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--- |
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license: mit |
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tags: |
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- biology |
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--- |
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# Model description |
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**MHC-I-EpiPred** (MHC-I-EpiPred, MHC I molecular epitope prediction) is a protein language model fine-tuned from [**ESM2**](https://github.com/facebookresearch/esm) pretrained model [(***facebook/esm2_t33_650M_UR50D***)](https://huggingface.co/facebook/esm2_t33_650M_UR50D) on a T cell MHC I epitope dataset. |
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**MHC-I-EpiPred** is is a classification model for predicting the class of MHC I epitope. |
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# Dataset |
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The original data was downloaded from IEDB data base at https://www.iedb.org/home_v3.php. |
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The full data can be downloaded at https://www.iedb.org/downloader.php?file_name=doc/tcell_full_v3.zip |
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This dataset comprises 543,717 T-cell epitope entries, spanning a variety of species and infections caused by diverse viruses. The epitope information included encompasses a broad range of potential sources, including data relevant to disease immunotherapy. |
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Finally, the dataset we used to train the model contains 41,060 positive and negative samples, which is stored in https://github.com/pengsihua2023/MHC-I-EpiPred/tree/main/data. |
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# Results |
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**MHC-I-EpiPred** achieved the following results: |
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Training Loss (cross-entropy loss, CEL): 0.1044 |
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Training Accuracy: 98.99% |
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Evaluation Loss (cross-entropy loss, CEL): 0.1576 |
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Evaluation Accuracy: 97.04% |
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Epochs: 492 |
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# Model training code at GitHub |
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https://github.com/pengsihua2023/MHC-I-EpiPred-ESM2 |
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# How to use **MHC-I-EpiPred** |
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### An example |
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Pytorch and transformers libraries should be installed in your system. |
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### Install pytorch |
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``` |
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pip install torch torchvision torchaudio |
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``` |
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### Install transformers |
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``` |
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pip install transformers |
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``` |
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### Run the following code |
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``` |
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Coming soon! |
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``` |
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## Funding |
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This project was funded by the CDC to Justin Bahl (BAA 75D301-21-R-71738). |
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### Model architecture, coding and implementation |
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Sihua Peng |
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## Group, Department and Institution |
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### Lab: [Justin Bahl](https://bahl-lab.github.io/) |
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### Department: [College of Veterinary Medicine Department of Infectious Diseases](https://vet.uga.edu/education/academic-departments/infectious-diseases/) |
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### Institution: [The University of Georgia](https://www.uga.edu/) |
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