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

#119 - How to accelerate the encoding time when using jax-unirep?

Issue - State: open - Opened by wushufang about 1 year ago - 1 comment

#118 - ModuleNotFoundError: No module named 'jax.example_libraries'

Issue - State: open - Opened by MohmedSoudy over 1 year ago - 1 comment

#117 - No module named 'jax.example_libraries'

Issue - State: closed - Opened by XiaoTigerHAO almost 2 years ago - 1 comment

#115 - Ask

Issue - State: open - Opened by GeorgyChistov about 2 years ago

#114 - Reverse `jax_unirep.get_reps(seq)`

Issue - State: open - Opened by mehradans92 about 2 years ago

#113 - Clear Map for on top classification with evotuned weights

Issue - State: open - Opened by mkd1996 about 2 years ago

#112 - Training classification model on top of UniRep

Issue - State: open - Opened by kvetab over 2 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 almost 3 years ago - 1 comment

#110 - ImportError: cannot import name 'cusolver'

Issue - State: closed - Opened by zhenzey about 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

#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 over 3 years ago - 8 comments

#96 - Add NaN test for sigmoid and grad of sigmoid

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

#95 - Evotuning log bugfix

Pull Request - State: closed - Opened by ElArkk over 3 years ago - 1 comment

#94 - Loss NaNs as a function of dataset size

Issue - State: closed - Opened by r-karimi over 3 years ago - 19 comments

#93 - Evotune log format

Issue - State: closed - Opened by jmahenriques over 3 years ago - 6 comments
Labels: bug

#92 - Changelog update and small fixes

Pull Request - State: closed - Opened by ElArkk over 3 years ago - 2 comments

#91 - Move CI infrastructure to Azure DevOps

Issue - State: closed - Opened by ericmjl over 3 years ago

#90 - Training mLSTM1900 weights from scratch

Issue - State: closed - Opened by jmahenriques over 3 years ago - 15 comments

#89 - Implement initial embedding layer

Issue - State: closed - Opened by ElArkk over 3 years ago

#88 - Embedding layer

Pull Request - State: closed - Opened by ElArkk over 3 years ago - 9 comments

#87 - Changelog update

Pull Request - State: closed - Opened by ElArkk over 3 years ago - 1 comment

#86 - Clearing GPU memory

Issue - State: closed - Opened by silenus092 over 3 years ago - 3 comments

#85 - Why is the embedding sequence one longer than the protein sequence?

Issue - State: closed - Opened by konstin over 3 years ago - 3 comments

#84 - #59 Removes params mutation during l2_normalization

Pull Request - State: closed - Opened by hypostulate over 3 years ago - 2 comments

#83 - embed_matrix:0.npy in evotuned dumped weights

Issue - State: closed - Opened by mengqvist over 3 years ago - 1 comment

#82 - Log batch size only when length-batching is used

Issue - State: closed - Opened by ericmjl almost 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 almost 4 years ago

#80 - Flexible output sizes

Pull Request - State: closed - Opened by ericmjl almost 4 years ago - 9 comments

#79 - Pin jax version to < 0.2

Pull Request - State: closed - Opened by maximz almost 4 years ago

#78 - GPU backend does not work in fit()

Issue - State: closed - Opened by mengqvist almost 4 years ago - 6 comments

#77 - get_reps broken for different-length protein lists

Issue - State: closed - Opened by ElArkk almost 4 years ago - 6 comments
Labels: bug

#76 - Embed sequences while evotuning.

Pull Request - State: closed - Opened by ElArkk almost 4 years ago - 2 comments

#75 - input_output_pairs memory consumption

Issue - State: closed - Opened by ElArkk almost 4 years ago - 1 comment
Labels: bug

#74 - Shifted step layer inside scope of batch function.

