Search Results for "graph algorithm"
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Showing 39 open source projects for "graph algorithm"
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Bifurcum
Software to run through a directional graph.
This software runs through a directional graph and writes the paths it found as test specifications. It has a simple algorithm (Deep First Search with modifications) and allows sorting children before traversing. This application sums up the authors 4-years experience when programming a commercial tool for graph traversing (which used a much more advanced algorithm) and coaching its users. -
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calculatorpp
Calculator++
Written in C++ (using template). Calculator++ is a application/library for Window (POSIX). The core of code is adaptable for posix. This algorithm support: + built-in operator + built-in functions + run-time functions and variables definition + run-time units system, units with prefix + constants definition + Pretty mathematical expressions - Process ascii files (dev) - vector and matrix (dev) - graph 2D and 3D (dev) - vector graph (dev) - symbolic calculate (dev) - Animations (dev) -
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TorchQuantum
A PyTorch-based framework for Quantum Classical Simulation
A PyTorch-based framework for Quantum Classical Simulation, Quantum Machine Learning, Quantum Neural Networks, Parameterized Quantum Circuits with support for easy deployments on real quantum computers. Researchers on quantum algorithm design, parameterized quantum circuit training, quantum optimal control, quantum machine learning, and quantum neural networks. Dynamic computation graph, automatic gradient computation, fast GPU support, batch model terrorized processing. -
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gml4gtk
small console GML or graphviz DOT graph viewer
directed graph layout program for GML (Graph-Markup-Language) graph or partial graphviz DOT graph -
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BifurcumLib
A library for running through a directional graph.
This is the library for the project Bifurcum. It does all the work. It has a simple algorithm (Deep First Search with modifications) and allows sorting children before traversing. This library sums up the authors 4-years experience when programming a commercial tool for graph traversing (which used a much more advanced algorithm) and coaching its users. -
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Pigale is a graph editor and a C++ algorithm library essentially concerned with planar graphs. This software, particularly intended for graph theoretical research, includes new algorithms based on our recent theoretical researches.
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popt4jlib
Parallel Optimization Library for Java
...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 network flow and other graph algorithms. A fast parallel implementation of the network simplex method, and some full-fledged parallel/distributed MIP solvers will be added in the next version. In general, emphasis is given in improving the efficiency of the algorithms in shared-memory models via java threads, since multi-core machines are so wide-spread today. -
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A spring-based 3D graph layout tool written in Java. Rendering is performed in OpenGL via the JOGL library.
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A star
it is an implementation of A* algorithm with examples of its usage.
A start (A*) is the algorithm for searching the shortest path in the weighted graphs. My implementation is provided with various interesting applications, i.e. 15 puzzle. This project is related to my other projects located at sourceforge as well: https://sourceforge.net/projects/path-finder-qt/ https://sourceforge.net/projects/shortest-path-graph-a-star/ For detail of A* algorithm see wiki page: https://en.wikipedia.org/wiki/A*_search_algorithm -
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Satsuma .NET Graph Library
a delicious .NET graph library
Satsuma is a graph library for .NET, written in C#. Satsuma is an easy-to-use and flexible library, which implements all the necessary graph structures, and the fastest possible graph algorithms. DOCUMENTATION: http://satsumagraph.sourceforge.net/ Satsuma is not a charting library. 'Graph' is used in the mathematical sense here (e.g. nodes connected with arcs). Satsuma is released under the zlib license. This license is very permissive and allows you to use Satsuma for both personal... -
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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
NOTE: Project moved to https://github.com/MolBIFFM/PTGLtools. The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/ -
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TAG
A tool for metatranscriptome assembly using metagenome graph
TAG is a tool for metatranscriptome assembly using de Bruijn graph of matched metagenome as the reference. TAG is an application of a reads mapping algorithm that we developed for mapping of short reads onto a de Bruijn graph of assemblies. A hash table of junction k-mers (k-mers spanning branching structures in the de Bruijn graph) is used to facilitate fast mapping of reads to the graph. -
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RT-alignment
Graph-based time alignment algorithms for multiple LC-MS datasets
...The main challenge in this task lies in correcting retention time shifts, which are inevitable even on the same instrument and under the same elution conditions. For large-scale studies, multiple instruments or multi-week experiments are often required, which exacerbates the problem. We present a new graph-based time alignment algorithm that can align these less similar LC-MS maps, which cannot be effectively handled by existing methods. -
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SplitMEM
Graphical pan-genome analysis with suffix skips
With the rise of improved sequencing technologies, genomics is expanding from a single reference per species paradigm into a more comprehensive pan-genome approach with multiple individuals represented and analyzed together. Here we introduce a novel O(n log n) time and space algorithm called splitMEM, that directly constructs the compressed de Bruijn graph for a pan-genome of total length n. To achieve this time complexity, we augment the suffix tree with suffix skips, a new construct that allows us to traverse several suffix links in constant time, and use them to efficiently decompose maximal exact matches (MEMs) during a suffix tree traversal. -
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Cell decomposition is one of the first applicable solution for path planning - robot path planning. The algorithm aims to find free areas (cells not occupied by obstacles) in the configuration space, and build a graph of adjacency for these cells.
