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EnsemblGSOC
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Ensembl-Repeat-Identification
A Deep Learning repository for predicting the location and type of repeat sequence in genome.
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Change the readme for gsoc
#57
yangtcai
closed
1 year ago
0
merge log.md to README
#56
williamstark01
opened
1 year ago
1
Fix test
#55
yangtcai
closed
1 year ago
1
Add mse metrics
#54
yangtcai
closed
1 year ago
0
predict a single class for all bases in a non-repeat subsequence
#53
williamstark01
opened
1 year ago
0
Log to file
#52
yangtcai
closed
1 year ago
1
Seq2seqmodel
#51
yangtcai
closed
1 year ago
0
test a simple Transformer network instead of DETR
#50
yangtcai
closed
1 year ago
0
Potential optimization of our model.
#49
yangtcai
opened
1 year ago
3
Add more metrics
#48
yangtcai
opened
1 year ago
1
print sample of predictions
#47
yangtcai
closed
1 year ago
1
Generate new datasets
#46
yangtcai
closed
1 year ago
1
print sample of predictions
#45
williamstark01
closed
1 year ago
2
split dataset to training, validation, and test sets
#44
williamstark01
closed
1 year ago
0
Refactor DETR model to pl lightning
#43
yangtcai
closed
1 year ago
7
missing arguments
#42
williamstark01
closed
1 year ago
4
Use label encoding and embedding
#41
yangtcai
closed
1 year ago
0
simple way to cache chromosome repeats lists
#40
williamstark01
closed
2 years ago
1
d_model parameter
#39
williamstark01
opened
2 years ago
8
submit training jobs to cluster GPU nodes
#38
williamstark01
closed
2 years ago
0
add mAP metric
#37
yangtcai
closed
2 years ago
4
customizable training dataset
#36
williamstark01
closed
2 years ago
1
organize hyperparameters
#35
williamstark01
closed
1 year ago
3
Deal with overfitting
#34
yangtcai
opened
2 years ago
4
Repeat list should contain genome start, not index
#33
yangtcai
closed
2 years ago
1
optimize segment length
#32
williamstark01
opened
2 years ago
1
selection of repeat type
#31
williamstark01
closed
1 year ago
5
repeat families and repeat type statistics
#30
williamstark01
closed
2 years ago
0
dataset statistics
#29
williamstark01
closed
2 years ago
2
Filter the no repeats fragments and add test stage
#28
yangtcai
closed
2 years ago
2
description of network architecture
#27
williamstark01
opened
2 years ago
0
explore PyTorch Lightning for the training loop
#26
williamstark01
closed
1 year ago
1
Implement evaluation metric
#25
yangtcai
closed
2 years ago
0
Training stage
#24
yangtcai
closed
2 years ago
1
Fix the labels
#23
yangtcai
closed
2 years ago
6
Simple data analysis about repeat sequence.
#22
yangtcai
closed
2 years ago
3
Convert the sequence to upper and make overlaps as hyperparameters
#21
yangtcai
closed
2 years ago
0
updates
#20
williamstark01
closed
2 years ago
3
Dealing with forward- and reverse-strand in datasets
#19
yangtcai
opened
2 years ago
2
Add Hungarian Matcher
#18
yangtcai
closed
2 years ago
3
use pyfaidx for FASTA sequences in Dataset and DataLoader
#17
yangtcai
closed
2 years ago
3
Implement Loss function
#16
yangtcai
closed
2 years ago
1
Implement Hungarian matcher
#15
yangtcai
closed
2 years ago
1
Constuct the DETR model
#14
yangtcai
closed
2 years ago
1
Add DETR main model
#13
yangtcai
closed
2 years ago
3
Implement neural network and training pipeline prototype
#12
williamstark01
closed
2 years ago
3
some refactoring and updates
#11
williamstark01
closed
2 years ago
2
generate repeats statistics
#10
williamstark01
opened
2 years ago
2
Implement sequence encoding, eg one hot
#9
williamstark01
closed
2 years ago
1
Implement dataloader function
#8
williamstark01
closed
2 years ago
1
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