 coolneng
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6dd0d7e0ba
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Add trained model
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2021-07-06 03:07:54 +02:00 |
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coolneng
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1311b9b945
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Apply isort to the project
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2021-07-06 03:01:43 +02:00 |
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coolneng
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92c6b54966
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Implement model inference of sequences
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2021-07-06 02:59:37 +02:00 |
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coolneng
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1333a9256b
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Remove logs directory
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2021-07-06 02:12:42 +02:00 |
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coolneng
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eabb7f0285
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Change model architecture to a MLP
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2021-07-06 01:44:58 +02:00 |
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coolneng
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1a1262b0b1
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Pad and mask the sequences in each batch
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2021-07-05 19:55:31 +02:00 |
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coolneng
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70363a82a0
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Refactor sequence preprocessing
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2021-07-05 19:54:48 +02:00 |
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coolneng
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72e3de945a
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Add type hints to the main module
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2021-07-05 03:52:26 +02:00 |
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coolneng
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bcc4f4b4d4
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Parse data and label files from CLI arguments
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2021-07-05 03:49:14 +02:00 |
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coolneng
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a3780c9761
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Move hyperparameters to a class
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2021-07-05 03:24:54 +02:00 |
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coolneng
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e07d0dcdbf
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Change Flatten layer, loss function and add Input
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2021-06-26 17:52:20 +02:00 |
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coolneng
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4d67bdac30
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Add poetry installation step to README
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2021-06-26 04:35:59 +02:00 |
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coolneng
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1237394bb1
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Perform one hot encoding on the sequences
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2021-06-25 00:05:14 +02:00 |
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coolneng
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e9582d0883
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Parallelize dataset transformations
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2021-06-24 19:54:19 +02:00 |
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coolneng
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b2f20f2070
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Revert "Remove dense Tensor transformation"
This reverts commit 0912600fdc.
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2021-06-24 17:10:07 +02:00 |
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coolneng
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c9466baa68
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Align altered sequence with the reference sequence
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2021-06-23 18:29:16 +02:00 |
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coolneng
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0912600fdc
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Remove dense Tensor transformation
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2021-06-23 18:28:09 +02:00 |
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coolneng
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1e433c123f
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Remove base counts from the dataset
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2021-06-16 13:02:49 +02:00 |
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coolneng
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a2ae7bbe11
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Add the Jupyter notebook
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2021-06-15 01:00:45 +02:00 |
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coolneng
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7a568f4f98
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Create logs directory
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2021-06-15 00:38:09 +02:00 |
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coolneng
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7029b64906
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Refactor the casting function using a loop
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2021-06-15 00:22:55 +02:00 |
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coolneng
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379303b440
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Cast the parsed features to int32
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2021-06-15 00:18:38 +02:00 |
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coolneng
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d2e5fd0fa3
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Build model incrementally
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2021-06-14 23:32:49 +02:00 |
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coolneng
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19ed847d12
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Convert sequence and label to VarLenFeature
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2021-06-14 19:33:42 +02:00 |
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coolneng
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c6d0d5959d
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Update gitignore
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2021-06-10 19:23:05 +02:00 |
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coolneng
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2c07c5975f
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Add usage instructions
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2021-06-10 19:22:41 +02:00 |
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coolneng
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498d93de2a
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Execute the training loop in the model module
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2021-06-10 13:27:55 +02:00 |
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coolneng
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3b2b6c4af9
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Remove deprecated org notebook
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2021-06-10 13:19:03 +02:00 |
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coolneng
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00e3389f5b
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Add datasets
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2021-06-10 13:18:25 +02:00 |
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coolneng
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08611de8e6
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Fix Tensorflow seed assignment
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2021-06-07 19:26:21 +02:00 |
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coolneng
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0ce582250d
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Implement the training loop and metrics evaluation
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2021-06-06 00:20:03 +02:00 |
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coolneng
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168a68b50d
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Update documentation about data splits
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2021-06-06 00:13:37 +02:00 |
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coolneng
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8870da8543
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Create a validation set
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2021-06-06 00:04:18 +02:00 |
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coolneng
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38903c5737
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Rename ref_sequence to label
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2021-06-06 00:03:15 +02:00 |
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coolneng
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035162bd8d
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Fix position weight matrix assignment
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2021-06-05 20:40:13 +02:00 |
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coolneng
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02d20d4e72
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Add reference sequence to each dataset instance
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2021-06-05 20:34:59 +02:00 |
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coolneng
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f30fc31c29
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Update README
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2021-06-04 12:18:44 +02:00 |
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coolneng
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c9de0c8320
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Add learning rate and l2 regularizer constants
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2021-06-03 18:52:26 +02:00 |
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coolneng
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ccaa8484c7
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Document read_dataset and process_input
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2021-06-03 18:51:49 +02:00 |
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coolneng
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f8c1a54be3
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Apply index-based encoding to the DNA sequence
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2021-06-03 18:29:43 +02:00 |
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coolneng
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d34e291085
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Generate a dataset from the TFRecords files
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2021-06-01 23:06:25 +02:00 |
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coolneng
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220c0482f1
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Move hardcorded data to a constants module
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2021-06-01 19:27:10 +02:00 |
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coolneng
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44ff69dc9e
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Document the preprocessing module
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2021-06-01 18:46:17 +02:00 |
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coolneng
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5ac81c049f
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Change BASES constant to a local variable
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2021-06-01 18:34:29 +02:00 |
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coolneng
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ad49e598db
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Update gitignore
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2021-06-01 18:27:16 +02:00 |
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coolneng
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16c01afbe7
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Create a dataset and write it to TFRecords files
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2021-06-01 18:26:13 +02:00 |
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coolneng
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59aa61112e
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Create a basic CNN model
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2021-05-31 20:02:44 +02:00 |
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coolneng
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731b76a0af
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Remove redundant modules
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2021-05-31 20:00:43 +02:00 |
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coolneng
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e957e714e6
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Replace tensorflow-io with biopython
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2021-05-31 12:30:57 +02:00 |
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coolneng
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6201e35e99
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Document the data parsing function
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2021-05-11 20:41:54 +02:00 |
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