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flatironinstitute
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deepblast
Neural Networks for Protein Sequence Alignment
BSD 3-Clause "New" or "Revised" License
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Use CPU aligner if no GPUs provided #109
#110
blackwer
closed
1 year ago
1
Make DeepBLAST CPU compatible
#109
mortonjt
closed
1 year ago
1
Distributed training
#108
tymor22
closed
1 year ago
7
WIP : Incorporating ESM2
#107
mortonjt
closed
1 year ago
1
File not found (deleted tm-vec repository)
#106
IrumHu
closed
2 years ago
1
Why was this repository reverted from TM-Vec to DeepBlast?
#105
ArnNag
closed
2 years ago
2
removing tm vec folder
#104
mortonjt
closed
2 years ago
0
Revert "Merge pull request #101 from flatironinstitute/tmvec"
#103
mortonjt
closed
2 years ago
0
Table S2 is missing in preprint
#102
konstin
closed
2 years ago
3
renaming to TM-vec
#101
mortonjt
closed
2 years ago
0
Index Error?
#100
sjanssen2
opened
2 years ago
1
Loading a pretrained model
#99
OliviaViessmann
closed
1 year ago
9
Updating dependencies
#98
mortonjt
closed
2 years ago
0
How to solve the following problems?
#97
mazhichong
closed
1 year ago
2
adding a regression test for hardmax Needleman-Wunsch
#96
sjanssen2
opened
3 years ago
0
subscript error
#95
sjanssen2
opened
3 years ago
0
wrong DP matrix init?
#94
sjanssen2
opened
3 years ago
0
wrong return type
#93
sjanssen2
opened
3 years ago
1
WIP : Adjoint trans
#92
mortonjt
closed
2 years ago
0
adding adjoint method. need to double check math
#91
mortonjt
closed
2 years ago
0
Link paper in readme
#90
nickbhat
closed
3 years ago
1
Weights can't be downloaded with python (User-Agent blocked)
#89
konstin
closed
2 years ago
4
Length bias in scores
#88
konstin
opened
3 years ago
1
Small setup.py fixes
#87
konstin
closed
3 years ago
1
deepblast-search fails with AttributeError: 'function' object has no attribute 'score'
#86
konstin
closed
1 year ago
4
Viterbi cuda
#85
blackwer
closed
3 years ago
2
WIP: K state paired hmm
#84
mortonjt
closed
2 years ago
0
standardizing mali
#83
mortonjt
closed
4 years ago
0
adding slip state and position specific transition probabilities
#82
mortonjt
closed
4 years ago
0
adding CNNs as per #74
#81
VGligorijevic
closed
1 year ago
2
WIP: Differentiable Viterbi algorithm with affine gaps
#80
mortonjt
closed
3 years ago
3
adding score metrics
#79
mortonjt
closed
4 years ago
2
Fasta search
#78
mortonjt
closed
1 year ago
2
Deprecation warning on alignment scores
#77
mortonjt
opened
4 years ago
0
updating version, adding docs, adding pretraining data
#76
mortonjt
closed
4 years ago
0
Off by 1 errors due to gaps at the ends
#75
mortonjt
closed
1 year ago
1
Using CNNs to estimate the gap / match scores
#74
mortonjt
closed
1 year ago
1
Test dataloader
#73
mortonjt
closed
4 years ago
1
Fasta search
#72
mortonjt
closed
4 years ago
1
Search functionality
#71
mortonjt
closed
1 year ago
1
Preprocess
#70
mortonjt
closed
4 years ago
2
weird validation results
#69
mortonjt
closed
4 years ago
0
Adding Priors
#68
mortonjt
closed
4 years ago
1
Add another attention layer
#67
mortonjt
opened
4 years ago
0
Add priors for match / gap scores
#66
mortonjt
opened
4 years ago
0
Percent identity being miscalculated
#65
mortonjt
closed
4 years ago
0
Remove enable_grad statements
#64
mortonjt
closed
4 years ago
1
Reduce memory footprint
#63
mortonjt
opened
4 years ago
0
adding methods for prediction / evaluation
#62
mortonjt
closed
4 years ago
0
Alignment prediction needs to be appropriately trimmed
#61
mortonjt
closed
1 year ago
0
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