Skip to content

Commit b8b324b

Browse files
committed
Update preliminary results ESM-DCA hybrid lowN model
1 parent b939639 commit b8b324b

File tree

2 files changed

+5
-0
lines changed

2 files changed

+5
-0
lines changed
482 KB
Loading

README.md

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -485,6 +485,11 @@ The performance of the GREMLIN model used is shown in the following for predicti
485485
486486
for ProteinGym datasets computed using the scripts located at [scripts/ProteinGym_runs](scripts/ProteinGym_runs).
487487
488+
A hybrid GREMLIN-ESM1v low-N-tuned model achieved even increased performances compared to the pure DCA-tuned model (script available at [scripts/ESM_finetuning](scripts/ESM_finetuning))
489+
<p align="center">
490+
<img src=".github/imgs/mut_performance_violin_DCA_ESM.png" alt="drawing" width="250"/>
491+
</p>
492+
488493
<a name="api-usage"></a>
489494
## API Usage for Sequence Encoding
490495
For script-based encoding of sequences using PyPEF and the available AAindex-, OneHot- or DCA-based techniques, the classes and corresponding functions can be imported, i.e. `OneHotEncoding`, `AAIndexEncoding`, `GREMLIN` (DCA), `PLMC` (DCA), and `DCAHybridModel`. In addition, implemented functions for CV-based tuning of regression models can be used to train and validate models, eventually deriving them to obtain performances on retained data for testing. An exemplary script and a Jupyter notebook for CV-based (low-*N*) tuning of models and using them for testing is provided at [scripts/Encoding_low_N/api_encoding_train_test.py](scripts/Encoding_low_N/api_encoding_train_test.py) and [scripts/Encoding_low_N/api_encoding_train_test.ipynb](scripts/Encoding_low_N/api_encoding_train_test.ipynb), respectively.

0 commit comments

Comments
 (0)