https://github.com/danvk/deepsea

Reimplementation of DeepSEA using TensorFlow
https://github.com/danvk/deepsea

Last synced: 28 days ago
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Reimplementation of DeepSEA using TensorFlow

• Host: GitHub
• URL: https://github.com/danvk/deepsea
• Owner: danvk
• License: apache-2.0
• Created: 2016-01-21T16:37:42.000Z (almost 9 years ago)
• Default Branch: master
• Last Pushed: 2016-01-25T20:19:51.000Z (almost 9 years ago)
• Last Synced: 2024-10-12T17:39:52.690Z (about 1 month ago)
• Language: Python
• Size: 11.7 KB
• Stars: 6
• Watchers: 5
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# deepsea

Reimplementation of DeepSEA using TensorFlow.

To get everything set up:

  1. [Install TensorFlow][tf] and numpy.

  1. Install other requirements, possibly in a virtualenv:

    `pip install -r requirements.txt`

  1. Download Jeff's [processed version][data] of the data (47 MB). You'll need to put `train10k.mat` in the repo's root directory.

  

To train a model, run:

    ./deepsea.py

While this is training, you can inspect its state using [TensorBoard][tb]:

    tensorboard /tmp/deepsea_logs

See also:

  * [DeepSEA paper][paper] in Nature Methods, including the supplemental

  * [Jeff's Notes][jn]

  * [Dan's Notes][dn]

[tf]: https://www.tensorflow.org/versions/master/get_started/os_setup.html

[tb]: https://www.tensorflow.org/versions/master/how_tos/summaries_and_tensorboard/index.html

[data]: https://drive.google.com/file/d/0ByrU_xuJMu6YWS1rN3p2bmFabzg/view

[paper]: http://www.nature.com/nmeth/journal/v12/n10/full/nmeth.3547.html

[jn]: https://docs.google.com/document/d/1dp2Kn7258Tttd_-FEnM05HOUJzevq9B9GJn2lngcrfo/edit#heading=h.nh8yx5qspnzv

[dn]: https://docs.google.com/document/d/1-PrZB7IcNiADFU84a0H4AcUxpcPCq3PXev1SQPsMwXE/edit