Enhance PARM_predict.py with error handling and evaluation improvements - #22

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luciabarb wants to merge 76 commits into

vansteensellab:mainfrom

Commits on Apr 1, 2026

Update the FEATname to avoid error
luciabarb
authored
e3edfb2

Commits on Apr 13, 2026

Commits on Apr 14, 2026

adding start_motif to avoid error
luciabarb
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199a551
add internal evaluation
luciabarb
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4c1ffe6
Fix import error of evaluation model
luciabarb
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cd141ca
fix importing libraries
luciabarb
committed
9e305ed
fix importing libraries
luciabarb
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aab6695
add info documentation
luciabarb
committed
47f15e4
adapt for multiple heads
luciabarb
committed
cdfe307
change default argument batch size
luciabarb
committed
8d9c229
change default argument batch size
luciabarb
committed
400fb66
change default argument batch size
luciabarb
committed
5e7a5e3

Commits on Apr 17, 2026

Add plots for evaluation of forward and reverse motif
luciabarb
committed
70ef307
Add plots for evaluation of forward and reverse motif
luciabarb
committed
bd6b4b6

Commits on Apr 21, 2026

make normalization_method (Log2RPM) a parameter for model evaluation
vhfsantos
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471e763
make normalization_method (Log2RPM) a parameter for model evaluation
vhfsantos
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3582d54
Add internal versioning control
vhfsantos
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d0138f5
Add internal versioning control
vhfsantos
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5d29c75
Make filter size a parameter for model evaluation
vhfsantos
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267ce38
Handle TSS_EnhA in feature selection in get_test_fold_predictions
vhfsantos
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69dc1a3
Version bump
vhfsantos
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643d1a7
Merge pull request #1 from luciabarb/vini_dev
luciabarb
authored
3cba854

Commits on Apr 22, 2026

Fixing issue calling hits while plotting
luciabarb
committed
4912e44
Merge branch 'main' of https://github.com/luciabarb/PARM_internal_use
luciabarb
committed
e95361b
Fixing issue calling hits while plotting
luciabarb
committed
940ae95
Merge branch 'main' into main
luciabarb
authored
c01c715

Commits on May 14, 2026

Add double head options in predictions
luciabarb
committed
5d3f965

Commits on May 15, 2026

Add double head options in predictions
luciabarb
committed
886d8b3
Add double head options in predictions
luciabarb
committed
514b848

Commits on May 19, 2026

Update pandas loading error
luciabarb
committed
c552a46

Commits on May 22, 2026

Add MIchiel enhancers to feature selection; fix compatibility with new torch version
vhfsantos
committed
521a9d3
Add michiel enha to model evaluation
vhfsantos
committed
82ce12c
fix import issue
vhfsantos
committed
1b22c09

Commits on May 25, 2026

Add number of conv blocks to model evaluation
vhfsantos
committed
860966a

Commits on May 26, 2026

Merge pull request #2 from luciabarb/dev
luciabarb
authored
8a71071

Commits on Jun 3, 2026

New evaluation step for SNPs
luciabarb
committed
aed2fca
Merge branch 'main' of https://github.com/luciabarb/PARM_internal_use
luciabarb
committed
7d0a487
New evaluation step for SNPs
luciabarb
committed
a805d22
New evaluation step for SNPs
luciabarb
committed
3ca95ce

Commits on Jun 4, 2026

fix taking abs values for evaluation step for SNPs
luciabarb
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4477a71
adding concordance for evaluation step for SNPs
luciabarb
committed
cfe5f52
Update pandas loading error
luciabarb
committed
79c2100

Commits on Jun 5, 2026

Commits on Jun 15, 2026

add michiel enha to test fold predictions
vhfsantos
committed
37eea19

Commits on Jun 23, 2026

Merge pull request #3 from luciabarb/dev_vini
luciabarb
authored
756e9c8
adapt for multiple heads
luciabarb
committed
2d0af40
adapt for multiple heads
luciabarb
committed
35c5a62
bump version to 0.2.5+internal.16
vhfsantos
committed
be0bd39
Remove weird import, bump new build
vhfsantos
committed
0b1e21f

Commits on Jun 24, 2026

Fix the double head model for loading data
luciabarb
committed
1e07ade
fix error adapt for multiple heads
luciabarb
committed
38d8f47
Plot model's performance also for training loop
vhfsantos
committed
836f749
Implement error handling for missing data
luciabarb
authored
9868837

Commits on Jul 1, 2026

Commits on Jul 9, 2026

Add regularization only in specific heads
luciabarb
committed
94df7a7
Merge branch 'main' of https://github.com/luciabarb/PARM_internal_use
luciabarb
committed
11ab28e

Commits on Jul 27, 2026

Add cuda checking in predictions
luciabarb
committed
299aef0
fix support for different motif DBs for PARM plot
vhfsantos
committed
65c94f0

Commits on Aug 4, 2026

Remove celltype arg from mutagenesis
vhfsantos
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2a9d835
Merge pull request #5 from luciabarb/vini
vhfsantos
authored
d1de96c
Fix parameters for loss type and convolution blocks
vhfsantos
committed
30d43b2
fix typo on n_blocks
vhfsantos
committed
bdcf4f1
fix typo on arg
vhfsantos
committed
6c2c9c4

Commits on Aug 5, 2026

Calls plot with motif_db
vhfsantos
committed
250c775