Pull Request - State: closed - Opened by ericmjl almost 4 years ago - 3 comments

#73 - Memory leak issues with lax.scan

Issue - State: closed - Opened by ericmjl almost 4 years ago

#72 - JMLR Submission

Pull Request - State: closed - Opened by ericmjl almost 4 years ago - 2 comments

#71 - Update to docs

Pull Request - State: closed - Opened by ericmjl almost 4 years ago - 2 comments

#70 - Integrating UniRep into bio_embeddings

Pull Request - State: closed - Opened by konstin almost 4 years ago - 3 comments

#69 - Non-standard Amino Acids

Issue - State: open - Opened by ericmjl almost 4 years ago - 4 comments

#68 - Update getting-started.md

Pull Request - State: closed - Opened by ericmjl almost 4 years ago - 1 comment

#67 - Update README.md

Pull Request - State: closed - Opened by ericmjl almost 4 years ago - 1 comment

#66 - Version 1.0

Pull Request - State: closed - Opened by ElArkk almost 4 years ago - 1 comment

#65 - Blessed developer who removes code

Pull Request - State: closed - Opened by ericmjl almost 4 years ago - 2 comments

#64 - Update docs

Pull Request - State: closed - Opened by ElArkk almost 4 years ago - 1 comment

#63 - Docs first pass attempt

Pull Request - State: closed - Opened by ericmjl almost 4 years ago - 2 comments

#62 - Feature request disclaimer

Pull Request - State: closed - Opened by ericmjl almost 4 years ago - 2 comments

#61 - GFP analysis fix

Pull Request - State: closed - Opened by ElArkk almost 4 years ago - 4 comments

#60 - GFP mutation to sequence question

Issue - State: closed - Opened by wward97 almost 4 years ago - 2 comments

#59 - Parameters not properly being passed into get_reps functions?

Issue - State: closed - Opened by hhefzi almost 4 years ago - 8 comments
Labels: bug

#58 - UI/UX updates

Pull Request - State: closed - Opened by ericmjl almost 4 years ago - 3 comments

#57 - [ENH] Speed up evotuning and improve evotuning ergonomics

Pull Request - State: closed - Opened by ericmjl about 4 years ago - 18 comments

#56 - Evotuning pairs can be sped up by switching to original NumPy

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

#55 - Evotuning with stop codons

Issue - State: closed - Opened by kbyang about 4 years ago - 6 comments

#54 - Move get params

Pull Request - State: closed - Opened by ElArkk about 4 years ago - 2 comments

#53 - Application notes

Pull Request - State: closed - Opened by ericmjl about 4 years ago - 2 comments

#52 - random batching memory issue for large number of training sequences

Issue - State: closed - Opened by ivanjayapurna about 4 years ago - 23 comments

#51 - Add optional dependencies

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

#50 - Missing deps

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

#49 - Upload coverage

Pull Request - State: closed - Opened by ElArkk about 4 years ago - 2 comments

#48 - Random batching

Pull Request - State: closed - Opened by ElArkk about 4 years ago - 7 comments

#47 - Add in batching

Issue - State: closed - Opened by ericmjl about 4 years ago - 1 comment
Labels: enhancement

#46 - 0-th row of embed_matrix:0.npy

Issue - State: closed - Opened by dlnp2 about 4 years ago - 3 comments

#45 - Possible XLA memory leak issue

Issue - State: closed - Opened by ericmjl about 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 about 4 years ago - 6 comments

#43 - Tests for loading and dumping params

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

#42 - dump_params function saves dense params with switched filenames

Issue - State: closed - Opened by andrewfavor95 about 4 years ago - 2 comments

#41 - 2 sets of weights in weights folder?

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

#40 - Evotune with "iters + batches" or "epochs"?

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

#39 - Fix params passing

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

#38 - Ivan fixes

Pull Request - State: closed - Opened by ericmjl about 4 years ago - 2 comments

#37 - Issue with NaNs

Issue - State: closed - Opened by ericmjl about 4 years ago - 10 comments

#36 - Modify evotuning function

Pull Request - State: closed - Opened by ivanjayapurna about 4 years ago - 13 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

#21 - Sequence sampler

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