Search Results for "syntax tree model"
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Showing 29 open source projects for "syntax tree model"
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DcmStoreService
A lightweight and robust Dicom server to archive medical images
Dicom storage service - DcmStoreService is a lightweight and robust package for implementing the Dicom Storage SCP Service. The application (C++ compiled x86/x64) runs on computer as automatic MS Windows system service (24 hrs). It has a variety of customizable options. -
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rethinking
Statistical Rethinking course and book package
This R package accompanies Richard McElreath’s Statistical Rethinking (2nd edition), offering utilities to fit and compare Bayesian models using both MAP estimation (quap) and Hamiltonian Monte Carlo via RStan (ulam). It supports specifying models via explicit distributional assumptions, providing flexibility for advanced statistical workflows. -
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Mayo 3D Cad Viewer
Free cad viewer for 3d drawings in different formats
A very nice 3d Cad viewer program. This software depends on the Opencascade library. To install opencascade V7.5.0 Beta on linux : sudo dpgk -i opencascade.deb To install mayo : sudo dpkg -i mayo-cad-viewer.deb -
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SCRAM
Probabilistic Risk Assessment Tool
SCRAM is a free and open source probabilistic risk analysis tool. The tool is under development to include fault tree, event tree, common cause, and other standard analyses. -
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popt4jlib
Parallel Optimization Library for Java
popt4jlib is an open-source parallel optimization library for the Java programming language supporting both shared memory and distributed message passing models. Implements a number of meta-heuristic algorithms for Non-Linear Programming, including Genetic Algorithms, Differential Evolution, Evolutionary Algorithms, Simulated Annealing, Particle Swarm Optimization, Firefly Algorithm, Monte-Carlo Search, Local Search algorithms, Gradient-Descent-based algorithms, as well as some well-known... -
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PyMathProg
An easy and flexible mathematical programming environment for Python.
PyMathProg is a Python reincarnation of AMPL and GNU MathProg modeling language, implemented in pure Python, connecting to GLPK via swiglpk. Create, optimize, report, change and re-optimize your model with Python, easily integrate database, plotting, etc. -
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Designed to help you with nonlinear, multidimensional, multi-parameter regression, using the Levenberg-Marquardt algorithm. The regression model can be set up using the input syntax of most modern cas. Full featured visualization and data edit mask. Regression Easy needs help. Especially need to catch exceptions and give reasonable error messages. (In the moment, the standard error handler is invoked. Simply click "resume" on any error.) For newest binary builds, look in the "/bin" directory of the Subversion distribution (code section). ...
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VeriSiMPL
Verification via biSimulations of Max-Plus-Linear models
...The LTS finite abstractions are shown to either simulate or to bisimulate the original MPL system. LTS models are to be verified against given specifications expressed as formulae in Linear Temporal Logic (LTL) and Computation Tree Logic (CTL). The toolbox intends to leverage the NuSMV model checker. Models are to be expressed in the C++ language. The abstraction procedure runs in C++. The generated LTS is exported to the NuSMV language. As such, it can be fed, along with a specification of interest, to the NuSMV model checker. If you are more familiar with JAVA language, we suggest you to try VeriSiMPL version 2.0 which is fully based on JAVA. ... -
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runjags
The 'runjags' R package and standalone JAGS extension module
This package provides high-level interface utilities for MCMC models via Just Another Gibbs Sampler (JAGS), facilitating the use of parallel (or distributed) processors for multiple chains, automated control of convergence and sample length diagnostics, and evaluation of the performance of a model using drop-k validation or against simulated data. Template model specifications can be generated using a standard lme4-style formula interface to assist users less familiar with the BUGS syntax. A JAGS extension module provides additional distributions including the Pareto family of distributions, the DuMouchel prior and the half-Cauchy prior. -
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Geophylobuilder is an extension for ArcGIS that builds a spatiotemporal phylogeographic GIS model from a tree and a set of geographical features.
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OVATION Prime
Seasonal model of the diffuse, monoenergetic, proton, and wave aurora.
...This is a community model. Users are invited to suggest and provide improvements. Documentation includes a model description and instructions for running the software. The README is available here: http://sourceforge.net/p/ovation-prime/code/HEAD/tree/trunk/README.pdf?format=raw A web interface for running the model for historical periods is available here: http://sd-www.jhuapl.edu/Aurora/ovation_prime/prime_display.html Realtime versions are running here: http://www.ngdc.noaa.gov/stp/ovation_prime/ http://www.swpc.noaa.gov/ovation/ -
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StatAlign
An extendable statistical multiple alignment tool.
