nf-core/deepmodeloptim

Issues

• [test] write unittest for analysis default block

  #135 opened 2 months ago
  1

• [feat] add noise to class labels

  #134 opened 2 months ago
  1

• [Docker] add matplotlib

  #133 opened 7 months ago
  0

• [fix] save config files without serialized objects when ray tune finish

  #130 opened 7 months ago
  0

• [test] Write tests for Predict class

  #129 opened 2 months ago
  1

• [feat] add padding/truncation as data modification

  #128 opened 2 months ago
  1

• [fix] DNA Experiment test is broken - needs to be fixed and added to the common tests

  #125 opened 5 months ago
  0

• If batch size to test is bigger than data size, it throws a not easy to understand error. Do a check or a warning.

  #124 opened 2 months ago
  1

• [fix] solve titanic experiment to be able to add noise to data

  #123 opened 3 months ago
  0

• Config yaml breaks (with no good error message) if data_params is not given.

  #121 opened 2 months ago
  0

• [feat] implement a ray tune results parser class

  #120 opened 7 months ago
  0

• [feat] tune config yaml should be able to take a simple value too

  #119 opened 4 months ago
  1

• [feat] take as input Yaml for transform and split information

  #117 opened 2 months ago
  1

• [bug] FloatRankEncoder and IntRankEncoder are currently applying a standardisation between range [0,1] and not really ranking the data

  #114 opened 2 months ago
  1

• [feat] ray tune report validation accuracy and alternative metrics

  #113 opened 7 months ago
  0

• [fix] put tune config `optimizer` into `optimizer_params`

  #112 opened 7 months ago
  1

• [feat] create a class to handle ray tune results

  #111 opened 7 months ago
  0

• [feat] Add data clipping as possible data modification

  #110 opened 3 months ago
  0

• [feat] How changes in the input contribute changes of the model

  #107 opened 2 months ago
  1

• [feat] convolution -> which filters are activated for which sequences

  #106 opened 2 months ago
  1

• [feat] how do model parameters affect model performance

  #105 opened 2 months ago
  1

• [feat] how do data variation affect model performance?

  #104 opened 2 months ago
  1

• [fea] motif discovery - analysis block

  #103 opened 2 months ago
  1

• [feat] dna sequence analysis block

  #102 opened 2 months ago
  1

• [feat] report robustness metric for the models

  #101 opened 7 months ago
  0

• [feat] report to show if the model is learning

  #100 opened 7 months ago
  0

• Improve parsing of initial CSV file and impose data types as defined in meta

  #99 opened 7 months ago
  0

• Add stub-run

  #98 opened 7 months ago
  0

• Adopt the nf-core template before migration

  #95 opened 2 months ago
  1

• [feat] save the models during tuning

  #94 opened 7 months ago
  1

• [bug] RayTune Learner is using the validation set to train, remove the if case statement

  #93 opened 7 months ago
  1

• [feat] use safetensors to save and load model weights

  #91 opened 2 months ago
  5

• use wave to build and deploy containers

  #89 opened 2 months ago
  1

• [improvement] change step -> epoch in model definition, as step is reserved for the Trainable class in RayTune

  #88 opened 7 months ago
  1

• [feat] save model and files during tuning

  #87 opened 7 months ago
  0

• The pipeline runs x times splitting based on the number of combinations of json

  #85 opened 6 months ago
  0

• downsampling block in stimulus

  #84 opened 2 months ago
  2

• [feat] check if model runs before launching full workflow

  #81 opened 7 months ago
  1

• [feature] store data

  #79 opened 2 months ago
  0

• Test on IBIS challenge data

  #78 opened 3 months ago
  0

• [good to have] shuffle prior to splitting

  #77 opened 7 months ago
  1

• [feat] allow for taking encoded data as input

  #76 opened 2 months ago
  2

• [feat] data augmentation

  #75 opened 7 months ago
  2

• [test] do a minimal test for Titanic Kaggle dataset

  #73 opened 7 months ago
  1

• stimulus to chose the arquitecture and finish the training of the best one(s) chosen by user

  #69 opened 3 months ago
  1

• Remove stuff in workDir when complete

  #68 opened 3 months ago
  1

• Adding shuffling block

  #67 opened 7 months ago
  2

• Data augmentation block

  #66 opened 7 months ago
  1

• Pass model weights from ray tune to training for fine tuning

  #65 opened 8 months ago
  2

• [future] how to pass a custom experiment file to the nextflow pipeline

  #64 opened 2 months ago
  4