flatironinstitute/deepblast issues and pull requests

#169 - Test dataset for CATHS40

Issue - State: open - Opened by haniulu 24 days ago

#167 - Comparison between two sequences

Issue - State: closed - Opened by AIM132 about 2 months ago - 5 comments

#100 - Index Error?

Issue - State: open - Opened by sjanssen2 over 2 years ago - 1 comment

#100 - Index Error?

Issue - State: open - Opened by sjanssen2 over 2 years ago - 1 comment

#99 - Loading a pretrained model

Issue - State: closed - Opened by OliviaViessmann over 2 years ago - 9 comments

#99 - Loading a pretrained model

Issue - State: closed - Opened by OliviaViessmann over 2 years ago - 9 comments

#98 - Updating dependencies

Pull Request - State: closed - Opened by mortonjt almost 3 years ago

#98 - Updating dependencies

Pull Request - State: closed - Opened by mortonjt almost 3 years ago

#97 - How to solve the following problems?

Issue - State: closed - Opened by mazhichong almost 3 years ago - 2 comments

#97 - How to solve the following problems?

Issue - State: closed - Opened by mazhichong almost 3 years ago - 2 comments

#96 - adding a regression test for hardmax Needleman-Wunsch

Pull Request - State: open - Opened by sjanssen2 almost 4 years ago

#96 - adding a regression test for hardmax Needleman-Wunsch

Pull Request - State: open - Opened by sjanssen2 almost 4 years ago

#95 - subscript error

Issue - State: open - Opened by sjanssen2 almost 4 years ago

#95 - subscript error

Issue - State: open - Opened by sjanssen2 almost 4 years ago

#94 - wrong DP matrix init?

Issue - State: open - Opened by sjanssen2 almost 4 years ago

#94 - wrong DP matrix init?

Issue - State: open - Opened by sjanssen2 almost 4 years ago

#93 - wrong return type

Issue - State: open - Opened by sjanssen2 almost 4 years ago - 1 comment

#93 - wrong return type

Issue - State: open - Opened by sjanssen2 almost 4 years ago - 1 comment

#92 - WIP : Adjoint trans

Pull Request - State: closed - Opened by mortonjt about 4 years ago

#92 - WIP : Adjoint trans

Pull Request - State: closed - Opened by mortonjt about 4 years ago

#91 - adding adjoint method. need to double check math

Pull Request - State: closed - Opened by mortonjt about 4 years ago

#91 - adding adjoint method. need to double check math

Pull Request - State: closed - Opened by mortonjt about 4 years ago

#90 - Link paper in readme

Issue - State: closed - Opened by nickbhat about 4 years ago - 1 comment

#90 - Link paper in readme

Issue - State: closed - Opened by nickbhat about 4 years ago - 1 comment

#89 - Weights can't be downloaded with python (User-Agent blocked)

Issue - State: closed - Opened by konstin about 4 years ago - 4 comments

#89 - Weights can't be downloaded with python (User-Agent blocked)

Issue - State: closed - Opened by konstin about 4 years ago - 4 comments

#88 - Length bias in scores

Issue - State: open - Opened by konstin about 4 years ago - 1 comment

#88 - Length bias in scores

Issue - State: open - Opened by konstin about 4 years ago - 1 comment

#87 - Small setup.py fixes

Pull Request - State: closed - Opened by konstin about 4 years ago - 1 comment

#87 - Small setup.py fixes

Pull Request - State: closed - Opened by konstin about 4 years ago - 1 comment

#86 - deepblast-search fails with AttributeError: 'function' object has no attribute 'score'

Issue - State: closed - Opened by konstin about 4 years ago - 4 comments

#86 - deepblast-search fails with AttributeError: 'function' object has no attribute 'score'

