OpenBioML protein-lm-scaling issues

OpenBioML / protein-lm-scaling

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Metrics for CL

#68 Muedi opened 3 months ago
0
Optuna super simple implementation

#67 hssn-20 opened 4 months ago
1
fix: training

#66 othertea closed 5 months ago
3
weird logic in positional embedding in APTModel (self.wpe)?

#65 othertea opened 5 months ago
3
Support MuParametrization and MuTransfer

#64 NZ99 opened 6 months ago
4
Create cluster_dataset.py

#63 jamaliki closed 5 months ago
0
Sample .a3m file

#62 jamesthesnake opened 7 months ago
0
Create evaluation utility to compute residue conservation from MSA

#61 jeffreyruffolo opened 8 months ago
0
Folder structure in evaluation

#60 Muedi opened 8 months ago
1
GQA Attention

#59 RishikeshMagar closed 5 months ago
1
Add continous value (plDDT and PPL) support for Curriculum Learning

#58 Leo-T-Zang closed 5 months ago
5
question to dynamic batch sizes

#57 wangleiofficial opened 8 months ago
0
Curriculum Learning for sequence_length

#56 talkhanz closed 9 months ago
0
Integrate Axial-RoPE

#55 pascalnotin closed 9 months ago
2
Add contact predictions to evaluation framework

#54 csjackson0 closed 9 months ago
3
Make an alternate gpu environment specification

#53 othertea closed 9 months ago
4
Integrate grouped-query attention into APT class

#52 pascalnotin opened 9 months ago
9
Training APT with toy example

#51 Muedi closed 9 months ago
2
Eval Script update

#50 Muedi closed 9 months ago
5
feat: add validation split, wandb logging, multigpu compatibility

#49 othertea closed 9 months ago
3
adding Huggingface compatible tokenizers

#48 justin-barton opened 9 months ago
1
Make tokenizer 100% API compatible with the Huggingface tokenizer

#47 justin-barton opened 9 months ago
1
Fixing sequence clipping bug in tokenizer

#46 justin-barton closed 6 months ago
1
Fix sequence clipping bug in tokenizer

#45 justin-barton opened 9 months ago
1
Integrate Linear and DynamicNTK Scaling Rotary position encoding

#44 csjackson0 closed 9 months ago
0
Create evaluation dataset for the contact prediction task

#43 pascalnotin opened 9 months ago
0
Add hierarchical cluster sampling strategy

#42 pascalnotin opened 9 months ago
0
Add flash attention

#41 pascalnotin opened 9 months ago
0
Add cluster sampling strategies

#40 pascalnotin opened 9 months ago
9
Add curriculum learning strategy

#39 pascalnotin opened 9 months ago
29
Update CONTRIBUTING.md

#38 pascalnotin closed 9 months ago
0
fix: allow max_steps training arg to be negative

#37 othertea closed 9 months ago
1
Epochs not changing

#36 talkhanz closed 9 months ago
4
Rerope implementation with unit tests

#35 talkhanz closed 9 months ago
0
Integrate ReRope position encoding

#34 pascalnotin closed 9 months ago
10
Perform data sharding for distributed learning

#33 pascalnotin closed 10 months ago
1
fill-in-the-middle collator

#32 csjackson0 closed 9 months ago
3
FIM collator

#31 csjackson0 closed 10 months ago
0
integrated alibi encoding + default_encoding is learned now

#30 talkhanz closed 10 months ago
0
Prepare ColabFoldDB

#29 NZ99 opened 10 months ago
6
Prepare OpenProteinSet

#28 NZ99 opened 10 months ago
6
Zero shot evaluation

#27 Muedi closed 9 months ago
4
feat: initial restructure of training script

#26 othertea closed 10 months ago
1
Clean up modeling code (with rotary embedding added)

#25 talkhanz closed 10 months ago
3
Extend data collator to support fill-in-the-middle modeling on the fly

#24 jeffreyruffolo closed 9 months ago
10
Integrate rotary positional encodings

#23 csjackson0 closed 10 months ago
3
Integrate ALiBi position encoding

#22 pascalnotin closed 10 months ago
4
Integrate rotary position encoding

#21 pascalnotin closed 10 months ago
3
Modeling task

#20 talkhanz closed 10 months ago
0
Add contact predictions to evaluation framework

#19 pascalnotin closed 9 months ago
4