...This approach eliminates common artifacts that traditional methods suffer from, at the cost of increased computational time. These artifacts include the dependency of the constructed phylogeny on a single (probably suboptimal) alignment and bias towards the guide tree upon which the alignment relies. The models behind the analysis permit the comparison of evolutionarily distant sequences: the TKF92 insertion-deletion model can be coupled to an arbitrary substitution model. A broad range of models for nucleotide and amino acid data is included in the package and the plug-in management system ensures that new models can be easily added. -
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Cost-sensitive Classifiers
Adaboost extensions for cost-sentive classification
Adaboost extensions for cost-sentive classification CSExtension 1 CSExtension 2 CSExtension 3 CSExtension 4 CSExtension 5 AdaCost Boost CostBoost Uboost CostUBoost AdaBoostM1 Implementation of all the listed algorithms of the cluster "cost-sensitive classification". They are the meta algorithms which requires base algorithms e.g. Decision Tree Moreover, Voting criteria is also required e.g. Minimum expected cost criteria Input also requires to load an arff file and a cost matrix (sample arff and cost files are uploaded for users' reference) This extension uses weka for classification and generates the classification model along with confusion matrix. For given dataset and cost matrix -
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A functional-structural model of tree growth based on carbon partitioning among individual organs that compete for resources.
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hrefinder
Detection of homologous recombination events from SNP data
...Based on SNP alleles calls and locations, it breaks the genomes into locally colinear blocks, and looks for cases where SNPs do not agree with the vertical pattern of inheritance in a phylogeny. It applies a dynamic programming algorithm to model whether changes within a block are likely a result of mutations, sequencing errors, or HRE. We use information from the nearby SNPs, so that if 1-2 alleles in a series of SNPs differs from the ancestral allele, it may be better explained as a mutation or sequencing error. But if a series of SNP alleles differ from the ancestral pattern, then it may be more likely that an HRE has occurred, particularly if the allele pattern matches that from another part of the tree better than that of the ancestral node. -
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GenNon-h
Simulating non-homogeneous multiple sequence alignments
...GenNon-H is the first package designed to generate multiple sequence alignments under the discrete-time Markov processes on phylogenetic trees, which samples directly from the transition matrices. Based on the input model and a phylogenetic tree in the Newick format (with branch lengths measured as the expected number of substitutions per site), the algorithm produces DNA alignments of desired length. GenNon-H is a collaborative project described at http://genome.crg.es/cgi-bin/phylo_mod_sel/AlgGenNonH.pl. -
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Rand Tree
Random Tree Generator for MatLab
RandTree is a MatLab based tree simulator program where the algorithm is based on Honda's model. We have used probabilistic generation of branches in order to simulate visually realistic tree structures. This program is designed to generate branching structures with bifurcation branching pattern (sympodial branching). By changing the probabilities and branching angles, you can generate different shapes of trees. -
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The fast2armc program translates source code of a counter automata model for FAST(er) tool to the ARMC prolog syntax.
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General purpose discrete event simulation (DES) framework for the Python programming language. Khronos gathers ideas from other simulation software and tries to provide a simple and poweful toolset for simulation of discrete systems.
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Vtgrep stands for Visual Tree Grep and is a GUI to tgrep. It allows the user to build graphical representations of tree structures and then translates them into the tgrep syntax. provides search functionality, as well as search and result logging.
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The SPASE Data Model Explorer is a web browser application that enables interactive exploration of the SPASE data model. The data model is organized in a tree and dictionary entries rendered for viewing in the browser.
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This research project seeks to use compiler techniques to perform an attribute-based data-flow analysis on (MOF/UML)models allowing for a syntax-driven validation of a model's static semantics as well as an abstract interpretation of i dynamic behavior.
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Free Open Source VoiceXML editor programmed in Java (Swing). The VoiceXML document is regularly parsed, a tree view is built and syntax errors are reported in a specific table.
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Latex editor with document structure tree view and project handling. Latex output allows direct jump to warnings/errors. Projects folders gives support for figures/graphs. Editor component includes usual features like search/replace and syntax highlight.
