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Dna joao#9

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marta-seq wants to merge 149 commits intomainBioSystemsUM/propythia:mainfrom dna-joaoBioSystemsUM/propythia:dna-joaoCopy head branch name to clipboard

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Commits on Feb 23, 2022

• first commit

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  6e7ad4f

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Commits on Feb 24, 2022

• add guides

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  a7f6dc2

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• .DS_Store banished!

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  ebe389c

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• add a few DNA descriptors

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• update requirements

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  28e5c32

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• add more descriptors and a get all function

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Commits on Feb 25, 2022

• fix get_kmer

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  c1b0127

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• add binary and accumulated nucleotide frequency descriptors

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  5513b4d

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• add binary and accumulated nucleotide frequency descriptors

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  61385f2

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• add enhanced nucleic acid composition descriptor

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• add header to descriptors_dna.py

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Commits on Mar 3, 2022

• add k spaced nucleic acid pairs descriptor

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Commits on Mar 5, 2022

• add get_PseDNC descriptor

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Commits on Mar 8, 2022

• add pseudo_k_composition descriptor

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Commits on Mar 10, 2022

• added all Autocorrelation descriptors

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  d629ffb

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• fix docs

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• add where code comes from

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Commits on Mar 11, 2022

• add dna deep ml template code

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• cifar10 template code

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Commits on Mar 15, 2022

• delete pickle file

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Commits on Mar 17, 2022

• add essential genes dataset

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Commits on Mar 24, 2022

• update

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Commits on Mar 25, 2022

• add enhancer dataset

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Commits on Mar 29, 2022

• update

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  25e9689

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• added essential genes fasta

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  2e65b5f

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Commits on Apr 4, 2022

• update

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Commits on Apr 5, 2022

• update

  

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• update

  

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Commits on Apr 6, 2022

• model with 62% acc for enhancers

  

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• test update

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  0ac4e3d

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• clean cdoe

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• update

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Commits on Apr 8, 2022

• with conda env now

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  a8dc599

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• remove unnecessary print

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• requirements file for conda env

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  8f565a4

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Commits on Apr 15, 2022

• one hot encoding attempt

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Commits on Apr 19, 2022

• change descriptors values to percentage

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  04969b2

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• delete ugly print

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  c50d6f5

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Commits on Apr 21, 2022

• good acc and mcc with a new dataset

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  8b9fa9c

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Commits on Apr 27, 2022

• remove enhancers and clean validate_descriptors

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Commits on Apr 28, 2022

• with more comments and models

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  1a9a7bc

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Commits on May 2, 2022

• fix linear svm feature importance

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  d7904e5

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Commits on May 18, 2022

• testing DL models

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Commits on May 19, 2022

• update testing

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  584ec1a

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• with more comments

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  04c9e7e

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Commits on May 20, 2022

• update

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  81095c2

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• update

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Commits on May 21, 2022

• with good acc and mcc

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  055f1bf

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• with early stopping

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• with early stopping and lr scheduler

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  51c39b6

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Commits on Jun 2, 2022

• clean up code

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  54e174e

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• creating module

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Commits on Jun 7, 2022

• just to not lose progress

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• just not to lose progress

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  34b5322

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• add readme

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• update

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• update

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• update

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Commits on Jun 8, 2022

• updating

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Commits on Jun 10, 2022

• update

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Commits on Jun 13, 2022

• update

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  f4d7e42

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• update

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  5f918b1

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• update

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Commits on Jun 14, 2022

• update

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  cfe8c93

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Commits on Jun 15, 2022

• features calculated and stored in pickle obj

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  8f7aeba

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• removed old DeepHE file

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  6da15a3

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• starting model with descriptors

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  a893677

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• testing models

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  acec716

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Commits on Jun 16, 2022

• removed extra descriptors and fixed accumulated

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  4f42b12

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Commits on Jun 17, 2022

• training with descriptors but guessing negatives

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  22c1764

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• features + DHE model in Primer and prepare_data.py

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  e1a118b

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• fix bug 0 MCC even when the classes were weighted

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  36fced1

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Commits on Jun 18, 2022

• created hyperparameter tuning script

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  27f646f

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• added more docs

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• primer with hyperparameter tuning

