus combing error-correction tool
Frame-Pro is a tool using Hidden Markov Model and directed acyclic graph to correct the errors in DNA sequencing reads.