Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / ElArkk/jax-unirep issues and pull requests
#121 - Bump actions/download-artifact from 2 to 4.1.7 in /.github/workflows
Pull Request -
State: open - Opened by dependabot[bot] about 1 month ago
Labels: dependencies
#120 - How to use jax-unirep throught GPU to embedding protein sequences. Now, it is very slow using CPU.
Issue -
State: open - Opened by shufangwu 9 months ago
#119 - How to accelerate the encoding time when using jax-unirep?
Issue -
State: open - Opened by wushufang over 1 year ago
- 1 comment
#118 - ModuleNotFoundError: No module named 'jax.example_libraries'
Issue -
State: open - Opened by MohmedSoudy almost 2 years ago
- 1 comment
#117 - No module named 'jax.example_libraries'
Issue -
State: closed - Opened by XiaoTigerHAO about 2 years ago
- 1 comment
#116 - fix: replace jax.experimental with jax.example_libraries to fix import deprecation in latest jax release
Pull Request -
State: closed - Opened by aaroncsolomon about 2 years ago
- 4 comments
#115 - Ask
Issue -
State: open - Opened by GeorgyChistov over 2 years ago
#114 - Reverse `jax_unirep.get_reps(seq)`
Issue -
State: open - Opened by mehradans92 over 2 years ago
#113 - Clear Map for on top classification with evotuned weights
Issue -
State: open - Opened by mkd1996 over 2 years ago
#112 - Training classification model on top of UniRep
Issue -
State: open - Opened by kvetab almost 3 years ago
- 2 comments
#111 - Rewrite `get_reps` to allow users to obtain reps from "256" and "64" models
Issue -
State: open - Opened by ericmjl about 3 years ago
- 1 comment
#110 - ImportError: cannot import name 'cusolver'
Issue -
State: closed - Opened by zhenzey over 3 years ago
- 3 comments
#109 - Question about weights and using different architectures
Issue -
State: closed - Opened by pkinn over 3 years ago
- 1 comment
#108 - Error when using get_reps with evotuned params
Issue -
State: closed - Opened by rushabh31 over 3 years ago
- 2 comments
#107 - Regression in v2: Embedding for `SEQWENCE` changed, while embedding for `PROTEIN` did not
Issue -
State: open - Opened by konstin over 3 years ago
- 2 comments
#106 - Add model weights
Pull Request -
State: closed - Opened by ElArkk over 3 years ago
- 6 comments
#105 - 64 weight file formatting
Issue -
State: closed - Opened by emilymak over 3 years ago
- 2 comments
#104 - Add auto-release GitHub action.
Pull Request -
State: closed - Opened by ericmjl over 3 years ago
- 2 comments
#103 - Output hidden state along sequence
Issue -
State: closed - Opened by golin010 over 3 years ago
- 4 comments
#102 - Release version restriction for jax
Pull Request -
State: closed - Opened by ericmjl over 3 years ago
- 5 comments
#101 - [ENV] Update environment to latest jax and jaxlib
Pull Request -
State: closed - Opened by ericmjl over 3 years ago
- 1 comment
#100 - Docs are back in action!
Issue -
State: closed - Opened by ericmjl over 3 years ago
#99 - [INF] Add Python setup action
Pull Request -
State: closed - Opened by ericmjl over 3 years ago
- 1 comment
#98 - Add autorelease github action
Pull Request -
State: closed - Opened by ericmjl over 3 years ago
- 1 comment
#97 - [WIP] GitHub actions ci
Pull Request -
State: closed - Opened by ericmjl almost 4 years ago
- 8 comments
#96 - Add NaN test for sigmoid and grad of sigmoid
Pull Request -
State: closed - Opened by ericmjl almost 4 years ago
- 4 comments
#95 - Evotuning log bugfix
Pull Request -
State: closed - Opened by ElArkk almost 4 years ago
- 1 comment
#94 - Loss NaNs as a function of dataset size
Issue -
State: closed - Opened by r-karimi almost 4 years ago
- 19 comments
#93 - Evotune log format
Issue -
State: closed - Opened by jmahenriques almost 4 years ago
- 6 comments
Labels: bug
#92 - Changelog update and small fixes
Pull Request -
State: closed - Opened by ElArkk almost 4 years ago
- 2 comments
#91 - Move CI infrastructure to Azure DevOps
Issue -
State: closed - Opened by ericmjl almost 4 years ago
#90 - Training mLSTM1900 weights from scratch
Issue -
State: closed - Opened by jmahenriques almost 4 years ago
- 15 comments
#89 - Implement initial embedding layer
Issue -
State: closed - Opened by ElArkk almost 4 years ago
#88 - Embedding layer
Pull Request -
State: closed - Opened by ElArkk almost 4 years ago
- 9 comments
#87 - Changelog update
Pull Request -
State: closed - Opened by ElArkk almost 4 years ago
- 1 comment
#86 - Clearing GPU memory
Issue -
State: closed - Opened by silenus092 almost 4 years ago
- 3 comments
#85 - Why is the embedding sequence one longer than the protein sequence?
