Search Results for "mining - software" - Page 3
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Showing 116 open source projects for "mining - software"
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1
MOGEN
The software for modeling the 3D structure of a genome using Hi-C data
The software builds 3D models of chromosomes or genome given chromosomal contacts data such as Hi-C, TCC, 5C. MOGEN was tested on simulated datasets. Using real Hi-C data of a human cell line, MOGEN built models that are consistent with knowledge about the genome of the cell line. Detail on how to use it: https://github.com/BDM-Lab/MOGEN It is published in Bioinformatics: http://bioinformatics.oxfordjournals.org/content/32/9/1286 Bioinformatics, Data Mining, Machine Learning (BDM) Laboratory, Jianlin Cheng, PhD Department of Computer Science University of Missouri, Columbia Email: chengji@missouri.edu -
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Random Bits Forest
RBF: a Strong Classifier/Regressor for Big Data
We present a classification and regression algorithm called Random Bits Forest (RBF). RBF integrates neural network (for depth), boosting (for wideness) and random forest (for accuracy). It first generates and selects ~10,000 small three-layer threshold random neural networks as basis by gradient boosting scheme. These binary basis are then feed into a modified random forest algorithm to obtain predictions. In conclusion, RBF is a novel framework that performs strongly especially on data... -
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LorDG
3D genome reconstruction with Lorentzian objective function
LorDG is a software to build 3D chromosomes and genome model from chromosomal contact data such as Hi-C, TCC, 5C. Detail on how to use it: https://github.com/BDM-Lab/Lordg It is published in Nucleic Acids Research : http://nar.oxfordjournals.org/content/early/2016/11/29/nar.gkw1155.long Bioinformatics, Data Mining, Machine Learning (BDM) Laboratory, Jianlin Cheng, PhD Department of Computer Science University of Missouri, Columbia Email: chengji@missouri.edu -
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Kohonen neural network library is a set of classes and functions for design, train and use Kohonen network (self organizing map) which is one of AI algorithms and useful tool for data mining and discovery knowledge in data (http://knnl.sf.net).
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5
DaMold
a data mining platform for variant annotation and visualization.
DaMold a powerful, integrated, web-based, and user-friendly tool to filter, annotate, cross-link, and visualize NGS, Sanger, and hotspot variants. It is easy-to-use software, which provides flexible input options and accepts variants in VCF and BED formats. For each variant DaMold predicts the variant effect, such as codon change, and amino acid change. Furthermore, it cross-links each variant with more than 30 clinically relevant public databases, which contain already reported SNPs and... -
6
Mass-based dissimilarity
A data dependent dissimilarity measure based on mass estimation.
This software calculates the mass-based dissimilarity matrix for data mining algorithms relying on a distance measure. References: Overcoming Key Weaknesses of Distance-based Neighbourhood Methods using a Data Dependent Dissimilarity Measure. KDD 2016 http://dx.doi.org/10.1145/2939672.2939779 The source code, presentation slide and poster are attached under "Files". -
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CCKDM
Concern Mining
This is a tool for concern mining which uses a KDM model as input and the output is the same model with annotated concerns. It uses a Concern Library and a modified String Clustering K-means algorithm with Levenshtein metric to cluster the strings. -
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RAFTS3
Rapid Alignment Free Tool for Sequences Similarity Search
...RAFTS3 performed searches many times faster than those with BLASTp against large protein databases such as NR and Pfam, with a small loss of sensitivity depending on the similarity degree of the sequences. RAFTS3 is a new alternative for fast comparison of protein sequences, genome annotation and biological data mining. Preprint: http://dx.doi.org/10.1101/055269 Precomputed databases evaluated on paper are available for download at http://www.bioinfo.ufpr.br/software/rafts3 -
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sgmweka
Weka wrapper for the SGM toolkit for text classification and modeling.
Weka wrapper for the SGM toolkit for text classification and modeling. Provides Sparse Generative Models for scalable and accurate text classification and modeling for use in high-speed and large-scale text mining. Has lower time complexity of classification than comparable software due to inference based on sparse model representation and use of an inverted index. The provided .zip file is in the Weka package format, giving access to text classification. Other functions are usable through either Java command-line commands or class inclusion into Java projects. -
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10
Web Application Protection
Tool to detect and correct vulnerabilities in PHP web applications
WAP automatic detects and corrects input validation vulnerabilities in web applications written in PHP Language (version 4.0 or higher) and with a low rate of false positives. WAP detects the following vulnerabilities: - SQL injection using MySQL, PostgreSQL and DB2 DBMS - Reflected cross-site scripting (XSS) - Stored XSS - Remote file inclusion - Local file inclusion - Directory traversal - Source code disclosure - OS command injection - PHP code injection WAP is a static... -
11
Gen3D
A tool for 3D genome and chromosome structural model construction
...It uses chromosomal contact data to construct three-dimensional conformations. This method can generate three-dimensional chromosomal models satisfying a large portion of chromosomal contacts. The software is developed in Prof. Jianlin Cheng's Bioinformatics, Data Mining and Machine Learning Laboratory in the Computer Science Department at the University of Missouri - Columbia, USA. The project is supported by the National Science Foundation (grant no. DBI1149224). If you use Gen3D in your research, please cite: Nowotny, Jackson, Sharif Ahmed, Lingfei Xu, Oluwatosin Oluwadare, Hannah Chen, Noelan Hensley, Tuan Trieu, Renzhi Cao, and Jianlin Cheng. ... -
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Bitcoin Mining Pool is a Software in which you can mine your Bitcoin directly into your Blockchain and Coinbase account.
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coinScripter
a light-weight tool made for easily generating mining scripts.
