{
    "info": {
        "author": "Eduardo Brito",
        "author_email": "eduardo.alfredo.brito.chacon@iais.fraunhofer.de",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Environment :: Console",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: Apache Software License",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Programming Language :: Python :: 3 :: Only",
            "Topic :: Scientific/Engineering :: Artificial Intelligence",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Scientific/Engineering :: Mathematics"
        ],
        "description": "RatVec\n======\nThis tool generates low-dimensional, continuous, distributed vector representations for non-numeric entities such as\ntext or biological sequences (e.g. DNA or proteins) via kernel PCA with rational kernels.\n\nThe current implementation accepts any input dataset that can be read as a list of strings.\n\nInstallation |pypi_version| |python_versions| |pypi_license|\n------------------------------------------------------------\nRatVec can be installed on Python 3.6+ from `PyPI <https://pypi.python.org/pypi/ratvec>`_ with the following code in\nyour favorite terminal:\n\n.. code-block:: sh\n\n    $ pip install ratvec\n\nor from the latest code on `GitHub <https://github.com/ratvec/ratvec>`_ with:\n\n.. code-block:: sh\n\n   $ pip install git+https://github.com/ratvec/ratvec.git\n\nIt can be installed in development mode with:\n\n.. code-block:: sh\n\n   $ git clone https://github.com/ratvec/ratvec.git\n   $ cd ratvec\n   $ pip install -e .\n\nThe ``-e`` dynamically links the code in the git repository to the Python site-packages so your changes get\nreflected immediately.\n\nHow to Use\n----------\n``ratvec`` automatically installs a command line interface. Check it out with:\n\n.. code-block:: sh\n\n   $ ratvec --help\n\nRatVec has three main commands: ``generate``, ``train``, and ``evaluate``:\n\n1. **Generate**. Downloads and prepare the SwissProt data set that is showcased in the RatVec paper.\n\n.. code-block:: sh\n\n   $ ratvec generate\n\n2. **Train**. Compute KPCA embeddings on a given data set. Please run the following command to see the arguments:\n\n.. code-block:: sh\n\n   $ ratvec train --help\n\n3. **Evaluate**. Evaluate and optimize KPCA embeddings. Please run the following command to see the arguments:\n\n.. code-block:: sh\n\n   $ ratvec evaluate --help\n\nShowcase Dataset\n----------------\nThe application presented in the paper (SwissProt dataset [1]_ used by Boutet *et al.* [2]_) can be downloaded directly\nfrom `here <https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/JMFHTN>`_ or running the following\ncommand:\n\n.. code-block:: sh\n\n   $ ratvec generate\n\nReferences\n----------\n.. [1] Boutet, E. *et al.* (2016). `UniProtKB/Swiss-Prot, the manually annotated section of the UniProt KnowledgeBase:\n   how to use the entry view. <https://doi.org/10.1007/978-1-4939-3167-5_2>`_. Plant Bioinformatics (pp. 23-54).\n\n.. [2] Asgari, E., & Mofrad, M. R. (2015). `Continuous distributed representation of biological sequences for deep\n   proteomics and genomics <https://doi.org/10.1371/journal.pone.0141287>`_. PloS one, 10(11), e0141287.\n\n\n.. |python_versions| image:: https://img.shields.io/pypi/pyversions/ratvec.svg\n    :alt: Python versions supported by RatVec\n\n.. |pypi_version| image:: https://img.shields.io/pypi/v/ratvec.svg\n    :alt: Current version of RatVec on PyPI\n\n.. |pypi_license| image:: https://img.shields.io/pypi/l/ratvec.svg\n    :alt: RatVec is distributed under the Apache 2.0 License\n\n\n",
        "description_content_type": "",
        "docs_url": null,
        "download_url": "https://github.com/ratvec/ratvec/releases",
        "downloads": {
            "last_day": -1,
            "last_month": -1,
            "last_week": -1
        },
        "home_page": "https://github.com/ratvec/ratvec",
        "keywords": "Representation Learning,Kernel PCA,Principle Component Analysis,PCA",
        "license": "Apache 2.0 License",
        "maintainer": "Eduardo Brito",
        "maintainer_email": "eduardo.alfredo.brito.chacon@iais.fraunhofer.de",
        "name": "ratvec",
        "package_url": "https://pypi.org/project/ratvec/",
        "platform": "",
        "project_url": "https://pypi.org/project/ratvec/",
        "project_urls": {
            "Bug Tracker": "https://github.com/ratvec/ratvec/issues",
            "Documentation": "https://ratvec.readthedocs.io",
            "Download": "https://github.com/ratvec/ratvec/releases",
            "Homepage": "https://github.com/ratvec/ratvec"
        },
        "release_url": "https://pypi.org/project/ratvec/0.1.2/",
        "requires_dist": [
            "click (>=7.0)",
            "requests",
            "distance",
            "numpy",
            "scipy",
            "tqdm",
            "sklearn",
            "cython",
            "click",
            "biopython"
        ],
        "requires_python": ">=3.6",
        "summary": "Generating dense embeddings for proteins using kernel PCA",
        "version": "0.1.2"
    },
    "last_serial": 5125170,
    "releases": {
        "0.1.0": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "0af7497f978be581ed19acc55e5d8761",
                    "sha256": "d68ca0b06bb607a1731f6540622f216526bc6f7b81a8441e1e7c0d3a418a5f97"
                },
