ElArkk jax-unirep issues

ElArkk / jax-unirep

Reimplementation of the UniRep protein featurization model.

GNU General Public License v3.0

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issues

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Bump actions/download-artifact from 2 to 4.1.7 in /.github/workflows

#121 dependabot[bot] opened 2 months ago
0
How to use jax-unirep throught GPU to embedding protein sequences. Now, it is very slow using CPU.

#120 shufangwu opened 9 months ago
0
How to accelerate the encoding time when using jax-unirep?

#119 wushufang opened 1 year ago
1
ModuleNotFoundError: No module named 'jax.example_libraries'

#118 MohmedSoudy opened 2 years ago
1
No module named 'jax.example_libraries'

#117 XiaoTigerHAO closed 2 years ago
1
fix: replace jax.experimental with jax.example_libraries to fix import deprecation in latest jax release

#116 aaroncsolomon closed 2 years ago
4
Ask

#115 GeorgyChistov opened 2 years ago
0
Reverse `jax_unirep.get_reps(seq)`

#114 mehradans92 opened 2 years ago
0
Clear Map for on top classification with evotuned weights

#113 mkd1996 opened 2 years ago
0
Training classification model on top of UniRep

#112 kvetab opened 2 years ago
2
Rewrite `get_reps` to allow users to obtain reps from "256" and "64" models

#111 ericmjl opened 3 years ago
1
ImportError: cannot import name 'cusolver'

#110 zhenzey closed 3 years ago
3
Question about weights and using different architectures

#109 pkinn closed 3 years ago
1
Error when using get_reps with evotuned params

#108 rushabh31 closed 3 years ago
2
Regression in v2: Embedding for `SEQWENCE` changed, while embedding for `PROTEIN` did not

#107 konstin opened 3 years ago
2
Add model weights

#106 ElArkk closed 3 years ago
6
64 weight file formatting

#105 emilymak closed 3 years ago
2
Add auto-release GitHub action.

#104 ericmjl closed 3 years ago
2
Output hidden state along sequence

#103 golin010 closed 3 years ago
4
Release version restriction for jax

#102 ericmjl closed 3 years ago
5
[ENV] Update environment to latest jax and jaxlib

#101 ericmjl closed 3 years ago
1
Docs are back in action!

#100 ericmjl closed 3 years ago
0
[INF] Add Python setup action

#99 ericmjl closed 3 years ago
1
Add autorelease github action

#98 ericmjl closed 3 years ago
1
[WIP] GitHub actions ci

#97 ericmjl closed 3 years ago
8
Add NaN test for sigmoid and grad of sigmoid

#96 ericmjl closed 3 years ago
4
Evotuning log bugfix

#95 ElArkk closed 3 years ago
1
Loss NaNs as a function of dataset size

#94 r-karimi closed 3 years ago
19
Evotune log format

#93 jmahenriques closed 3 years ago
6
Changelog update and small fixes

#92 ElArkk closed 3 years ago
2
Move CI infrastructure to Azure DevOps

#91 ericmjl closed 3 years ago
0
Training mLSTM1900 weights from scratch

#90 jmahenriques closed 3 years ago
15
Implement initial embedding layer

#89 ElArkk closed 3 years ago
0
Embedding layer

#88 ElArkk closed 3 years ago
9
Changelog update

#87 ElArkk closed 3 years ago
1
Clearing GPU memory

#86 silenus092 closed 3 years ago
3
Why is the embedding sequence one longer than the protein sequence?

#85 konstin closed 3 years ago
3
#59 Removes params mutation during l2_normalization

#84 hypostulate closed 4 years ago
2
embed_matrix:0.npy in evotuned dumped weights

#83 mengqvist closed 3 years ago
1
Log batch size only when length-batching is used

#82 ericmjl closed 3 years ago
0
[DOC] Add annotation on how to install JAX compiled for GPU

#81 ericmjl opened 4 years ago
0
Flexible output sizes

#80 ericmjl closed 3 years ago
9
Pin jax version to < 0.2

#79 maximz closed 4 years ago
0
GPU backend does not work in fit()

#78 mengqvist closed 3 years ago
6
get_reps broken for different-length protein lists

#77 ElArkk closed 4 years ago
6
Embed sequences while evotuning.

#76 ElArkk closed 4 years ago
2
input_output_pairs memory consumption

#75 ElArkk closed 4 years ago
1
Shifted step layer inside scope of batch function.

#74 ericmjl closed 4 years ago
3
Memory leak issues with lax.scan

#73 ericmjl closed 4 years ago
0
JMLR Submission

#72 ericmjl closed 4 years ago
2