| ---
|
| license: mit
|
| ---
|
|
|
| # Dataset Description
|
|
|
|
|
| ## Dataset Summary
|
|
|
| This dataset was derived from the Stanford HIV Genotype-Phenotype database and contains 1,733 HIV protease sequences. A
|
| pproximately half of the sequences are resistant to at least one antiretroviral therapeutic (ART).
|
|
|
| Supported Tasks and Leaderboards: None
|
|
|
| Languages: English
|
|
|
| ## Dataset Structure
|
|
|
| ### Data Instances
|
| Each column represents the protein amino acid sequence of the HIV protease protein. The ID field indicates the Genbank reference ID for future cross-referencing. There are 1,733 total protease sequences.
|
|
|
| Data Fields: ID, sequence, fold, FPV, IDV, NFV, SQV
|
|
|
| Data Splits: None
|
|
|
| ## Dataset Creation
|
|
|
| Curation Rationale: This dataset was curated to train a model (HIV-BERT-PI) designed to predict whether an HIV protease sequence would result in resistance to certain antiretroviral (ART) drugs.
|
|
|
| Initial Data Collection and Normalization: Dataset was downloaded and curated on 12/21/2021.
|
|
|
| ## Considerations for Using the Data
|
|
|
| Social Impact of Dataset: Due to the tendency of HIV to mutate, drug resistance is a common issue when attempting to treat those infected with HIV.
|
| Protease inhibitors are a class of drugs that HIV is known to develop resistance via mutations.
|
| Thus, by providing a collection of protease sequences known to be resistant to one or more drugs, this dataset provides a significant collection of data that could be utilized to perform computational analysis of protease resistance mutations.
|
|
|
| Discussion of Biases: Due to the sampling nature of this database, it is predominantly composed of subtype B sequences from North America and Europe with only minor contributions of Subtype C, A, and D.
|
| Currently, there was no effort made to balance the performance across these classes.
|
| As such, one should consider refinement with additional sequences to perform well on non-B sequences.
|
|
|
| ## Additional Information:
|
| - Dataset Curators: Will Dampier
|
| - Citation Information: TBA
|
|
|
|
|
|
|