                "downloads": -1,
                "filename": "ratvec-0.1.0-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "0af7497f978be581ed19acc55e5d8761",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": ">=3.6",
                "size": 35812,
                "upload_time": "2019-04-10T13:41:19",
                "url": "https://files.pythonhosted.org/packages/bf/a7/bcf77a6f28a519900ae1b80d267e27c0a3ea44542f44c314743bf633bce7/ratvec-0.1.0-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "8744615f63c12ddb7c8fdd0e16f4455b",
                    "sha256": "1c98046ed0bdb48a53bf4e531cec11c48ed538b7f35bb538a1118baf7affc795"
                },
                "downloads": -1,
                "filename": "ratvec-0.1.0.tar.gz",
                "has_sig": false,
                "md5_digest": "8744615f63c12ddb7c8fdd0e16f4455b",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.6",
                "size": 25483,
                "upload_time": "2019-04-10T13:41:21",
                "url": "https://files.pythonhosted.org/packages/1e/1f/af45fb5524fb2cfedc426b0720c18911f8ab4054548c457959436ea7310b/ratvec-0.1.0.tar.gz"
            }
        ],
        "0.1.1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "421f22819e83801996dcf104587e3782",
                    "sha256": "764a9aa7b8be54d4354e8717e19f5a068fec3916ec07fbd7cb256c0f33445dd4"
                },
                "downloads": -1,
                "filename": "ratvec-0.1.1-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "421f22819e83801996dcf104587e3782",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": ">=3.6",
                "size": 23777,
                "upload_time": "2019-04-10T14:03:58",
                "url": "https://files.pythonhosted.org/packages/b9/15/deb5965c559f133f30c0fa21a5de32d60944a6ae513c5350df7379a205cb/ratvec-0.1.1-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "538198c62acdf628f15aeb4f515f5192",
                    "sha256": "4602778525c84079221ef87b1080b5efb051877dcc9998ff11490bc9904f5773"
                },
                "downloads": -1,
                "filename": "ratvec-0.1.1.tar.gz",
                "has_sig": false,
                "md5_digest": "538198c62acdf628f15aeb4f515f5192",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.6",
                "size": 22162,
                "upload_time": "2019-04-10T14:04:00",
                "url": "https://files.pythonhosted.org/packages/b5/35/6aece06611f0530799d7cc75590532c7ec67f1df01734772821afd8a1a47/ratvec-0.1.1.tar.gz"
            }
        ],
        "0.1.2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "98e2e9656e68167cb07c1a7984669d3e",
                    "sha256": "7bcba08243c0eb741158a447239ca202a5fd7cf6f5966eb2a149aefa17e31914"
                },
                "downloads": -1,
                "filename": "ratvec-0.1.2-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "98e2e9656e68167cb07c1a7984669d3e",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": ">=3.6",
                "size": 23956,
                "upload_time": "2019-04-10T14:27:59",
                "url": "https://files.pythonhosted.org/packages/ed/b2/19709fed9c8bb3a782bcf7d18dced012f7e9d64fb096b68cecb3365aad85/ratvec-0.1.2-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "a8d757ba08afb5c0c971f34bcbd3e2b1",
                    "sha256": "b6142ad1cccb65540be3e2e1cdfa163ee23bd064d1ccedaaf043312123f65753"
                },
                "downloads": -1,
                "filename": "ratvec-0.1.2.tar.gz",
                "has_sig": false,
                "md5_digest": "a8d757ba08afb5c0c971f34bcbd3e2b1",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.6",
                "size": 22615,
                "upload_time": "2019-04-10T14:28:01",
                "url": "https://files.pythonhosted.org/packages/e4/5f/159e89b8c425adc6c338a058dedfd77fca1a979d8e16ef13436abf7e2145/ratvec-0.1.2.tar.gz"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "98e2e9656e68167cb07c1a7984669d3e",
                "sha256": "7bcba08243c0eb741158a447239ca202a5fd7cf6f5966eb2a149aefa17e31914"
            },
            "downloads": -1,
            "filename": "ratvec-0.1.2-py3-none-any.whl",
            "has_sig": false,
            "md5_digest": "98e2e9656e68167cb07c1a7984669d3e",
            "packagetype": "bdist_wheel",
            "python_version": "py3",
            "requires_python": ">=3.6",
            "size": 23956,
            "upload_time": "2019-04-10T14:27:59",
            "url": "https://files.pythonhosted.org/packages/ed/b2/19709fed9c8bb3a782bcf7d18dced012f7e9d64fb096b68cecb3365aad85/ratvec-0.1.2-py3-none-any.whl"
        },
        {
            "comment_text": "",
            "digests": {
                "md5": "a8d757ba08afb5c0c971f34bcbd3e2b1",
                "sha256": "b6142ad1cccb65540be3e2e1cdfa163ee23bd064d1ccedaaf043312123f65753"
            },
            "downloads": -1,
            "filename": "ratvec-0.1.2.tar.gz",
            "has_sig": false,
            "md5_digest": "a8d757ba08afb5c0c971f34bcbd3e2b1",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": ">=3.6",
            "size": 22615,
            "upload_time": "2019-04-10T14:28:01",
            "url": "https://files.pythonhosted.org/packages/e4/5f/159e89b8c425adc6c338a058dedfd77fca1a979d8e16ef13436abf7e2145/ratvec-0.1.2.tar.gz"
        }
    ]
}