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sync-greedy

A greedy algorithm to find the combination of features that maximized the Younden J statistic.

https://github.com/climerlab/sync-greedy

Science Score: 52.0%

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    CITATION.cff file
    Found CITATION.cff file
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    Organization climerlab has institutional domain (www.cs.umsl.edu)
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    Low similarity (6.8%) to scientific vocabulary

Keywords

cpp discrete-optimization greedy-algorithms youden-jstatistic
Last synced: 6 months ago · JSON representation ·

Repository

A greedy algorithm to find the combination of features that maximized the Younden J statistic.

Basic Info
  • Host: GitHub
  • Owner: ClimerLab
  • License: bsd-3-clause
  • Language: C++
  • Default Branch: main
  • Homepage:
  • Size: 27.3 KB
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Topics
cpp discrete-optimization greedy-algorithms youden-jstatistic
Created over 2 years ago · Last pushed about 2 years ago
Metadata Files
Readme License Citation

README.md

sync-greedy

Greedy implementation of the Sync feature selection algorithm.

To Use

Configure the Makefile with the locaion of open mpi libraries and binary

Compile with the Makefile by navigating to the root directory and entering: make

Update configuration file

Run the program. For an example enter: mpirun -np 4 ./sync

Configuration File

DATAFILE - Tab seperated file where the first NUMCASES columns are cases and the next NUM_CTRLS columns are controls. The row indicate features.

SCRATCH_DIR - Directory where ouputs are recorded.

NUMCASES - Number of cases in DATAFILE.

NUMCTRLS - Numbr of controls in DATAFILE.

NUMEXPRS - Number of features in DATAFILE.

NUMHEADROWS - Number of header rows in DATA_FILE.

NUMHEADCOLS - Number of header columns in DATA_FILE.

RISK - Boolean that indicates if risk patterns (true) or protective patterns should be found.

MAX_PS - Maximum pattern size to search.

MIN_OBJ - Minimum Younden J value that will be kept for PS=1 patterns.

USESOLPOOL - Boolean that indicates if a solution pool will be kept.

SOLPOOLSIZE - Size of solution pool to keep.

MISSINGSYMBOL - String used to indicate missing data in DATAFILE.

SETNATRUE - Boolean used to indicate if missing data is treated as both high and low.

HIGHVALUE - Value in DATAFILE that indicates high expression.

NORMVALUE - Value in DATAFILE that indicates normal expression.

LOWVALUE - Value in DATAFILE that indicates low expression.

Outputs

PS#.solPool - Files containing a collection of patterns of size #

markerPairs.csv - Contains a count of individuals from G_1 that contain each pair of markers

Notes

Requires Open MPI

DATA_FILE should be tab seperate, the columns represent individuals and the rows represent features

Owner

  • Name: Climer Lab
  • Login: ClimerLab
  • Kind: organization
  • Location: Saint Louis Missouri

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Smith"
  given-names: "Ken"
  orcid: "https://orcid.org/0000-0002-7292-8268"
title: "Sync-greedy"
version: 1.0.0
license: BSD-3-Clause
license-url: "https://github.com/ClimerLab/sync-greedy/blob/main/LICENSE"
repository-code: "https://github.com/ClimerLab/sync-greedy/"
keywords:
  - feature selection
  - youden j
  - greedy algorithm
type: software
url: "https://github.com/ClimerLab/sync-greedy/"

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