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set out_dim dynamically #74

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set out_dim dynamically #74

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@aditya0by0 aditya0by0 commented Feb 23, 2025 •
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Dependency with below PRs (should only be merged after below PRs are merged)

@aditya0by0
script to evaluate go predictions
bdba442
@aditya0by0
Merge branch 'dev' into protein_prediction
264bd94
@aditya0by0
add fmax to evaluation script
6c0fce1
@aditya0by0
Merge branch 'dev' into protein_prediction
154e827
@aditya0by0
add base code for deep_go data migration
58ae92d 
- migration from deep go format to chebai->go_uniprot format
@aditya0by0
varry fmax threshold as per paper
78a38de
@aditya0by0
go_uniprot: add sequence len to docstring
3a4e007
@aditya0by0
update experiment evidence codes as per DeepGo SE
227a014 
- #36 (comment)
@aditya0by0
Merge branch 'dev' into protein_prediction
33436e8
@aditya0by0
consIder X as a valid amino acid as per DeepGO-SE
c6d60cd 
- #36 (comment)
@aditya0by0
deepgo se mirgration : add class to migrate
ca5461f
@aditya0by0
Merge branch 'dev' into protein_prediction
af54954
@aditya0by0
migration: rectify errors
dfb9430
@aditya0by0
protein trigram containing tokenS with X
085b13b 
- #36 (comment)
@aditya0by0
protein token unigram contain X
3e0bae0 
- #36 (comment)
@aditya0by0
add migration for deepgo1 - 2018 paper
99b5af1
@aditya0by0
deepgo1: create non-exclusive val set as a placeholder
a15d492
@aditya0by0
deepgo1: further split train set into train and val for
e0a8524 
- +migration structure changes
@aditya0by0
migration script update
093be28
@aditya0by0
add classes to use migrated deepgo data
14db9d6
@aditya0by0
deepgo: minor code change
8922d4d
@aditya0by0
modify prints to display actual file name
796356c
@aditya0by0
create sub dir for deego dataset and move rel files
3c11a69
@aditya0by0
update imports as per new deepGO dir
2b571c5
@aditya0by0
update import dir for pretrain test
f75e30b
@aditya0by0
migration fix : truncate seq and save data with labels
1b8b270
@aditya0by0
Delete protein_protein_interactions.py
bcda11c
@aditya0by0
migration: replace invalid amino acid with "X" notation
85c47a0 
- #64 (comment)
@aditya0by0
update deepgo configs
fbb5c58
@aditya0by0
add esm2 reader for deepGO
272446d
aditya0by0 and others added 26 commits January 24, 2025 15:21
@aditya0by0
scope: add documentation
6735e41
@aditya0by0
scope: add OverX classes and their derivaties
c3ba8da
@aditya0by0
scope: modify select classes and labels save operation
764b812
@aditya0by0
scope: data config
b23f1f6
@aditya0by0
deepgo: remove label_number from docstring
6370572
@aditya0by0
ffn: update for as per deepgo2 mlp architecture
191c979
@aditya0by0
scope: map invalid amino acids to "X"
b7ca0e5
@sfluegel05
fix MLPBlock hidden_dim
ad24fa7
@aditya0by0
esm2 reader: save reader to default global data dir
357752f
@aditya0by0
configs: move configs to data specific sub-dir
a52d8de
@sfluegel05
adding SCOPe50 dataset
b2f51f9
@sfluegel05
add scope50 config
e0bbb0e
@sfluegel05
Merge branch 'protein_prediction' of https://github.com/ChEB-AI/pytho…
e3659cb 
…n-chebai into protein_prediction
@aditya0by0
scope: version number should str not float
22aa985 
- as we are not doing any processing for number so its compatible to pass it as str
@aditya0by0
Merge branch 'protein_prediction' of https://github.com/ChEB-AI/pytho…
45c1015 
…n-chebai into protein_prediction
@aditya0by0
scope: data filtering update
d3fd0f2 
- consider proteins domain in the dataset which maps to any selected node irrespective of the hierarchy level
@aditya0by0
scope: avoid data fragmentation and add progress bar
c791893
@aditya0by0
scope: vectorized operation instead of df.itterows
aad16d9 
- https://stackoverflow.com/a/24871316/17626445
@aditya0by0
scope: fix multiple chain filtering
13b8795
@aditya0by0
scope: tutorial for scope data exploration
4572272
@aditya0by0
scope: update tutorial
eba0417
@aditya0by0
scope: add more scope details to tutorial
dad6f76
@aditya0by0
minor changes: deepgo configs + scope
fd6dd01
@aditya0by0
datamodule: store num_of_labels to hparms
acd487e
@aditya0by0
lightning module: retrieve num_of_labels from data module
9a48fdf
@aditya0by0
fnn: move layer initializaton to setup method
381452e
@aditya0by0 aditya0by0 self-assigned this Feb 23, 2025
@aditya0by0 aditya0by0 linked an issue Feb 23, 2025 that may be closed by this pull request
Generate out_dim dynamically #73
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Generate out_dim dynamically
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@aditya0by0 @sfluegel05