issues
search
kuleshov-group
/
caduceus
Bi-Directional Equivariant Long-Range DNA Sequence Modeling
Apache License 2.0
137
stars
14
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Conda environment doesn't work out of the box
#43
edenlum
closed
1 week ago
0
About pretrain GPUS
#42
wyhsleep
closed
1 week ago
3
The TF binding or enhancer activation is orientation independent
#41
freedom-cognit
closed
1 month ago
3
error when using hf model in genomic_benchmark pretrain
#40
lyksj200
closed
1 month ago
4
Does Caduceus Support Variable-Length Inputs in Batches?
#39
yangzhao1230
closed
1 month ago
1
Strange results using mcc on genomic benchmark?
#38
leannmlindsey
closed
1 month ago
2
Difficulty Reproducing Downstream Task Finetune Results with HF Trainer
#37
yangzhao1230
closed
1 month ago
10
"omegaconf.errors.InterpolationKeyError: Interpolation key 'metric' not found" in NucelotideTransformer Benchmark
#36
yangzhao1230
closed
1 month ago
1
Customize dimension and layers
#35
zyj1729
closed
1 month ago
5
loss nan in Genomic Benchmark
#34
multydoffer
opened
1 month ago
8
runtime terminal behaves
#33
yongrenr
closed
1 month ago
3
loss nan in Genomic Benchmark
#32
multydoffer
closed
1 month ago
2
"Unexpected segmentation fault encountered in worker" in multi-gpu training
#31
yangzhao1230
closed
1 month ago
0
Package requirements issue
#30
amelie-iska
closed
1 month ago
3
num_workers=1 warning
#29
leannmlindsey
closed
1 month ago
2
High Storage Requirements for Running vep_embeddings.py in EQTL VEP Analysis
#28
yangzhao1230
closed
1 month ago
11
Error using seq classification with d_model 256
#27
leannmlindsey
closed
1 month ago
5
reproducing the pre-training
#26
GengGengJiuXi
closed
1 month ago
8
Fine Tuning on custom datasets
#25
leannmlindsey
closed
2 months ago
1
question about training lengths
#24
leannmlindsey
closed
2 months ago
1
import quesition
#23
GengGengJiuXi
closed
2 months ago
0
val/loss=nan.0 when training with ddp (distributed data parallel)
#22
leannmlindsey
closed
2 months ago
7
pretraining parameters for caduceus-ph and caduceus w/o equivariance
#21
leannmlindsey
closed
2 months ago
2
Unexpected data loader error during pre-training
#20
zhan8855
closed
2 months ago
3
Unexpected low test accuracy in reproducing dummy_mouse_enhancers_ensembl experiments
#19
zhan8855
closed
2 months ago
4
Slurm scripts for downstream tasks
#18
zhan8855
closed
2 months ago
2
The size of the vocab is inconsistent with the output dimension of the lm_head
#17
jaminzzz
closed
2 months ago
1
Error when reproducing the pre-training
#16
richardsun-voyager
opened
2 months ago
12
Inconsistency between pre-training slurm scripts and the training details in the paper
#15
zhan8855
closed
2 months ago
2
How to load pre-trained model for fine-tuning?
#14
zhan8855
closed
2 months ago
6
CPU
#13
yongrenr
closed
2 months ago
3
Small typo in wrapper scripts
#12
leannmlindsey
closed
3 months ago
1
Question about pre-training
#11
leannmlindsey
closed
2 months ago
5
Update README.md
#10
eltociear
closed
3 months ago
0
Issues with genomic_benchmark Experiment code in Caduceus
#9
xwx1999
closed
3 months ago
3
1.9million parameters, 470K parameters Caduceus model query
#8
MarcAmil30
closed
3 months ago
1
Something about specifying the GPU
#7
yongrenr
closed
3 months ago
5
What does the length extension mean for pre-training dataset?
#6
KatarinaYuan
closed
3 months ago
1
There seems a bug of related to d_model in class "CaduceusForSequenceClassification" for the RCPS case
#5
qiaoqiaoLF
closed
3 months ago
4
Unable to run the model on input sequence with length of 131072
#4
qiaoqiaoLF
closed
3 months ago
4
Questions about experimental code
#3
yongrenr
closed
3 months ago
5
LLVM ERROR: Cannot select: intrinsic %llvm.nvvm.shfl.sync.bfly.i32
#2
Jellymoon
closed
3 months ago
9
Refactor/create package
#1
jorenretel
opened
4 months ago
3