Pretrained supervised task-specific weights for fluorescence task?

[spark157]

Hello,

I'm trying to run the fluorescence task with fully pretrained model weights (ie. for both the unsupervised pretraining and weights for the supervised task as well). I have downloaded the pretrained UniRep model but I'm thinking this does not include the model weights for the supervised task (fluorescence). Are these available or am I confusing something?

In the README.md|Loading a Model there is a bit about loading supervised task-specific weights but it wasn't clear to me.

Thanks for any guidance you have.

Scott

[thomas-a-neil]

Hi Scott,

You can find the fluorescence task model weights here, where *_pretrain* indicates the model was first pretrained on language modeling, then fine-tuned to fluorescence. You should be able to load them with load_task_from=</path/to/supervised_weights.h5> note that this is different than the load_from argument

http://s3.amazonaws.com/proteindata/fluorescence_weights/bepler_pretrain_weights.h5
http://s3.amazonaws.com/proteindata/fluorescence_weights/lstm_pretrain_weights.h5
http://s3.amazonaws.com/proteindata/fluorescence_weights/lstm_weights.h5
http://s3.amazonaws.com/proteindata/fluorescence_weights/one_hot_weights.h5
http://s3.amazonaws.com/proteindata/fluorescence_weights/resnet_pretrain_weights.h5
http://s3.amazonaws.com/proteindata/fluorescence_weights/resnet_weights.h5
http://s3.amazonaws.com/proteindata/fluorescence_weights/transformer_pretrain_weights.h5
http://s3.amazonaws.com/proteindata/fluorescence_weights/transformer_weights.h5
http://s3.amazonaws.com/proteindata/fluorescence_weights/unirep_pretrain_weights.h5

I will work on making the other pretrained task models available, and making the instructions on how to access them clearer in the README.

[jannisborn]

Hi @CaptainCapsaicin and @spark157
it seems that that the links have expired. Do you still have those weights available?
A quick reply would be greatly appreciated. I'm working toward a deadline and would like to include this as a comparison for a paper

[thomas-a-neil]

Hi @jannisborn, we recently migrated our S3 hosting. The updated URLs for fluorescence task model weights are here.

http://s3.amazonaws.com/songlabdata/proteindata/fluorescence_weights/bepler_pretrain_weights.h5
http://s3.amazonaws.com/songlabdata/proteindata/fluorescence_weights/lstm_pretrain_weights.h5
http://s3.amazonaws.com/songlabdata/proteindata/fluorescence_weights/lstm_weights.h5
http://s3.amazonaws.com/songlabdata/proteindata/fluorescence_weights/one_hot_weights.h5
http://s3.amazonaws.com/songlabdata/proteindata/fluorescence_weights/resnet_pretrain_weights.h5
http://s3.amazonaws.com/songlabdata/proteindata/fluorescence_weights/resnet_weights.h5
http://s3.amazonaws.com/songlabdata/proteindata/fluorescence_weights/transformer_pretrain_weights.h5
http://s3.amazonaws.com/songlabdata/proteindata/fluorescence_weights/transformer_weights.h5
http://s3.amazonaws.com/songlabdata/proteindata/fluorescence_weights/unirep_pretrain_weights.h5

Keep in mind that this repo is an archived version from our neurips 2019 submission, while https://github.com/songlab-cal/tape is under development

[jannisborn]

Thanks for the quick reply @CaptainCapsaicin 👍🏼
But unfortunately the buckets dont seem to be publicly exposed. I get "AccessDenied" errors for all files :/

[thomas-a-neil]

Thanks for catching that, they should be publicly exposed now.

[jannisborn]

Indeed, works now, thanks a lot!