Search Results for "combinatorial"
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Showing 35 open source projects for "combinatorial"
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InferOpt.jl
Combinatorial optimization layers for machine learning pipelines
InferOpt.jl is a toolbox for using combinatorial optimization algorithms within machine learning pipelines. It allows you to create differentiable layers from optimization oracles that do not have meaningful derivatives. Typical examples include mixed integer linear programs or graph algorithms. -
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OR-Tools - Google Optimization Tools
Google's software suite for combinatorial optimization
Google Optimization Tools, also known as OR-Tools is an open-source, fast and portable software suite for solving combinatorial optimization problems. These encompass problems in vehicle routing, flows, integer and linear programming, and constraint programming. This suite contains a number of solvers, namely: a constraint programming solver; a linear programming solver; wrappers for commercial solvers (like Gurobi or CPLEX) and other open source solvers (SCIP, GLPK, etc.); among others. ... -
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CGAL
The Computational Geometry Algorithms Library
CGAL or the Computational Geometry Algorithms Library is a C++ library that gives you easy access to a myriad of efficient and reliable geometric algorithms. These algorithms are useful in a wide range of applications, including computer aided design, robotics, molecular biology, medical imaging, geographic information systems and more. CGAL features a great range of data structures and algorithms, including Voronoi diagrams, cell complexes and polyhedra, triangulations, arrangements of... -
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AlphaZero.jl
A generic, simple and fast implementation of Deepmind's AlphaZero
Beyond its much publicized success in attaining superhuman level at games such as Chess and Go, DeepMind's AlphaZero algorithm illustrates a more general methodology of combining learning and search to explore large combinatorial spaces effectively. We believe that this methodology can have exciting applications in many different research areas. Because AlphaZero is resource-hungry, successful open-source implementations (such as Leela Zero) are written in low-level languages (such as C++) and optimized for highly distributed computing environments. This makes them hardly accessible for students, researchers and hackers. ... -
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ECLiPSe CLP
ECLiPSe Constraint Logic Programming System
The ECLiPSe Constraint Logic Programming System is designed for solving combinatorial optimization problems, for the development of new constraint solver technology and their hybrids, and for the teaching of modelling, solving and search techniques. -
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nars2000
NARS2000: An Experimental APL Interpreter
APL is an arrary-oriented language initially conceived in the 1960s by Kenneth E. Iverson, IBM Fellow and 1979 ACM Turing Award recipient. It is ideally suited to computer programming because it subsumes the tedious aspects of the job allowing the programmer to concentrate on the heart of the project. NARS2000 is a Free Open Source implementation of APL. For more details on this project, visit the NARS2000.org website. -
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Combinatorial Game Suite
A computer algebra system for research in combinatorial game theory.
STARTING WITH VERSION 2.0, CGSUITE HAS MOVED TO GITHUB. The latest version can be found at the CGSuite homepage: https://www.cgsuite.org/ This page is preserved for archival purposes only and is no longer being maintained. -
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Jack LIRE (Linked Record)
Quantum universal object system with referencing and genetics
Jack LIRE (Linked Record) is a quantum database-backed life-long text record diary with referencing (linking) between records, and a data library for life-long keeping of files such as documents, photographs, music and more. The diary records are fully searchable. Files can be mentioned in diary records to preserve memories, document knowledge and ideas, and more. Massive numbers of diary records and files can be permanently kept. A database located on one computer can be accessed from... -
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CompleXChange
differential analysis of combinatorial protein complexes
The increasing wealth of transcriptomic data and current computational tools enable to infer how protein interactomes and complexomes may be assembled in specific samples. With CompleXChange this information can be exploited to conduct differential analyses of the dynamic protein complexome in a quantitative manner. The corresponding publication can be found on https://doi.org/10.1186/s12859-019-2852-z. -
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DACO-algorithm
A novel transcription factor complex prediction algorithm.
...The metric is locally maximized on the holistic level of protein interactions while sophisticated connectivity constraints on the domain level are utilized to account for the exclusive and thus inherently combinatorial nature of the interactions within such assemblies. The original publication can be found on http://bioinformatics.oxfordjournals.org/content/30/17/i415 . -
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...Furthermore, we observed that the identified regulatory modules and chromatin states may jointly determine the motif preference for specific class of proteins. Thus, our results reveal a relation between chromatin states and combinatorial binding of proteins in the complex transcriptional regulatory process.
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Plant Metabolite Annotation Toolbox (PlantMAT) is a computational tool combining library search and combinatorial enumeration to facilitate the structural identification of plant specialized metabolites, e.g., saponins and flavonoid glycosides.
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The complexity of cellular networks is an outstanding challenge for documentation, visualisation and mathematical modelling. In this project, we develop a new way to describe these networks that minimises the combinatorial complexity and allows an automatic visualisation and export of mathematical (ODE/rulebased) models.
