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DeepGraphLearning
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GearNet
GearNet and Geometric Pretraining Methods for Protein Structure Representation Learning, ICLR'2023 (https://arxiv.org/abs/2203.06125)
MIT License
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How to pass the protein pdb file to the released model weight: (mc_gearnet_edge.pth)
#69
Tizzzzy
opened
1 month ago
1
How to check the representation of a 3D structure data
#68
Tizzzzy
opened
1 month ago
0
How to Fine-Tune My Pretrained Model on Downstream Tasks
#67
fourier20laplace
closed
1 month ago
0
Working with batches of proteins with different sizes
#66
mpedraza98
opened
2 months ago
0
Why is the Batch Size for Downstream Tasks Set to 2? It Seems Quite Slow
#65
minjiecheng
opened
2 months ago
0
About data_setting from species_start: 0 to species_end: 22 of alphafolddb_v2
#64
minjiecheng
opened
3 months ago
0
how Fmax and AUPRC are calculated?
#63
Qzhangyx
opened
4 months ago
0
Problems in using "fold_mc_gearnet_edge_ieconv.pth"
#62
haniulu
opened
5 months ago
0
Problems in using FC dataset
#61
Yangqy-16
opened
6 months ago
2
Seeking help for dataset
#60
zsc2003
opened
6 months ago
4
RuntimeError: shape '[31, 147]' is invalid for input of size 651 in extracting embbeding from pdb files
#59
blazexpire
opened
9 months ago
6
Extract the structure embeddings
#58
Jerry888Chen
opened
9 months ago
1
What is input (Tensor) – input node representations for GearNet
#57
Heisenburger2020
opened
9 months ago
1
TypeError: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases
#56
blazexpire
closed
10 months ago
2
Inference on PDB file by conversion into torchdrug.data.PackedProtein or TorchDrug.data.Protein
#55
gtamer2
closed
10 months ago
5
Passing CIF files directly into GearNet?
#54
gtamer2
closed
11 months ago
2
Asking about implementation of series connection of PLM & GNN in the FusionNetwork.
#53
yunxiaoliCB
closed
11 months ago
2
Custom dataset. Data preprocessing
#52
Chicky-Picky
opened
11 months ago
1
Node classification tasks
#51
mpedraza98
opened
1 year ago
3
secondary structure evaluation
#50
ejko99
closed
9 months ago
2
Pre-trained weight for ESM-GearNet
#49
hxu105
opened
1 year ago
4
Pre-training on different datasets
#48
DuanhaoranCC
closed
1 year ago
1
RuntimeError: addmm: Argument #3 (dense), for training ESM_GearNet on EC
#47
hxu105
closed
1 year ago
0
Solution when alpha carbon coordinate is missing
#46
YanjingLiLi
opened
1 year ago
1
A dataset not found when I run "python script/pretrain.py -c config/pretrain/mc_gearnet_edge.yaml --gpus [0]"
#45
horacehht
opened
1 year ago
5
confusion on epochs
#44
Siirui
opened
1 year ago
3
Non-deterministic embeddings
#43
andrew7shen
closed
1 year ago
2
atom view
#42
karel-w
opened
1 year ago
1
The pre-trained GearNet-Edge model for Fold Classification
#41
arantir123
opened
1 year ago
5
Edge_list set to [0,0,0]
#40
andrew7shen
closed
1 year ago
2
About Dataset
#39
DuanhaoranCC
closed
1 year ago
2
a question about the downstream tasks
#38
onlyonewater
closed
1 year ago
2
asking about how to obtain the new graph based on contrast learning
#37
Yanara-Tian
closed
1 year ago
6
An error occurring when using the StepLR scheduler on the FOLD3D dataset
#36
arantir123
closed
1 year ago
2
Asking about the default config option `save_interval: 5` when pretraining on AlphaDB
#35
yunxiaoliCB
closed
1 year ago
2
Add Dockerfile
#34
inc0
closed
1 year ago
1
none
#33
Yanara-Tian
closed
1 year ago
0
Attribution information of the Fold3D dataset
#32
YanjingLiLi
closed
1 year ago
1
Training details of basic GearNet on Fold prediction task
#31
YanjingLiLi
closed
1 year ago
7
TypeError: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases
#30
Brian-hongyan
closed
1 year ago
2
max_length=100 for TruncateProtein in pretrain config files
#29
yunxiaoliCB
closed
1 year ago
2
What information that the hidden dimensions respectively represent
#28
BenardChase
closed
1 year ago
3
Explainability
#27
MichailChatzianastasis
opened
1 year ago
1
RuntimeError: CUDA error: the provided PTX was compiled with an unsupported toolchain.
#26
dabianzhixing
closed
1 year ago
4
Error:General Union types are not currently supported. Only Union[T, NoneType] (i.e. Optional[T]) is supported.: File "/home/lvqy/anaconda3/envs/ZernikeMetric/lib/python3.8/site-packages/torch_cluster/rw.py", line 18
#25
dabianzhixing
closed
1 year ago
1
shape mismatch
#24
pearl-rabbit
closed
1 year ago
4
how to use the GearNet to extract the protein feature?
#23
onlyonewater
closed
1 year ago
15
How to download and preprocess the PDB experimentally-determined protein.
#22
Dreamer312
closed
1 year ago
2
Error in Fold3D config file
#21
valegiunchiglia
closed
1 year ago
2
error in mc_esm_gearnet
#20
hxu105
opened
1 year ago
3
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