nf-core deepmodeloptim issues

nf-core / deepmodeloptim

Stochastic Testing and Input Manipulation for Unbiased Learning Systems

https://nf-co.re/deepmodeloptim

MIT License

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issues

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computation cost of pipeline (in terms of money)

#59 alessiovignoli closed 1 month ago
1
Implement better parsing of configuration for hyperparameter tuning

#58 luisas closed 7 months ago
1
Check which is the relationship of iterations and epochs

#57 luisas closed 7 months ago
2
Add tests that considers the reproducibility & random seeds

#56 suzannejin closed 7 months ago
1
[nf-tests] Assure reproducibility

#55 suzannejin opened 7 months ago
3
Issue51

#54 alessiovignoli closed 7 months ago
0
noise only train set and not the others or viceversa.

#53 alessiovignoli closed 1 month ago
2
change behaviour of bin/launch_split_csv.py when both json split and csv split parameters are present.

#52 alessiovignoli closed 1 month ago
1
errata in bin/launch_split_csv.py

#51 alessiovignoli closed 7 months ago
1
Checking correctness of Json for noise and split parameters.

#50 alessiovignoli closed 1 month ago
2
Implement nextflow modules/workflows for training

#49 luisas closed 7 months ago
1
Polish trainer implementation (with tests!)

#48 luisas closed 7 months ago
1
[tests] Add global pipeline tests (nf-tests)

#47 mathysgrapotte closed 4 months ago
0
Add split functionality

#46 luisas closed 7 months ago
0
Noise module

#45 alessiovignoli closed 7 months ago
0
written description of JsonSchema functions and descriptio of launch_…

#44 alessiovignoli closed 7 months ago
0
[future] splitting CSV to parralelize bash code (samtools, bedtools...) and python noising functions

#43 mathysgrapotte closed 2 months ago
0
Firstpipe module

#42 alessiovignoli closed 7 months ago
0
Check type hints

#41 suzannejin closed 2 months ago
0
reproducibility in model

#40 mathysgrapotte closed 5 months ago
1
add masking to allow for better use of padding

#39 mathysgrapotte closed 2 months ago
1
All encoders should output either a numpy array (when all elements are the same shape) or a list of numpy arrays (when shapes are different)

#38 mathysgrapotte closed 7 months ago
0
Add add_split method inside CsvProcessing and corresponding tests

#37 suzannejin closed 8 months ago
0
implement the noise_all_combination() in the JsonSchema class

#36 alessiovignoli closed 1 month ago
3
Firstpipe module

#35 alessiovignoli closed 8 months ago
0
convert split into a standalone optional category, implement add noise function inside CsvProcessing, and add protein experiment

#34 suzannejin closed 8 months ago
0
Improving TorchDataset

#33 mathysgrapotte closed 7 months ago
0
Taking care of split:meta:int column present in the input csv

#32 mathysgrapotte closed 8 months ago
9
Add functionalities to the CsvParser class

#31 mathysgrapotte closed 7 months ago
0
Csvhandlerpolar

#30 mathysgrapotte closed 8 months ago
7
updated the Json schema to be column_name oriented instead of noise f…

#29 alessiovignoli closed 8 months ago
0
Readable way of providing combinations of configuration files to python

#28 suzannejin closed 8 months ago
0
Pipeline integration

#27 alessiovignoli closed 8 months ago
0
Replacing data_types by dictionaries of encoders and noisers

#26 mathysgrapotte closed 8 months ago
0
Add protein type

#25 suzannejin closed 8 months ago
0
Json to noise func call

#24 mathysgrapotte closed 8 months ago
0
fixed the bug while slicing the encoded_item using idx

#23 suzannejin closed 8 months ago
0
Remove self data

#22 suzannejin closed 8 months ago
0
Write protein data type

#21 suzannejin closed 8 months ago
3
add .vscode/settings.json to allow testing and debugging of the unit tests inside vscode

#20 suzannejin closed 8 months ago
6
finished handletorch implementation

#19 mathysgrapotte closed 8 months ago
0
Call from get attribute instead of using if else in the encoder class

#18 mathysgrapotte closed 8 months ago
2
Remove self.data from csv parser class

#17 mathysgrapotte closed 8 months ago
0
Use a config in json format to parse de parameters in nextflow through the python code

#16 mathysgrapotte closed 7 months ago
3
Dataset dataloader

#15 mathysgrapotte closed 9 months ago
0
added noise generator gaussian class tests

#14 alessiovignoli closed 9 months ago
0
fixed multiproccess screwing up setting seed

#13 alessiovignoli closed 9 months ago
0
Encoding variable size input

#12 mathysgrapotte closed 9 months ago
1
test CI #2

#11 alessiovignoli closed 9 months ago
0
test CI #2

#10 alessiovignoli closed 9 months ago
0

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