Issue -
State: closed - Opened by konstin almost 4 years ago
- 3 comments
#84 - #59 Removes params mutation during l2_normalization
Pull Request -
State: closed - Opened by hypostulate almost 4 years ago
- 2 comments
#83 - embed_matrix:0.npy in evotuned dumped weights
Issue -
State: closed - Opened by mengqvist almost 4 years ago
- 1 comment
#82 - Log batch size only when length-batching is used
Issue -
State: closed - Opened by ericmjl about 4 years ago
Labels: enhancement, help wanted, good first issue
#81 - [DOC] Add annotation on how to install JAX compiled for GPU
Issue -
State: open - Opened by ericmjl about 4 years ago
#80 - Flexible output sizes
Pull Request -
State: closed - Opened by ericmjl about 4 years ago
- 9 comments
#79 - Pin jax version to < 0.2
Pull Request -
State: closed - Opened by maximz about 4 years ago
#78 - GPU backend does not work in fit()
Issue -
State: closed - Opened by mengqvist about 4 years ago
- 6 comments
#77 - get_reps broken for different-length protein lists
Issue -
State: closed - Opened by ElArkk about 4 years ago
- 6 comments
Labels: bug
#76 - Embed sequences while evotuning.
Pull Request -
State: closed - Opened by ElArkk about 4 years ago
- 2 comments
#75 - input_output_pairs memory consumption
Issue -
State: closed - Opened by ElArkk about 4 years ago
- 1 comment
Labels: bug
#74 - Shifted step layer inside scope of batch function.
Pull Request -
State: closed - Opened by ericmjl about 4 years ago
- 3 comments
#73 - Memory leak issues with lax.scan
Issue -
State: closed - Opened by ericmjl about 4 years ago
#72 - JMLR Submission
Pull Request -
State: closed - Opened by ericmjl about 4 years ago
- 2 comments
#71 - Update to docs
Pull Request -
State: closed - Opened by ericmjl about 4 years ago
- 2 comments
#70 - Integrating UniRep into bio_embeddings
Pull Request -
State: closed - Opened by konstin about 4 years ago
- 3 comments
#69 - Non-standard Amino Acids
Issue -
State: open - Opened by ericmjl about 4 years ago
- 4 comments
#68 - Update getting-started.md
Pull Request -
State: closed - Opened by ericmjl about 4 years ago
- 1 comment
#67 - Update README.md
Pull Request -
State: closed - Opened by ericmjl about 4 years ago
- 1 comment
#66 - Version 1.0
Pull Request -
State: closed - Opened by ElArkk about 4 years ago
- 1 comment
#65 - Blessed developer who removes code
Pull Request -
State: closed - Opened by ericmjl about 4 years ago
- 2 comments
#64 - Update docs
Pull Request -
State: closed - Opened by ElArkk about 4 years ago
- 1 comment
#63 - Docs first pass attempt
Pull Request -
State: closed - Opened by ericmjl about 4 years ago
- 2 comments
#62 - Feature request disclaimer
Pull Request -
State: closed - Opened by ericmjl about 4 years ago
- 2 comments
#61 - GFP analysis fix
Pull Request -
State: closed - Opened by ElArkk about 4 years ago
- 4 comments
#60 - GFP mutation to sequence question
Issue -
State: closed - Opened by wward97 about 4 years ago
- 2 comments
#59 - Parameters not properly being passed into get_reps functions?