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  8422653

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Commits on Jun 19, 2022

• hyperparam tuning in DHE, primer and testing

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  42aaf24

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Commits on Jun 21, 2022

• chemical enc, deepHE stats

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  c33db3a

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Commits on Jun 22, 2022

• rnn-lstm model. primer works for every model

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  2fa291d

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Commits on Jul 5, 2022

• update

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Commits on Jul 6, 2022

• update

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  6172078

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Commits on Jul 8, 2022

• with cnn-lstm model

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  a654c9d

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• cnn-lstm works for primer and h3

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  da9f74a

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Commits on Jul 11, 2022

• add bidirectional option for LSTM and CNN-LSTM

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• add daniel buckle thesis model

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  a4dee74

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Commits on Jul 28, 2022

• implemented kmer_one_hot encoding

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  0005399

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• clean up of repo

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  de594a5

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• clean up of repo

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  030533f

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• update readme

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  45b131e

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• removed unnecessary files

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  e91dba5

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• update README

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  e195cb5

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• primer added again

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  d540a2c

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Commits on Aug 2, 2022

• fix PseDNC and PseKNC

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  70d24f1

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• descriptors better commented

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  1b3093f

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• remove unnecessary code

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  2483b13

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• calculation list descriptors, read_sequence module

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  f8aeae4

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• quick start notebook for descriptors

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  1b04065

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• update readme

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  b25c714

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• update text

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  4632d6a

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• made quick start smaller

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  8a02aec

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• fix table

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  4ff3722

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• fix table

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  0d19414

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• fix table

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  47fb670

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• fix table 4

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• asdasd

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  b6c3d71

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• fix table 5

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  1af3db5

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• prettify

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  1d6c4ce

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• prettify

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• grammar update on quick start and gru model

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  5bcb8c0

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• allows train without tuning

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Commits on Aug 3, 2022

• calculates descriptors when they havent been

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  da72bd8

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• update texts

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  678f154

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• refactored to 1 big folder instead of 2

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  a5f641f

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• joined utils files and fixed imports

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Commits on Aug 4, 2022

• testing.py brough back (?) starting quick start DL

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• quick start DL until hyper tuning

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• renamed testing to deep_ml

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  c17e4d8

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Commits on Aug 5, 2022

• with config file

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Commits on Aug 8, 2022

• change read me

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Commits on Aug 9, 2022

• commit test

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Commits on Aug 10, 2022

• update

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Commits on Aug 17, 2022

• quick start dl done

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Commits on Aug 25, 2022

• with num layers in MLP as hyperparameter

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Commits on Sep 5, 2022

• fc layer of CNN similar to MLP's

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Commits on Sep 7, 2022

• added bi_gru, mlp_half and cnn_half models

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Commits on Sep 8, 2022

• Delete Primer.ipynb

  JoaoNunoAbreu

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  65ae1e2

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Commits on Sep 14, 2022

• update

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Commits on Sep 23, 2022

• update

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  2dbc374

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• Merge branch 'dna-joao' of https://github.com/BioSystemsUM/propythia into dna-joao

  JoaoNunoAbreu

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Commits on Oct 6, 2022

• final version of models i hope

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• remove dynamic num_layers

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Commits on Oct 10, 2022

• com hyper tuning reproducible

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Commits on Oct 12, 2022

• reproducible results with new scheduler

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Commits on Oct 18, 2022

• refactoring of a lot of things

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  d3c98dc

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• fix typo on quicker start

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Commits on Oct 19, 2022

• with SMOTE and cutting length

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  66182d4

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• with choice of reading from pickle

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• with more and pretty metrics

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• remove unnecessary parameter from oversample

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• smote in training

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  477b27a

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• fix

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• martelada

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Commits on Oct 20, 2022

• Revert "smote in training"

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• revert to last week

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• working so far

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• still working with prepare_and_train

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Commits on Oct 22, 2022

• update

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  c8c2e4f

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• fix last update

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Commits on Oct 27, 2022

• gg

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Commits on Jul 2, 2023

• Rename requirements to requirements_dna

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