lgragert nn-sero-pytorch issues

lgragert / nn-sero-pytorch

PyTorch version of neural network HLA serology prediction

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Store latest stable version of repo

#43 gbiagini closed 2 years ago
0
Broad-split serology assignments are inconsistent.

#42 gbiagini closed 3 years ago
1
Feature/imputation

#41 gbiagini closed 3 years ago
0
Rewrite NN using vanilla PyTorch

#40 gbiagini opened 3 years ago
0
Bring in changes from master branch

#39 gbiagini closed 4 years ago
0
Feature/imputation

#38 gbiagini closed 4 years ago
0
Check to see if using the `_nuc.msf` files from ANHIG/IMGTHLA is sufficient for getting only the coding sequences

#37 gbiagini closed 4 years ago
0
Feature/imputation

#36 gbiagini closed 4 years ago
0
Rework imputation algorithm to function based on nucleotide sequence instead of AA sequence

#35 gbiagini closed 4 years ago
2
Feature/imputation

#34 gbiagini closed 4 years ago
0
Imputation of missing HLA sequences

#33 gbiagini closed 4 years ago
1
Update feature/imputation

#32 gbiagini closed 4 years ago
0
Inconsistencies between new and old polymorhphic AAs

#31 gbiagini closed 4 years ago
1
Retrain and test on new serology labels based on AA motif patterns.

#30 lgragert opened 4 years ago
0
Measure performance using test set instead of just making predictions on test set

#29 lgragert closed 3 years ago
0
NMDP HLA Dictionary refresh

#28 lgragert opened 4 years ago
0
Determine polymorphism limit of R-SNNS

#27 lgragert closed 3 years ago
1
Recreation

#26 gbiagini closed 4 years ago
0
Restore original training and validation sets so that new data is entirely in the testing set

#25 gbiagini closed 4 years ago
1
minor change to fix the sorting of the train, validation, and test sets.

#24 gbiagini closed 4 years ago
0
Update nn-sero-pytorch/recreation for generation of .pat files

#23 gbiagini closed 4 years ago
0
compare predictions from R-SNNS to any lab-generated serology types that have been confirmed for the testing set

#22 gbiagini closed 3 years ago
1
create .pat files to run R-SNNS on new data

#21 gbiagini closed 4 years ago
1
merge and add more information to summary table

#20 gbiagini closed 3 years ago
1
assign alleles to training or validation sets appropriately

#19 gbiagini closed 4 years ago
1
add in broad specificities for serology labels with only specific specificities to new training/validation sets

#18 gbiagini closed 4 years ago
1
Try nearest neighbor

#17 gbiagini opened 4 years ago
0
Try Gaussian process regression

#16 gbiagini opened 4 years ago
0
Try Support Vector Machines (SVM)

#15 gbiagini opened 4 years ago
0
Random Forest

#14 gbiagini closed 3 years ago
1
PyTorch-Optimized: Autoencoder

#13 gbiagini opened 4 years ago
0
PyTorch-Optimized: Cross-Entropy Loss

#12 gbiagini closed 3 years ago
1
PyTorch-Optimized: Stochastic Gradient Descent (SGD)

#11 gbiagini closed 3 years ago
0
Update training/validation/test set using latest WHO serology assignments

#10 gbiagini closed 4 years ago
1
Port 'uli' Perl script to Python and code all alleles in the IMGT/HLA v3.39.0 into AA polymorphism vectors using the aa_matching Python modules

#9 gbiagini closed 4 years ago
1
Modify aa_matching.py to load latest MSF files (HLADB v3.39.0)

#8 gbiagini closed 4 years ago
1
Bringing testground up to date

#7 gbiagini closed 4 years ago
0
Recreation

#6 gbiagini closed 4 years ago
0
Develop a strategy to implement a random forest classifier with SKLearn

#5 gbiagini closed 4 years ago
0
Develop a strategy to implement an SVM (Support Vector Machine) with SKLearn

#4 gbiagini closed 4 years ago
0
Modify the parser to generate CSV files with the information for each locus

#3 gbiagini closed 4 years ago
1
Update parse.py

#2 gbiagini closed 4 years ago
0
Fix

#1 gbiagini closed 4 years ago
0