Congratulations to the winners and many thanks to Zindi and InstaDeep for hosting this interesting competition.

My solution is a transformer model with no ensembling or fold averaging. The code is written in Pytorch.

Approach

• Fine tune a pre-trained prot_bert_bfd model from the Hugging Face library (prot_bert_bfd was trained on amino acid sequences).
• Map rare amino acids (U, Z, O, B) to X. This is how the data was pre-processed when prot_bert_bfd was trained.
• Use a max sequence length of 256.
• Use 11000 samples per class and train for 2 epochs.
• Use dropout and weight decay to regularize the model.
• Set aside creature4 and creature5 data for validation.

I trained the model in Kaggle notebooks (1 x P100 GPU). Training time was approx. 8.3 hours per epoch. Inference time was approx. 2.2 hours. I used 11000 samples per class and a max length of 256 in order to stay within the 9 hour GPU runtime limit.

Edit

Please note that this solution does not comply with the competition rules i.e. < 8 hours for training and < 2 hours for inference.