AmelieSchreiber
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Update README.md
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README.md
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@@ -36,7 +36,14 @@ One of the primary goals in training this model is to prove the viability of usi
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for binary token classification tasks like predicting binding and active sites of protein sequences based on sequence alone. This project
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is also an attempt to make deep learning techniques like LoRA more accessible and to showcase the competative or even superior performance
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of simple models and techniques. This however may not be as viable as other methods. The model seems to show good performance, but
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testing based on [this notebook]()
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Since most proteins still do not have a predicted 3D fold or backbone structure, it is useful to
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have a model that can predict binding residues from sequence alone. We also hope that this project will be helpful in this regard.
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for binary token classification tasks like predicting binding and active sites of protein sequences based on sequence alone. This project
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is also an attempt to make deep learning techniques like LoRA more accessible and to showcase the competative or even superior performance
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of simple models and techniques. This however may not be as viable as other methods. The model seems to show good performance, but
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testing based on [this notebook](https://huggingface.co/AmelieSchreiber/esm2_t12_35M_lora_binding_sites_v2_cp3/blob/main/testing_esmb.ipynb)
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seems to indicate otherwise.
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The other potentially important finding is that Low Rank Adaptation (LoRA) helps dramatically improve overfitting of the models. We initially
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finetuned without LoRA and found overfitting to be a serious issue. However, after using LoRA, we found the overfitting improved quite a lot
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without any other modification. Due to the simplicity of LoRA, this may prove an important regularization technique for learning on proteins
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in the future. Keep in mind though, this did not really solve the overfitting problem despite the improvements (the finetuned model wihtout LoRA
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was *very* overfit).
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Since most proteins still do not have a predicted 3D fold or backbone structure, it is useful to
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have a model that can predict binding residues from sequence alone. We also hope that this project will be helpful in this regard.
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