Bio::T...:SVMLoc(3pm)

✨ Bio::Tools::PSort::SVMLoc 💖

okay so bestie, this is a page from the User Contributed Perl Documentation (yes, that whole "Bio::T...:SVMLoc(3pm)" thing at the top is just the manual name doing its little header strut) and it's literally about Perl bindings for the libsvm Support Vector Machine library in Psortb. Buckle up 🎀

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🌸 NAME 🌸

Bio::Tools::PSort::SVMLoc — Perl bindings for the libsvm Support Vector Machine library in Psortb.

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✨ SYNOPSIS ✨

use Bio::Tools::PSort::SVMLoc;

# Load the model stored in the file 'sample.model' and Frequent Patterns in 'FreqPatt'
$svm = new Bio::Tools::PSort::SVMLoc(Model => 'sample.model', FreqPattern => 'FreqPatt');

# Classify a sequence in $seq, do not include FASTA headers!
$svm->classify($seq);

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💜 DESCRIPTION 💜

Bio::Tools::PSort::SVMLoc implements a Support Vector Machine for Perl. And what do Support Vector Machines do, you ask? They give you a method for creating classification functions from a set of labeled training data, which then lets you make predictions for subsequent data sets. It's giving trained-model-girlboss energy 👑

Now here's the tea: Bio::Tools::PSort::SVMLoc is a stripped down version of Algorithm::SVM designed specifically for PSortb. So if you need functionality like training of SVM, please use that module instead. This one is not the training arc, it's the glow-up-that-already-happened arc 💅

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🦋 CONSTRUCTOR 🦋

# Load an existing SVM.
$svm = new Bio::Tools::PSort::SVMLoc(Model  => 'sample.model', FreqPattern => 'FreqPatt');

A Bio::Tools::PSort::SVMLoc object must be created loaded from an existing model file. No model, no vibe check, no object. Periodt.

An existing SVM is loaded from a file using the Model named parameter and the frequent patterns set. The model file should be of the format produced by the svm->train program (distributed with the libsvm library) or from the $svm->save() method in Algorithm::SVM. So like, your model needs to come from one of those two places or it's not gonna slay 🙈

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🌈 METHODS 🌈

$result = $svm->classify($seq);

The classify method is used to classify a set of data according to the loaded model. The method accepts a single parameter, which should be a protein sequence object. Returns a floating point number corresponding to the predicted value. That's it, that's the whole method, and honestly? Iconic minimalism 🫶

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👑 MAINTAINER 👑

Matthew Laird <matt@brinkman.mbb.sfu.ca>

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⭐ SEE ALSO ⭐

The libsvm homepage: http://www.csie.ntu.edu.tw/~cjlin/libsvm/

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💖 ACKNOWLEDGEMENTS 💖

Thanks go out to Fiona Brinkman and the other members of the Simon Fraser University Brinkman Laboratory for providing me the opportunity to develop this module. Additional thanks go to Chih-Jen Lin, one of the libsvm authors, for being particularly helpful during the development process. Shoutout to the whole squad fr fr 🌸🧚

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and that's a wrap on this little manual, bestie — this page is from perl v5.34.0, dated 2022-02-06, and it lives in the Bio::T...:SVMLoc(3pm) corner of the User Contributed Perl Documentation. go classify something, you got this 💅✨