Issue - State: closed - Opened by konstin about 4 years ago - 4 comments

#85 - Viterbi cuda

Pull Request - State: closed - Opened by blackwer over 4 years ago - 2 comments

#85 - Viterbi cuda

Pull Request - State: closed - Opened by blackwer over 4 years ago - 2 comments

#84 - WIP: K state paired hmm

Pull Request - State: closed - Opened by mortonjt over 4 years ago

#84 - WIP: K state paired hmm

Pull Request - State: closed - Opened by mortonjt over 4 years ago

#83 - standardizing mali

Pull Request - State: closed - Opened by mortonjt over 4 years ago

#83 - standardizing mali

Pull Request - State: closed - Opened by mortonjt over 4 years ago

#82 - adding slip state and position specific transition probabilities

Pull Request - State: closed - Opened by mortonjt over 4 years ago

#82 - adding slip state and position specific transition probabilities

Pull Request - State: closed - Opened by mortonjt over 4 years ago

#81 - adding CNNs as per #74

Pull Request - State: closed - Opened by VGligorijevic over 4 years ago - 2 comments

#81 - adding CNNs as per #74

Pull Request - State: closed - Opened by VGligorijevic over 4 years ago - 2 comments

#80 - WIP: Differentiable Viterbi algorithm with affine gaps

Pull Request - State: closed - Opened by mortonjt over 4 years ago - 3 comments

#79 - adding score metrics

Pull Request - State: closed - Opened by mortonjt over 4 years ago - 2 comments
Labels: URGENT

#79 - adding score metrics

Pull Request - State: closed - Opened by mortonjt over 4 years ago - 2 comments
Labels: URGENT