Issue -
State: closed - Opened by hhefzi about 4 years ago
- 8 comments
Labels: bug
#58 - UI/UX updates
Pull Request -
State: closed - Opened by ericmjl about 4 years ago
- 3 comments
#57 - [ENH] Speed up evotuning and improve evotuning ergonomics
Pull Request -
State: closed - Opened by ericmjl over 4 years ago
- 18 comments
#56 - Evotuning pairs can be sped up by switching to original NumPy
Issue -
State: closed - Opened by ericmjl over 4 years ago
- 4 comments
#55 - Evotuning with stop codons
Issue -
State: closed - Opened by kbyang over 4 years ago
- 6 comments
#54 - Move get params
Pull Request -
State: closed - Opened by ElArkk over 4 years ago
- 2 comments
#53 - Application notes
Pull Request -
State: closed - Opened by ericmjl over 4 years ago
- 2 comments
#52 - random batching memory issue for large number of training sequences
Issue -
State: closed - Opened by ivanjayapurna over 4 years ago
- 23 comments
#51 - Add optional dependencies
Pull Request -
State: closed - Opened by ericmjl over 4 years ago
- 1 comment
#50 - Missing deps
Issue -
State: closed - Opened by phiweger over 4 years ago
- 1 comment
#49 - Upload coverage
Pull Request -
State: closed - Opened by ElArkk over 4 years ago
- 2 comments
#48 - Random batching
Pull Request -
State: closed - Opened by ElArkk over 4 years ago
- 7 comments
#47 - Add in batching
Issue -
State: closed - Opened by ericmjl over 4 years ago
- 1 comment
Labels: enhancement
#46 - 0-th row of embed_matrix:0.npy
Issue -
State: closed - Opened by dlnp2 over 4 years ago
- 3 comments
#45 - Possible XLA memory leak issue
Issue -
State: closed - Opened by ericmjl over 4 years ago
- 1 comment
Labels: bug
#44 - How can I use 'get_reps' on many long amino acid squences?
Issue -
State: closed - Opened by KotaroTsuboyama over 4 years ago
- 6 comments
#43 - Tests for loading and dumping params
Pull Request -
State: closed - Opened by ElArkk over 4 years ago
#42 - dump_params function saves dense params with switched filenames
Issue -
State: closed - Opened by andrewfavor95 over 4 years ago
- 2 comments
#41 - 2 sets of weights in weights folder?
Issue -
State: closed - Opened by ivanjayapurna over 4 years ago
- 1 comment
#40 - Evotune with "iters + batches" or "epochs"?
Issue -
State: closed - Opened by ericmjl over 4 years ago
- 4 comments
#39 - Fix params passing
Pull Request -
State: closed - Opened by ElArkk over 4 years ago
- 1 comment
#38 - Ivan fixes
Pull Request -
State: closed - Opened by ericmjl over 4 years ago
- 2 comments
#37 - Issue with NaNs
Issue -
State: closed - Opened by ericmjl over 4 years ago
- 10 comments
#36 - Modify evotuning function
Pull Request -
State: closed - Opened by ivanjayapurna over 4 years ago
- 13 comments
#35 - RuntimeError: Resource exhausted: Failed to allocate request for 87.48GiB (93935126000B) on device ordinal 0
Issue -
State: closed - Opened by DorJake over 4 years ago
- 2 comments
#34 - Code fixes for correctness and readability
Pull Request -
State: closed - Opened by ivanjayapurna over 4 years ago
- 10 comments
#33 - deleted "apply_fun" in get_rep() and added a comma to evotune example
Pull Request -
State: closed - Opened by ivanjayapurna over 4 years ago
- 1 comment
#32 - Error with get_rep() in latest update
Issue -
State: closed - Opened by ivanjayapurna over 4 years ago
#31 - Fix featurization
Pull Request -
State: closed - Opened by ElArkk over 4 years ago
#30 - Unirep stax
Pull Request -
State: closed - Opened by ElArkk over 4 years ago
- 3 comments
#29 - Paper post review edits
Pull Request -
State: closed - Opened by ElArkk over 4 years ago
#28 - Finetuning the paper
Pull Request -
State: closed - Opened by ElArkk over 4 years ago
- 3 comments
#27 - Added single chain sampler
Pull Request -
State: closed - Opened by ericmjl over 4 years ago
#26 - Temporarily delegating probability vector checks to numpy multinomial
Pull Request -
State: closed - Opened by ElArkk over 4 years ago
#25 - Implemented biased sampling
Pull Request -
State: closed - Opened by ericmjl over 4 years ago
#24 - Learning rate
Pull Request -
State: closed - Opened by ElArkk over 4 years ago
- 3 comments
#23 - Made step_size a kwarg in evotuning
Pull Request -
State: closed - Opened by ElArkk over 4 years ago
#22 - Sampler
Pull Request -
State: closed - Opened by ElArkk over 4 years ago