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Grammar based Combinatorial Solver
Solver with Applications in Computer Network Systems Design
The solver performs an exhaustive search on the space defined using simple formal language grammar constructs to identify solutions that meet the objective and constraints. It can be used to easily define complex discrete multi-dimensional combinatorial problems that are otherwise difficult to model using Mixed Integer Linear Programming solvers. The solver does not make any assumptions on continuity of the search space. The solver is implemented in PHP. A GoJS based visualization is provided for model's grammar. Two system design model samples are provided. One uses the solver to identify low power network design for Passive Optical Networks given a set of choices for provider and customer premises equipment and a set of optical domain constraints. ... -
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CCH
A genetics tool that identifies genomic regions of shared ancestry
Combinatorial Conflicting Homozygosity (CCH) uses dense Single Nucleotide Polymorphism (SNP) genotypes to identify regions of the genome inherited from a common ancestor among any or all subsets of a group. Analysis is rapid and can identify loci containing genes for dominant traits. CCH is robust to the presence of phenocopies and can detect undisclosed shared common ancestry. -
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caplib
Correct, translate and analyze combinatorial library sequencing data
Originally developped to handle PacBio CCS data for an AAV capsid library. This program will extract, correct, translate and analyze the sequencng data, starting from the CCS fastq file. -
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JConstraints
Java Framework to implement solutions to solve constraints problems
JConstraints is a Java Framework that enables implementations of advanced solutions for combinatorial problems as constraints satisfaction problems. The architecture was built thinking in the constraints satisfaction paradigm. The Framework is easy to use. Therefore, with few interfaces implementations you can already run advanced combinatory solutions. Just to name a few algorithms, the Framework can solve any constraints problems using: - Regular Backtracking; - A variety of Backjumping algorithms; - A variety of arc-consistency algorithms; - Local search algorithm; - Tabu search algorithm; - Maximize solutions: comming soon; - Minimize solutions: comming soon; The Framework also enables heuristic injections so that the developers can achieve greater performance of algorithms using their own heuristics. ... -
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RaTrav
mean first passage times and node occupancies calculations
...The tool approves arbitrary networks (graphs) where a dynamics of the Markovian type takes place. Two methods are made available for which their efficiency is strongly dependent on the topology of the defined network: the combinatorial Hill technique and the Monte Carlo simulation method. References: M. Torchala, P. Chelminiak, M. Kurzynski and P. A. Bates, 'RaTrav: a tool for calculating mean first-passage times on biochemical networks', BMC Syst. Biol. 7, 130 (2013). M. Torchala, P. Chelminiak and P. A. Bates, 'Mean first-passage time calculations: comparison of the deterministic Hill's algorithm with Monte Carlo simulations', Eur. ... -
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Java Combinatorial Optimization Platform is used to solve combinatorial problems using common interface, providing means to easily add new algorithms and problems and to benchmark them.
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FJSP Software
A Software for Flexible Job Shop Scheduling
Flexible job shop scheduling problem (FJSP) is very important in many fields such as production management, resource allocation and combinatorial optimization. In the real manufacturing systems, each operation could be processed on more than one machine and each machine can also process several operations. This feature is known as flexibility. You can define your problem in this software and get an optimal solution as a Gantt Chart. This software is based on my M.Sc. thesis of Shahed university (Tehran, Iran). -
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Asteroid
A CBLS Engine in SCALA, NOW part of OscaR
Asteroid has been merged with Scampi, to give rise to OScar. Follow us on https://bitbucket.org/oscarlib/oscar/wiki/Home Asteroid offers a powerful framework for developing constraint-based local search solution to combinatorial problems. This technique provides good scalability to real-world problems. It includes a library of standard constraints and invariants to declaratively define the problem you want to solve, and it also provides powerful search mechanisms. -
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MARC Library ( SobekCM )
Another C# MARC Record implementation
This is a C# library which contains classes for working in memory with MARC records ( http://www.loc.gov/marc/ ). This allows records to be read from MarcXML and Marc21 formats. Once in memory any field or subfield can be edited, added, or deleted. Then the record can be queried or saved again in either a MarcXML or Marc21 file format. In addition, version 1.1 includes Z39.50 capability and auto-translation from the most common MARC8 characters into Unicode. -
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ORganic Virtual Library (ORVIL) Program
ORganic VIrtual Library (ORVIL)
ORganic VIrtual Library (ORVIL) –A COMBINATORIAL LIBRARY CONSTRUCTION BASED ON ORGANIC CONSTITUENTS AND WITHOUT SCAFFOLD HOPPING Abstract Rapid construction of virtual combinatorial library is a prerequisite for in silico library enumeration and design. ORganic VIrtual Library (ORVIL) is a perl program to generate a combinatorial library using most frequently observed 200 organic substituents. -
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Intelligent Water Drops Algorithm
Solving optimization problems by the Intelligent Water Drops algorithm
This project deals with the Intelligent Water Drops algorithm or the IWD algorithm. The IWD algorithm is a population & nature-inspired combinatorial optimization algorithm. It tries to imitate the behavior that natural water drops conduct in river beds where they create complex paths that seem optimistic considering the environment, obstacles, and the surrounding terrain. One way to use the IWD algorithm is to map our optimization problem into a graph over which Intelligent Water Drops (IWDs) travel from node to node to gradually create complete solutions. ...