#78 - Fasta search

Pull Request - State: closed - Opened by mortonjt over 4 years ago - 2 comments

#78 - Fasta search

Pull Request - State: closed - Opened by mortonjt over 4 years ago - 2 comments

#77 - Deprecation warning on alignment scores

Issue - State: open - Opened by mortonjt over 4 years ago

#77 - Deprecation warning on alignment scores

Issue - State: open - Opened by mortonjt over 4 years ago

#76 - updating version, adding docs, adding pretraining data

Pull Request - State: closed - Opened by mortonjt over 4 years ago

#76 - updating version, adding docs, adding pretraining data

Pull Request - State: closed - Opened by mortonjt over 4 years ago

#75 - Off by 1 errors due to gaps at the ends

Issue - State: closed - Opened by mortonjt over 4 years ago - 1 comment

#75 - Off by 1 errors due to gaps at the ends

Issue - State: closed - Opened by mortonjt over 4 years ago - 1 comment

#74 - Using CNNs to estimate the gap / match scores

Issue - State: closed - Opened by mortonjt over 4 years ago - 1 comment

#74 - Using CNNs to estimate the gap / match scores

Issue - State: closed - Opened by mortonjt over 4 years ago - 1 comment

#73 - Test dataloader

Pull Request - State: closed - Opened by mortonjt over 4 years ago - 1 comment

#73 - Test dataloader

Pull Request - State: closed - Opened by mortonjt over 4 years ago - 1 comment

#72 - Fasta search

Pull Request - State: closed - Opened by mortonjt over 4 years ago - 1 comment

#72 - Fasta search

Pull Request - State: closed - Opened by mortonjt over 4 years ago - 1 comment

#71 - Search functionality

Issue - State: closed - Opened by mortonjt over 4 years ago - 1 comment

#71 - Search functionality

Issue - State: closed - Opened by mortonjt over 4 years ago - 1 comment

#70 - Preprocess

Pull Request - State: closed - Opened by mortonjt over 4 years ago - 2 comments

#70 - Preprocess

Pull Request - State: closed - Opened by mortonjt over 4 years ago - 2 comments

#69 - weird validation results

Issue - State: closed - Opened by mortonjt over 4 years ago

#69 - weird validation results

Issue - State: closed - Opened by mortonjt over 4 years ago

#68 - Adding Priors

Pull Request - State: closed - Opened by mortonjt over 4 years ago - 1 comment

#68 - Adding Priors

Pull Request - State: closed - Opened by mortonjt over 4 years ago - 1 comment

#67 - Add another attention layer

Issue - State: open - Opened by mortonjt over 4 years ago

#67 - Add another attention layer

Issue - State: open - Opened by mortonjt over 4 years ago

#66 - Add priors for match / gap scores

Issue - State: open - Opened by mortonjt over 4 years ago

#66 - Add priors for match / gap scores

Issue - State: open - Opened by mortonjt over 4 years ago

#65 - Percent identity being miscalculated

Issue - State: closed - Opened by mortonjt over 4 years ago

#65 - Percent identity being miscalculated

Issue - State: closed - Opened by mortonjt over 4 years ago

#64 - Remove enable_grad statements

Issue - State: closed - Opened by mortonjt over 4 years ago - 1 comment

#64 - Remove enable_grad statements

Issue - State: closed - Opened by mortonjt over 4 years ago - 1 comment

#63 - Reduce memory footprint

Issue - State: open - Opened by mortonjt over 4 years ago

#63 - Reduce memory footprint

Issue - State: open - Opened by mortonjt over 4 years ago

#62 - adding methods for prediction / evaluation

Pull Request - State: closed - Opened by mortonjt over 4 years ago

#62 - adding methods for prediction / evaluation

Pull Request - State: closed - Opened by mortonjt over 4 years ago

#61 - Alignment prediction needs to be appropriately trimmed

Issue - State: closed - Opened by mortonjt over 4 years ago

#61 - Alignment prediction needs to be appropriately trimmed

Issue - State: closed - Opened by mortonjt over 4 years ago

#60 - Affine gap functionality

Pull Request - State: closed - Opened by mortonjt over 4 years ago

#60 - Affine gap functionality

Pull Request - State: closed - Opened by mortonjt over 4 years ago

#59 - WIP: Preprocess

Pull Request - State: closed - Opened by mortonjt over 4 years ago

#59 - WIP: Preprocess

Pull Request - State: closed - Opened by mortonjt over 4 years ago

#58 - Edge edge : single sequence alignment

Issue - State: closed - Opened by mortonjt over 4 years ago - 1 comment
Labels: good first issue

#58 - Edge edge : single sequence alignment

Issue - State: closed - Opened by mortonjt over 4 years ago - 1 comment
Labels: good first issue

#57 - Edge case in collate_f

Issue - State: closed - Opened by mortonjt over 4 years ago - 1 comment

#57 - Edge case in collate_f

Issue - State: closed - Opened by mortonjt over 4 years ago - 1 comment

#56 - Edge case in Dataset test

Issue - State: closed - Opened by mortonjt over 4 years ago - 1 comment

#56 - Edge case in Dataset test

Issue - State: closed - Opened by mortonjt over 4 years ago - 1 comment

#55 - Summary stats are nan

Issue - State: closed - Opened by mortonjt over 4 years ago - 1 comment

#55 - Summary stats are nan

Issue - State: closed - Opened by mortonjt over 4 years ago - 1 comment

#54 - Padding is off

Issue - State: closed - Opened by mortonjt over 4 years ago - 1 comment

#54 - Padding is off

Issue - State: closed - Opened by mortonjt over 4 years ago - 1 comment

#53 - WIP: Affine gap

Pull Request - State: closed - Opened by mortonjt over 4 years ago - 3 comments

#53 - WIP: Affine gap

Pull Request - State: closed - Opened by mortonjt over 4 years ago - 3 comments

#52 - Affine gap

Pull Request - State: closed - Opened by mortonjt over 4 years ago

#52 - Affine gap

Pull Request - State: closed - Opened by mortonjt over 4 years ago

#51 - Multitask loss

Pull Request - State: closed - Opened by mortonjt over 4 years ago

GitHub / flatironinstitute/deepblast issues and pull requests