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VespaG: Expert-Guided Protein Language Models enable Accurate and Blazingly Fast Fitness Prediction

VespaG is a blazingly fast single amino acid variant effect predictor, leveraging embeddings of the protein language model ESM-2 (Lin et al. 2022) as input to a minimal deep learning model.

To overcome the sparsity of experimental training data, we created a dataset of 39 million single amino acid variants from a subset of the Human proteome, which we then annotated using predictions from the multiple sequence alignment-based effect predictor GEMME (Laine et al. 2019) as a proxy for experimental scores.

Assessed on the ProteinGym (Notin et al. 2023) benchmark, VespaG matches state-of-the-art methods while being several orders of magnitude faster, predicting the entire single-site mutational landscape for a human proteome in under a half hour on a consumer-grade laptop.

More details on VespaG can be found in the corresponding preprint.

Quick Start

Running Inference with VespaG

1. Install necessary dependencies using conda (or, interchangeably, mamba or micromamba): conda env create -f environment.yml -n vespag and conda activate vespag
2. Run python -m vespag predict with the following options:
   Required:

• --input/-i: Path to FASTA-formatted file containing protein sequence(s).
  Optional:
• --output/-o:Path for saving created CSV and/or H5 files. Defaults to ./output.
• --embeddings/-e: Path to pre-computed ESM2 (esm2_t36_3B_UR50D) input embeddings. Embeddings will be generated from scratch if no path is provided and saved in ./output. Please note that embedding generation on CPU can be slow.
• --mutation-file: CSV file specifying specific mutations to score. If not provided, the whole single-site mutational landscape of all input proteins will be scored.
• --id-map: CSV file mapping embedding IDs (first column) to FASTA IDs (second column) if they're different. Does not have to cover cases with identical IDs.
• --single-csv: Whether to return one CSV file for all proteins instead of a single file for each protein.
• --no-csv: Whether no CSV output should be produced.
• --h5-output: Whether a file containing predictions in HDF5 format should be created.
• --zero-idx: Whether to enumerate protein sequences (both in- and output) starting at 0.
• --normalize: Whether to normalize predicted scores to [0,1] interval by applying a sigmoid to the predicted GEMME substitution scores (which are on a broader spectrum of about [-10,2], although some predicted values fall out of this).

Examples

After installing the dependencies above and cloning the VespaG repo, you can try out the following examples:

• Run VespaG without precomputed embeddings for the example fasta file with 3 sequences in data/example/example.fasta:
  • python -m vespag predict -i data/example/example.fasta. This will save a CSV file for each sequence in the folder ./output
• Run VespaG with precomputed embeddings for the example fasta file with 3 sequences in data/example/example.fasta:
  • python -m vespag predict -i data/example/example.fasta -e output/esm2_embeddings.h5 --single-csv. This will save a single CSV file for all sequences in the folder ./output

Re-training VespaG

VespaG uses DVC for pipeline orchestration and WandB for experiment tracking.

Using WandB is optional; a username and project for WandB can be specified in params.yaml.

Using DVC is non-optional. There is a dvc.yaml file in place that contains stages for generating pLM embeddings from FASTA files, but you can also download pre-computed embeddings and GEMME scores from our Zenodo repository. Adjust paths in params.yaml to your context, and feel free to play around with model parameters. You can simply run a training run using dvc repro -s train@<model_type>-{esm2|prott5}-<dataset>, with <model_type> and <dataset> each corresponding to a named block in params.yaml.

Evaluation

You can reproduce our evaluation using the eval subcommand, which pre-processes data into a format usable by VespaG, runs predict, and computes performance metrics.

ProteinGym217

Based on the ProteinGym (Notin et al. 2023) DMS substitutions benchmark, dubbed ProteinGym217 by us. Run it with python -m vespag eval proteingym, with the following options: Optional:

• --reference-file: Path to ProteinGym reference file. Will download to data/test/proteingym217/reference.csv or data/test/proteingym87/reference.csv if not provided.
• --dms-directory: Path to directory containing per-DMS score files in CSV format. Will download to data/test/proteingym217/raw_dms_files/ or data/test/proteingym87/raw_dms_files/ if not provided.
• --output/-o:Path for saving created CSV with scores for all assays and variants as well as a CSV with Spearman correlation coefficients for each DMS. Defaults to ./output/proteingym217 or ./output/proteingym87.
• --embeddings/-e, --id-map, --normalize-scores: identical to predict, used for the internal call to it.
• --v1 if you want to get a result for the first iteration of ProteinGym with 87 assays.

Preprint Citation

If you find VespaG helpful in your work, please be so kind as to cite our pre-print:

@article{vespag,
	author = {Celine Marquet and Julius Schlensok and Marina Abakarova and Burkhard Rost and Elodie Laine},
	title = {VespaG: Expert-guided protein Language Models enable accurate and blazingly fast fitness prediction},
	year = {2024},
	doi = {10.1101/2024.04.24.590982},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/early/2024/04/28/2024.04.24.590982},
	journal = {bioRxiv}}