Giter VIP home page Giter VIP logo

dna_sequence_covid_classification's Introduction

DNA_Sequence_Covid_Classification

This work is a sequence classification, we predict whether a DNA sequence belongs to the SARS-CoV-2 (Covid-19).

  1. **Data description**
    • Xtr.csv - the training sequences.
    • Xte.csv - the test sequences.
    • Ytr.csv - the sequence labels of the training sequences indicating Covid-19 DNA (1) or not (0).
    • Xtr_vectors- the training vectors which contain the encoding vector of each DNA sequencing reads from training.
    • Xte_vectors- the testing vectors which contain the encoding vector of each DNA sequencing reads from testing.
    • Each row of Xtr.csv represents a sequence.
    • Xte.csv contains 1000 test sequences, for which you need to predict the labels.
    • Ytr.csv contains the labels corresponding to the training data, in the same format as a submission file.

  2. **Pre-processing**
  3. For features use the vectors dataset which are already encoded but still we need to convert the values 0 to -1. Therefore transforming {0,1} classification problem to {-1,1} classification problem. To do that we computed : $y=2y-1$

  4. **Models**
  5. We used many models to make classification like Logistic Ridge Regression (Newton-Ralphson ,SGD), Kernel Logistic Regression, Kernel Ridge Regression, Kernel SVM and HardMarginSVM. We got the best accuracy with using Kernel SVM using RBF kernel. Our model performs an accuracy of **100%** for training and **97%** for validation. We got this result by looking for the good hyper-parameters
    • kernel = 'rbf'
    • sigma =0.1407035175879397
    • degree = 2
    • C = 10.0
    • tol = 1e-4

dna_sequence_covid_classification's People

Contributors

gildarech avatar

Stargazers

Mikhaël Presley KIBINDA-MOUKENGUE avatar  avatar

Watchers

 avatar

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.