PLEASE DOWNLOAD THE LATEST VERSION :) coinScripter is a light-weight tool made for easily generating basic scripts (batch files) for mainstream cryptocurrency mining tools. Support Mining Tools: - bfgminer - cgminer - cudaminer - cpuminer (minerd) Supported Operating Systems: - Microsoft Windows Please post feedback/reviews :) They help alot (just please don't be mean). UNFORTUNATELY: THIS PROJECT MAY NO LONGER BE UPDATED. -
14
Mr.FSM
Large-Scale Frequent Subgraph Mining in MapReduce
This is the program used in the following paper: Wenqing Lin, Xiaokui Xiao, and Gabriel Ghinita. Large-Scale Frequent Subgraph Mining in MapReduce. In Proceedings of the 30th IEEE International Conference on Data Engineering (ICDE), pages 844-855, 2014. Please cite the paper if you choose to use the program. If having any problems, please report to {wlin1 at ntu dot edu dot sg}. -
15
libVMR
VMR - machine learning library
libVMR is a class library written in Java which implements code generator for group method of data handling - GMDH. The library is intended for users, with machine learning skills. libVMR provides an effective framework for the research and development of data mining and predictive analytics. libVMR is based on the most popular neural network model with a higher generalization ability from kernel tricks - vector machine by Reshetov (VMR). The library has been designed to learn from... -
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riecoin
riecoin cryptocurrency
...It still has support for Litecoin, Bitcoin and other cryptocurrencies. Currently supported algorithms are RIECOIN style prime sextuplets, SHA-256d and scrypt(1024, 1, 1). It supports the getwork mining protocol as well as the Stratum mining protocol, and can be used for both solo and pooled mining. Notice: Please see here to understand why this package is recognized as a threat by some antivirus software: https://github.com/pooler/cpuminer/issues/13 -
17
MRA
A general recommender system with basic models and MRA
Multi-categorization Recommendation Adjusting (MRA) is to optimize the results of recommendation based on traditional(basic) recommendation models, through introducing objective category information and taking use of the feature that users always get the habits of preferring certain categories. Besides this, there are two advantages of this improved model: 1) it can be easily applied to any kind of existing recommendation models. And 2) a controller is set in this improved model to provide... -
18
giServer
giServer the easy to use and extensible batch and integration server
The giServer is an easy-to-use integration server for process automation and event-driven or scheduled execution of batch jobs. Instead of using complex XML configuration files an elaborate GUI for batch job management is included. Some possible usage scenarios are: - Automatic processing of incoming data files - Big Data applications - Process automation - Data Mining/Aggregation applications - Automatic Reporting - Processing and analysis of database records -
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Genome Microsatellite Analyzing Tool
GMATO : Microsatellite Analyzing Tool for Huge Genome at any size
...GMATo also has easy and graphical user interface scripted in Java and command line interface in Perl, either running in Windows, Linux and Mac etc. platforms with easily customized parameters control for biologists and bio-informatician. Software GMATo is a better tool for SSR characterization in a huge genome cite this paper: Wang X. et al , Bioinformation [2013, 9(10):541-544] -
20
GaltCo.in
GaltCoin - Escape Ordinary Currency
...Galtcoin uses peer-to-peer technology to operate with no central authority: managing transactions and issuing money are carried out collectively by the network. Galtcoin is also the name of the open source software which enables the use of this currency. For mining, we've included a recent-ish build of https://sourceforge.net/projects/cpuminer/ though we recommend building it from source. -
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RedLDA
Redundancy Aware LDA Gibbs Sampler
Redundancy-Aware Topic Modeling Copy Paste Redundancy or Data Duplication are prevalent in many corpora.This redundancy has a negative impact on the quality of text mining and topic modeling in particular. This is a software package of a novel variant of Latent Dirichlet Allocation (LDA) topic modeling, Red-LDA, which takes into account the inherent redundancy of corpora when modeling content. My site: http://www.cs.bgu.ac.il/~cohenrap/ Lab site: http://www.cs.bgu.ac.il/~nlpproj/ Sister project: http://sourceforge.net/projects/corpusredundanc/ -
22
Mining Overlord
Automated Bitcoin mining monitor and up-time enforcer
...This program is cross-platform compatible and has been tested on: Windows XP/Vista/7 Linux (Ubuntu 12.04 and Raspian) Mac OS 12.04 It requires that Python 2.7.3 or above be installed on the host to run. Currently, Mining Overlord only supports installations where one instance of the mining software is running. -
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GISBox by Citiviz
Ready-to-use appliance for GIS, Data Mining and Analysis, Modelling...
GISBox by Citiviz is a ready-to-use virtual appliance containing an assortment of powerful, free and open source GIS, Data Mining and Analysis, Modelling and Programming software and packages. The pre-configured and tested GISBox allows you to try and use in few minutes a variety of software used by data scientists, engineers, physicists, mathematicians, geomatics engineers, and geographers from around the globe, without installing anything more than once the Oracle VirtualBox™ software (https://www.virtualbox.org/) on your Linux, Windows or Mac computer. ... -
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Math tools in Python to tackle down problems in Operational Research fields. Comes with a Django based web interface to allow remote access to complex simulation means.
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Approximate Subgraph Matching Algorithm
Approximate Subgraph Matching Algorithm for Dependency Graphs
The subgraph matching problem (subgraph isomorphism) is NP-complete. Previously, we designed an exact subgraph matching (ESM) algorithm for dependency graphs using a backtracking approach (http://esmalgorithm.sourceforge.net). We further designed an approximate subgraph matching (ASM) algorithm that is capable of detecting approximate subgraph matching based on a subgraph distance. Assume that the graph G and the subgraph Gs have m and n vertices, and km and kn edges respectively,...
