mathysgrapotte/stimulus

Issues

• [feat] have test data in a different repo

  #146 opened 5 months ago by luisas
  2

• [feat] outsource python package to a different repo ready for pip deployment

  #179 opened 5 months ago by mathysgrapotte
  1

• [feat] dna sequence analysis block

  #102 opened 6 months ago by suzannejin
  1

• [fea] motif discovery - analysis block

  #103 opened 6 months ago by suzannejin
  1

• [feat] how do model parameters affect model performance

  #105 opened 6 months ago by suzannejin
  1

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

  #117 opened 6 months ago by alessiovignoli
  1

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

  #114 opened 6 months ago by suzannejin
  1

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

  #106 opened 6 months ago by suzannejin
  1

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

  #107 opened 6 months ago by suzannejin
  1

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

  #121 opened 6 months ago by luisas
  0

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

  #104 opened 6 months ago by suzannejin
  1

• [feat] add padding/truncation as data modification

  #128 opened 6 months ago by luisas
  1

• [feat] add noise to class labels

  #134 opened 6 months ago by suzannejin
  1

• [feat] add a check on split parameters values.

  #151 opened 6 months ago by alessiovignoli
  1

• ray init does not automaticly detect GPUs

  #157 opened 10 months ago by alessiovignoli
  1

• 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 6 months ago by luisas
  1

• [test] Write tests for Predict class

  #129 opened 6 months ago by luisas
  1

• [test] write unittest for analysis default block

  #135 opened 6 months ago by suzannejin
  1

• [analysis] provide a report of auc vs data modification

  #136 opened 6 months ago by suzannejin
  1

• [feat] add an early stopper for ray tune

  #142 opened 6 months ago by suzannejin
  2

• [feat] resume ray tune

  #144 opened 6 months ago by suzannejin
  1

• Performance: define metrics per class

  #147 opened 6 months ago by luisas
  1

• [bug] If there is only one metric, analysis step crashes

  #148 opened 6 months ago by luisas
  1

• [feat] robust way of defining and importing the model class

  #158 opened 6 months ago by suzannejin
  1

• [feat] GaussianChunk to nf-test handle_data.nf.test

  #165 opened 6 months ago by alessiovignoli
  1

• [feat] python module to validate the tune config fields.

  #167 opened 6 months ago by alessiovignoli
  2

• [feat] parallelize predict wrapper

  #178 opened 6 months ago by suzannejin
  3

• [feat] add a way to assess the impact of different initial weights on the learning

  #171 opened 6 months ago by suzannejin
  1

• [feat] experiment conf json "custom" section should provide a slot "name" for the naming of each configuration

  #176 opened 6 months ago by suzannejin
  1

• [feat] analysis default should provide figures about the prediction values

  #175 opened 6 months ago by suzannejin
  1

• [feat] Add data clipping as possible data modification

  #110 opened 7 months ago by luisas
  0

• [bug] multiprocessing doesn't work in ikernels

  #173 opened 7 months ago by mathysgrapotte
  1

• [fix] ray tune runs forever sometimes

  #143 opened 9 months ago by suzannejin
  3

• [feat] force raytune to have maximum running time

  #159 opened 8 months ago by suzannejin
  1

• [feat] custom function for tune to sample x number from space

  #160 opened 9 months ago by suzannejin
  0

• [Docker] add matplotlib

  #133 opened a year ago by suzannejin
  0

• [fix] the output of the forward step should be tensor, never dict

  #137 opened a year ago by suzannejin
  0

• [fix] we want to transform the entire data

  #139 opened a year ago by suzannejin
  0

• [feat] implement a ray tune results parser class

  #120 opened a year ago by suzannejin
  0

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

  #123 opened 7 months ago by suzannejin
  0

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

  #125 opened 9 months ago by luisas
  0

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

  #130 opened a year ago by suzannejin
  0

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

  #111 opened a year ago by suzannejin
  0

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

  #112 opened a year ago by suzannejin
  1

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

  #113 opened a year ago by suzannejin
  0

• [feature] add logging functionalities

  #138 opened a year ago by mathysgrapotte
  0

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

  #119 opened 8 months ago by suzannejin
  1

• [seqera platform] on seqera platform, pipeline crashes since it is allowed just 1.GB of memory by default

  #155 opened 8 months ago by mathysgrapotte
  1

• Make pipeline run on GPU (+checks)

  #149 opened 10 months ago by luisas
  1

• Add `ps` to all containers

  #141 opened a year ago by evanfloden
  2