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fbp

Frequency Based Pruning (FBP) is a feature selection algorithm based upon maximizing the Youden J statistic. FBP intelligently enumerates through combinations of features, using the frequency of smaller patterns to prune away large regions of the solution space.

https://github.com/climerlab/fbp

Science Score: 62.0%

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    Organization climerlab has institutional domain (www.cs.umsl.edu)
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    Low similarity (7.8%) to scientific vocabulary

Keywords

cpp discrete-optimization enumeration feature-selection pruning-optimization
Last synced: 6 months ago · JSON representation ·

Repository

Frequency Based Pruning (FBP) is a feature selection algorithm based upon maximizing the Youden J statistic. FBP intelligently enumerates through combinations of features, using the frequency of smaller patterns to prune away large regions of the solution space.

Basic Info
  • Host: GitHub
  • Owner: ClimerLab
  • License: bsd-3-clause
  • Language: C++
  • Default Branch: main
  • Homepage:
  • Size: 38.1 KB
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Topics
cpp discrete-optimization enumeration feature-selection pruning-optimization
Created over 2 years ago · Last pushed almost 2 years ago
Metadata Files
Readme License Citation

README.md

FBP

Frequency Based Pruning (FBP) is a feature selection algorithm based upon maximizing the Youden J statistic. FBP intelligently enumerates through combinations of features, using the frequency of smaller patterns to prune away large regions of the solution space.

Details on FBP 1.0.0 from 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

FBP 1.1.0 updates how the FBP_worker enumerates the patterns.

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 ./fbp

Configuration

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 - Directoty where results are recorded

SOLPOOLFILE - File File with the best and worst objective values from the solution pool of each pattern size.

RUN_TAG - Run tag appended to output file

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

NUMCASES - The number of cases in DATAFILE.

NUMCTRLS - The number of controls in DATAFILE.

NUMEXPRS - The number of features in DATAFILE.

NUMHEADROWS - The number of header rows in DATA_FILE.

NUMHEADCOLS - The number of header columns in DATA_FILE.

PATTERN_SIZE - The number of marker states in the pattern(s) to be found.

MISSINGSYMBOL - String used to indicate missing data in DATAFILE.

MAX_PS - Maximum size patterns to find

USESOLUTIONPOOL - A boolean indicating if all pattens above a threshold should be found (true) or just an optimal solution. If true, the worst objective value for each patter size from SOLPOOLFILE is used as the lower bound.

HIGHVALUE - Value in DATAFILE that indicates high expression.

NORMVALUE - Value in DATAFILE that indicates normal expression.

LOWVALUE - Value in DATAFILE that indicates low expression.

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

Outputs

_runtimes.csv - File containing runtimes for each pattern size

PS#_.log - File containing the selected feature sets of size #.

Notes

Recommend using sync-greedy to generate SOLPOOLFILE.

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/0000-0000-0000-0000"
title: "Frequency Based Pruning"
version: 1.1.0
license: BSD-3-Clause
license-url: "https://github.com/ClimerLab/FBP/blob/main/LICENSE"
repository-code: "https://github.com/ClimerLab/FBP/"
keywords:
  - feature selection
  - youden j
type: software
url: "https://github.com/ClimerLab/FBP/"

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