nowittynamesleft protein_function_description issues

nowittynamesleft / protein_function_description

Describing protein sets' functions with natural language.

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Improve generation with oversmoothing regularization

#31 nowittynamesleft opened 2 years ago
1
Length transform should be described in methods section

#30 nowittynamesleft closed 1 year ago
0
Sample distinct sets of proteins with the same common functions of each set

#29 nowittynamesleft closed 2 years ago
0
Related work

#28 nowittynamesleft closed 1 year ago
0
Write motivations for protein function description model

#27 nowittynamesleft closed 2 years ago
0
How to handle the "multiple answers" problem

#26 nowittynamesleft opened 2 years ago
0
Clean up train_and_test_model.py

#25 nowittynamesleft closed 1 year ago
0
Make all prediction and training batched/vectorized

#24 nowittynamesleft closed 2 years ago
1
Length converter needs to be looked through carefully for any bugs

#23 nowittynamesleft closed 2 years ago
0
Clean up code

#22 nowittynamesleft closed 2 years ago
1
Zero-shot protein function prediction performance is bad

#21 nowittynamesleft closed 2 years ago
3
label smoothing

#20 nowittynamesleft closed 2 years ago
1
large scale prediction with disBatch doesn't use GPU much (0-3% mostly) vs. using it on a single GPU uses 10-50%

#19 nowittynamesleft opened 2 years ago
1
early stopping with validation loss

#18 nowittynamesleft closed 2 years ago
0
scheduled sampling

#17 nowittynamesleft opened 2 years ago
4
length penalty (or rather shortness penalty) in beam search

#16 nowittynamesleft closed 2 years ago
1
byte-pair encoding

#15 nowittynamesleft closed 2 years ago
1
Checkpointing and restarting

#14 nowittynamesleft closed 2 years ago
0
Make pytorch lightning logging work with tensorboard or some other thing

#13 nowittynamesleft opened 2 years ago
1
Enable Multi-gpu training

#12 nowittynamesleft closed 1 year ago
1
Evaluation

#11 nowittynamesleft closed 2 years ago
5
add <start> and <end> tokens to GO term descriptions

#10 nowittynamesleft closed 2 years ago
0
inference code: greedy decoder, and beam search

#9 nowittynamesleft closed 2 years ago
2
GO preprocessing and fasta alignment scripts

#8 nowittynamesleft closed 2 years ago
0
new dataloader for NMT code: length-transform, GO term selection and protein sequence sampling

#7 nowittynamesleft closed 2 years ago
1
create 'seqCLIP' python package

#6 VGligorijevic opened 3 years ago
2
pytorch lightning integration

#5 nowittynamesleft closed 2 years ago
4
add neural translation model as keyword/GO description generator

#4 nowittynamesleft closed 2 years ago
1
separate code into more specific files

#3 nowittynamesleft closed 3 years ago
2
adding transformer layers

#2 VGligorijevic closed 3 years ago
0
top-10 accuracy reduces after first epoch

#1 nowittynamesleft closed 2 years ago
1