This tool generates low-dimensional, continuous, distributed vector representations for non-numeric entities such as text or biological sequences (e.g. DNA or proteins) via kernel PCA with rational kernels.
The current implementation accepts any input dataset that can be read as a list of strings.
Installation 
RatVec can be installed on Python 3.6+ from PyPI with the following code in your favorite terminal:
$ pip install ratvecor from the latest code on GitHub with:
$ pip install git+https://github.com/ratvec/ratvec.gitIt can be installed in development mode with:
$ git clone https://github.com/ratvec/ratvec.git
$ cd ratvec
$ pip install -e .The -e dynamically links the code in the git repository to the Python site-packages so your changes get reflected immediately.
How to Use
ratvec automatically installs a command line interface. Check it out with:
$ ratvec --helpRatVec has three main commands: generate, train, and evaluate:
Generate. Downloads and prepare the SwissProt data set that is showcased in the RatVec paper.
$ ratvec generateTrain. Compute KPCA embeddings on a given data set. Please run the following command to see the arguments:
$ ratvec train --helpEvaluate. Evaluate and optimize KPCA embeddings. Please run the following command to see the arguments:
$ ratvec evaluate --helpShowcase Dataset
The application presented in the paper (SwissProt dataset [1] used by Boutet et al. [2]) can be downloaded directly from here or running the following command:
$ ratvec generateReferences
Release files for ratvec 0.1.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| ratvec-0.1.2.tar.gz | 22.6 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| ratvec-0.1.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 46.6 kB
Release files / ratvec-0.1.2.tar.gz
| Download URL | ratvec-0.1.2.tar.gz |
|---|---|
| Size | 22.6 kB |
| Tags | Source |
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SHA-256 checksum How to use checksums |
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Release files / ratvec-0.1.2-py3-none-any.whl
| Download URL | ratvec-0.1.2-py3-none-any.whl |
|---|---|
| Size | 24.0 kB |
| Tags | Python 3 |
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SHA-256 checksum How to use checksums |
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twine/1.13.0 pkginfo/1.5.0.1 requests/2.21.0 setuptools/41.0.0 requests-toolbelt/0.9.1 tqdm/4.31.1 CPython/3.7.2
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