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29 Commits

Author SHA1 Message Date
coolneng 0ce582250d
Implement the training loop and metrics evaluation 2021-06-06 00:20:03 +02:00
coolneng 168a68b50d
Update documentation about data splits 2021-06-06 00:13:37 +02:00
coolneng 8870da8543
Create a validation set 2021-06-06 00:04:18 +02:00
coolneng 38903c5737
Rename ref_sequence to label 2021-06-06 00:03:15 +02:00
coolneng 035162bd8d
Fix position weight matrix assignment 2021-06-05 20:40:13 +02:00
coolneng 02d20d4e72
Add reference sequence to each dataset instance 2021-06-05 20:34:59 +02:00
coolneng f30fc31c29
Update README 2021-06-04 12:18:44 +02:00
coolneng c9de0c8320
Add learning rate and l2 regularizer constants 2021-06-03 18:52:26 +02:00
coolneng ccaa8484c7
Document read_dataset and process_input 2021-06-03 18:51:49 +02:00
coolneng f8c1a54be3
Apply index-based encoding to the DNA sequence 2021-06-03 18:29:43 +02:00
coolneng d34e291085
Generate a dataset from the TFRecords files 2021-06-01 23:06:25 +02:00
coolneng 220c0482f1
Move hardcorded data to a constants module 2021-06-01 19:27:10 +02:00
coolneng 44ff69dc9e
Document the preprocessing module 2021-06-01 18:46:17 +02:00
coolneng 5ac81c049f
Change BASES constant to a local variable 2021-06-01 18:34:29 +02:00
coolneng ad49e598db
Update gitignore 2021-06-01 18:27:16 +02:00
coolneng 16c01afbe7
Create a dataset and write it to TFRecords files 2021-06-01 18:26:13 +02:00
coolneng 59aa61112e
Create a basic CNN model 2021-05-31 20:02:44 +02:00
coolneng 731b76a0af
Remove redundant modules 2021-05-31 20:00:43 +02:00
coolneng e957e714e6
Replace tensorflow-io with biopython 2021-05-31 12:30:57 +02:00
coolneng 6201e35e99
Document the data parsing function 2021-05-11 20:41:54 +02:00
coolneng 34fefed3ed
Add literate programming notebook 2021-05-06 20:44:22 +02:00
coolneng eb072836a1
Parse a FASTQ file into a Tensor 2021-05-06 20:34:39 +02:00
coolneng 62fcf0974d
Add gitignore 2021-05-06 18:59:08 +02:00
coolneng 223bf16a8a
Add Tensorflow workarounds to shell.nix 2021-05-06 00:12:24 +02:00
coolneng fba5578adc
Resolve dependencies with Poetry 2021-05-05 23:54:48 +02:00
coolneng a4ba69feed
Change python version to 3.8 2021-05-05 23:54:20 +02:00
coolneng 38ea414b69
Change nixpkgs channel to unstable 2021-05-05 23:53:48 +02:00
coolneng dd7386ff73
Pin dependencies with niv 2021-05-04 21:17:02 +02:00
coolneng 5c30ede7d5
Initial commit 2021-02-17 18:06:14 +01:00