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frederikkemarin
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BEND
Benchmarking DNA Language Models on Biologically Meaningful Tasks
BSD 3-Clause "New" or "Revised" License
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Clarification multi_hot
#65
tdsone
closed
1 week ago
3
Embedder logits
#64
fteufel
closed
1 week ago
0
dnabert unk offsetting bug fix
#63
fteufel
closed
1 week ago
0
Cannot run Hyena-DNA
#62
HelloWorldLTY
closed
1 week ago
1
Enable embedders to return logits
#61
fteufel
closed
1 week ago
1
A bug in the readme file
#60
HelloWorldLTY
closed
2 weeks ago
3
nucleotide transformer embedding
#59
hongruhu
closed
1 month ago
1
Incorrect DNABERT behavior?
#58
canallee
closed
1 month ago
4
Slow Training for Downstream Tasks with Low GPU Utilization
#57
1159556229
closed
3 months ago
2
Clarification on MCC Calculation Method
#56
yangzhao1230
closed
3 months ago
2
Discrepancy in Genome Versions Used for Chromatin Accessibility Compared to Other ENCODE-Based Studies
#55
yangzhao1230
closed
4 months ago
1
Fix broken link
#54
tdsone
opened
5 months ago
0
Add missing packages to requirements.txt
#53
tdsone
opened
5 months ago
1
Inconsistent number of classes for histone modification task
#52
kirill-vish
closed
6 months ago
2
dirty data exists in variant dataset
#51
yangzhao1230
closed
6 months ago
3
Add GROVER LM + fix some bugs
#50
fteufel
closed
8 months ago
0
'N' exists in variant datasets
#49
yangzhao1230
closed
8 months ago
2
Issue with Separator in retrieve_from_bed.py Causing Misalignment in variant_effects_disease.bed
#48
yangzhao1230
closed
8 months ago
1
Update hydra.rst
#47
eltociear
opened
9 months ago
0
Enhancer annotation hdf5 issue
#46
gonzalobenegas
closed
10 months ago
3
Random seed
#45
gonzalobenegas
opened
10 months ago
1
Error with train_on_task.py
#44
gonzalobenegas
closed
11 months ago
4
Enable NT V2
#43
fteufel
closed
11 months ago
0
use webdataset
#42
fteufel
closed
11 months ago
0
Merge docs to main
#41
fteufel
closed
11 months ago
0
Chunk embedding
#40
frederikkemarin
closed
11 months ago
0
Crash at higher `wandb` versions
#39
fteufel
closed
11 months ago
1
Better handling of specified chunks
#38
fteufel
closed
11 months ago
0
Chunk embedding
#37
frederikkemarin
closed
11 months ago
0
enable basset training
#36
fteufel
closed
11 months ago
0
Skip bad embeddings
#35
fteufel
closed
11 months ago
0
update
#34
fteufel
closed
11 months ago
0
Added supervised resnet embedding-dim
#33
frederikkemarin
closed
1 year ago
0
resnet supervised in conf
#32
frederikkemarin
closed
1 year ago
0
Supervised resnet config
#31
frederikkemarin
closed
1 year ago
0
Restructure configs
#30
frederikkemarin
closed
1 year ago
0
Feature tf compression
#29
frederikkemarin
closed
1 year ago
0
Multirun embedding
#28
frederikkemarin
closed
1 year ago
0
Add documentation
#27
fteufel
closed
1 year ago
0
update variant effect file names
#26
fteufel
closed
1 year ago
0
update variant effect commands
#25
fteufel
closed
1 year ago
0
delete local paths
#24
fteufel
closed
1 year ago
0
update
#23
fteufel
closed
1 year ago
0
get task confs
#22
fteufel
closed
1 year ago
0
Bend dev
#21
fteufel
closed
1 year ago
1
Merge pull request #18 from frederikkemarin/bend-dev
#20
fteufel
closed
1 year ago
0
update bend-dev
#19
fteufel
closed
1 year ago
0
delete evaluate.py
#18
fteufel
closed
1 year ago
0
Add DNABert2Embedder
#17
fteufel
closed
1 year ago
1
Run Enhancer Annotation task with new embedder
#16
frederikkemarin
closed
1 year ago
0
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