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The MaxParser is written in c++ and can parse with first, second, third and fourth order projective Graph-based Dependency parsing algorithm. The project is the new version of the project "Max-MSTParser". If you want to use this software for research, please reference this web address in your papers
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MolSig
The Stereo Signature Molecular Descriptor
An algorithm to compute molecular graph descriptors considering the stereochemistry of the molecular structure, based on our previously introduced signature molecular descriptor. The algorithm can generate two types of descriptors, one which is compliant with the Cahn-Ingold-Prelog priority rules, and a faster one based on our previous definition of a directed acyclic graph that isaugmented to a chiral molecular graph. -
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TSPLib.Net
TSPLib wrapper for .Net
TSPLib is a set of Traveler Salesman and related graph problems gathered by the Heidelberg university. This project provides .Net library wrapping up library files loading code, implements distance functions and all the TSPLib features. If you'd like to test your graph tour searching algorithm on a TSP lib will save you hours of reading in a data and adjusting your code to ensure that result are comparable. -
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LTS: Learning to Search
Discriminative subgraph mining by learning from search history
LTS (Learning to Search) is an implementation of an algorithm described in "LTS: Discriminative Subgraph Mining by Learning from Search History" in Data Engineering (ICDE), IEEE 27th International Conference, pages 207-218, 2011. The purpose of LTS is to find discriminative subgraphs, which are smaller graphs that are embedded in larger graphs that all share a certain trait. A discriminative subgraph can help to characterize a complex graph and can be used to classify new graphs with unknown traits. ... -
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Mix
Mix is a tool to combine multiple assemblies from NGS data.
Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a path in the extension graph that maximizes the cumulative contig length. Please note that Mix has moved to: https://github.com/massyah/MIX -
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PID Simulator
Version 2 is out!
Try version 2! Total separation of physical simulation, PID algorithm and GUI. The setup is intended to realistically mimic a physical body with a specific heat capacity, a measurement delay, and an input delay + low pass filter (heater delay) for more realism. This is a simple PID simulator I wrote in .NET, created to get a feel of how to tune a PID by adjusting the various properties. -
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Track Animation
A simple application which simulates Disk Scheduling Algorithms.
Track Animation is an easy to use Windows application that simulates the following Disk Scheduling Algorithms : FCFS (First Come First Serve), SJF (Shortest Job First) aka SSTF (Shortest Seek Time First), SCAN (Elevator Algorithm), LOOK, C-SCAN (Circular SCAN) and C-LOOK. This application enables the user to play and pause the simulation after providing the necessary simulation requirements. -
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Grafoanalizator
Graphanalyzer is an environment for visualization of graphsand process
Graphanalyzer is an environment for visualization of graphsand processes with different algorithms. Program supports about 20 algorithms. Program shows visual result of algorithm. You can solve lot of engineering tasks with Graphanalyzer. Learn more about program Graphanalyzer. Features: 1. About 20 algorithms. 2. Visualization of all the processes of graph processing. 3. Supporting helper function for graph creating as map. 4. Feedback. -
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BIL++ is a set of standalone C++ packages for data processing in Bioinformatics (Graph mining, Bayesian networks, Genetic algorithm, Discretization, Gene expression data analysis, Hypothesis testing).
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The E* algorithm is a path planner for (mobile) robotics. Unlike A*, which constrains movements to graph edges, it produces smooth trajectories by interpolating between edges. Like D*, it supports dynamic replanning after local path cost changes.
