CSCI4949-6969 Assign4

Assign4: Protein Contextual Embeddings via BERT

Due Date: Mar 6, before midnight (EST 11:59:59PM)

In this assignment, you will implement the BERT embedding method for protein sequences.

Your code should implement on your own the transformer approach with masked language model for learning contextual embeddings for input sequences. You can use the pytorch layer norm and feed forward layers, but you must implement the multi-head attention on your own. The details of BERT training can be found in BERT, and those for the transformer in Transformer. You must implement at least one transformer block, but you may play with the full model too (12 layers!). You have to also implement the masked language model.

For training the BERT model, you will use the same large set of 524532 protein sequences uniprot-reviewed-lim_sequences.txt. This data is from the paper Learned protein embeddings for machine learning. For prototyping the algorithm you can make use of the dataset of 1000 proteins small_uniprot.txt.

One complication in BERT training is what tokenization to use. You can try the basic character-level tokenization, i.e., each amino acid is a token, i.e., kmer=1. On the training dataset, the max sequence length is 999, so you should use a block size of 1000, with the first token being "CLS".

If you are feeling ambitious, you an also try a kmer-3 tokenization, in which case, each sequence can either be represented via a sliding window of all kmers, or you can create three different sequences based on the starting offset, and use non-overlapping kmers for pre-training.


Once you have pre-trained the BERT model, you will evaluate it on the protein family classification described in the paper Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics. The dataset is available online at In particular, use the testing sequences in the file "family_classification_sequences.csv". This file has 324018 sequences from different protein families. The true class for these sequences is listed in the "FamilyID" of the file "".

For each family, you should as positive class the sequences that have the given family label, and then you should select an equal number of random sequences from the whole dataset as negative class to train an MLP model for binary classification. The MLP model will use the pre-trained BERT model to learn a representation for each example sequence in the dataset.

Finally, you should also compare the benefit of BERT over ProtVec by using the pre-trained word2vec based embeddings in the "family_classification_protVec.csv" file. This file has the final embedding vector for each of the 324018 sequences, which can be used directly as input for a MLP model for classification.


Submit your jupyter notebooks (or python scripts) via submitty.

The first notebook is for the BERT model. The output of your code should include the pre-trained BERT model for the pre-training code.

The second notebook is for the classification. Next, you need to report the classification accuracy using the pre-trained BERT model, as well as the prot2vec model on the protein family classification dataset. Report the classification results (accuracy) for the first 20 families (in decreasing order of size).

You should acknowledge the source of any code you use from the web.