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Adding model.yaml

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  1. model.yaml +49 -0
model.yaml ADDED
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+ defined_as: kipoi.model.KerasModel
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+ args: # arguments of kipoi.model.KerasModel
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+ arch:
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+ url: https://zenodo.org/record/5502060/files/DeepSTARR.model.json?download=1
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+ md5: 9b796f79441e53dc75dd79b911fff872
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+ weights:
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+ url: https://zenodo.org/record/5502060/files/DeepSTARR.model.h5?download=1
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+ md5: 7e53a9351b2520a4713a5ffdb5f1566c
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+
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+ default_dataloader:
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+ defined_as: kipoiseq.dataloaders.SeqIntervalDl
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+
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+ default_args: # Optional arguments to the SeqIntervalDl dataloader
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+ auto_resize_len: 249
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+ alphabet_axis: 1
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+ dummy_axis: 2
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+ alphabet: "ACGT"
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+ ignore_targets: False
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+
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+ info:
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+ authors:
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+ - name: Bernardo P. de Almeida
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+ github: bernardo-de-almeida
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+ email: bernardo.almeida94@gmail.com
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+ doc: Model predicting the activities of developmental and housekeeping enhancers in Drosophila S2 cells
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+ cite_as: https://doi.org/10.1101/2021.10.05.463203
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+ trained_on: Developmental and housekeeping quantitative enhancer activity. Held-out second half of chromosome 2R.
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+ license: MIT
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+
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+ dependencies:
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+ conda:
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+ - python=3.7
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+ - h5py=3.6.0
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+ - pip=21.2.2
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+ pip:
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+ - keras==2.7.0
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+ - tensorflow==2.7.0
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+
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+ schema:
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+ inputs:
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+ shape: (249,4,1)
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+ doc: DNA sequence
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+
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+ targets:
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+ shape: (2,)
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+ doc: Developmental and housekeeping enhancer activity
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+
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+
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+