https://github.com/weekend37/string-kernels

Implementation of the Polynomial String Kernel and linear time String Kernel implementation. Compatible and ready for easy plug-in to Scikit-Learn's Support Vector Machines and supports multithreading.
https://github.com/weekend37/string-kernels

algorithms genomics kernelsvm machine-learning multithreading sequence-analysis

Last synced: about 1 month ago
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Implementation of the Polynomial String Kernel and linear time String Kernel implementation. Compatible and ready for easy plug-in to Scikit-Learn's Support Vector Machines and supports multithreading.

• Host: GitHub
• URL: https://github.com/weekend37/string-kernels
• Owner: weekend37
• License: other
• Created: 2021-10-26T20:39:30.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2025-08-25T04:02:54.000Z (6 months ago)
• Last Synced: 2025-09-29T18:05:11.151Z (5 months ago)
• Topics: algorithms, genomics, kernelsvm, machine-learning, multithreading, sequence-analysis
• Language: Python
• Homepage:
• Size: 371 KB
• Stars: 5
• Watchers: 1
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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# String Kernels

This package contains an implementation of the **Polynomial String Kernel** and a linear time **String Kernel** algorithm as described in our paper, [High Resolution Ancestry Deconvolution for Next Generation Genomic Data](https://www.biorxiv.org/content/10.1101/2021.09.19.460980v1). 





It offers

- Linear time computation of two effective string kernels.

- Compatibility with Scikit-Learn's Support Vector Machines (easy plug-in).

- Multithreading.

## Usage

To install the package, execute from the command line

```

pip install string-kernels

```

And then you're all set!

Assuming you have [Scikit-Learn](https://scikit-learn.org/) already installed, you can use Lodhi's string kernel via

```python

from sklearn import svm

from stringkernels.kernels import string_kernel

model = svm.SVC(kernel=string_kernel())

```

and the polynomial string kernel,

```python

from sklearn import svm

from stringkernels.kernels import polynomial_string_kernel

model = svm.SVC(kernel=polynomial_string_kernel())

```

For morer information read the [docs](https://github.com/weekend37/string-kernels/blob/master/doc/docs.md) or take a look at the notebook [example.ipynb](https://github.com/weekend37/string-kernels/blob/master/example.ipynb) for further demonstration of usage.

If you end up using this in your research we kindly ask you to cite us! :)