Update parquet files

.gitattributes

@@ -1,37 +0,0 @@
-*.7z filter=lfs diff=lfs merge=lfs -text
-*.arrow filter=lfs diff=lfs merge=lfs -text
-*.bin filter=lfs diff=lfs merge=lfs -text
-*.bin.* filter=lfs diff=lfs merge=lfs -text
-*.bz2 filter=lfs diff=lfs merge=lfs -text
-*.ftz filter=lfs diff=lfs merge=lfs -text
-*.gz filter=lfs diff=lfs merge=lfs -text
-*.h5 filter=lfs diff=lfs merge=lfs -text
-*.joblib filter=lfs diff=lfs merge=lfs -text
-*.lfs.* filter=lfs diff=lfs merge=lfs -text
-*.model filter=lfs diff=lfs merge=lfs -text
-*.msgpack filter=lfs diff=lfs merge=lfs -text
-*.onnx filter=lfs diff=lfs merge=lfs -text
-*.ot filter=lfs diff=lfs merge=lfs -text
-*.parquet filter=lfs diff=lfs merge=lfs -text
-*.pb filter=lfs diff=lfs merge=lfs -text
-*.pt filter=lfs diff=lfs merge=lfs -text
-*.pth filter=lfs diff=lfs merge=lfs -text
-*.rar filter=lfs diff=lfs merge=lfs -text
-saved_model/**/* filter=lfs diff=lfs merge=lfs -text
-*.tar.* filter=lfs diff=lfs merge=lfs -text
-*.tflite filter=lfs diff=lfs merge=lfs -text
-*.tgz filter=lfs diff=lfs merge=lfs -text
-*.xz filter=lfs diff=lfs merge=lfs -text
-*.zip filter=lfs diff=lfs merge=lfs -text
-*.zstandard filter=lfs diff=lfs merge=lfs -text
-*tfevents* filter=lfs diff=lfs merge=lfs -text
-# Audio files - uncompressed
-*.pcm filter=lfs diff=lfs merge=lfs -text
-*.sam filter=lfs diff=lfs merge=lfs -text
-*.raw filter=lfs diff=lfs merge=lfs -text
-# Audio files - compressed
-*.aac filter=lfs diff=lfs merge=lfs -text
-*.flac filter=lfs diff=lfs merge=lfs -text
-*.mp3 filter=lfs diff=lfs merge=lfs -text
-*.ogg filter=lfs diff=lfs merge=lfs -text
-*.wav filter=lfs diff=lfs merge=lfs -text

README.md

@@ -1,46 +0,0 @@
----
-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
- 
-

data/train-00000-of-00001.parquet → damlab--HIV_PI/parquet-train.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:9ffdcd1eaedcd5d88a9a2ac8c6dfab0b96438485ac5f3e3b63ecc2bd8175c08b
-size 69238
+oid sha256:b8bfc66e7628bc6a50d105a748e2f800cfef364e95442fbae58ba5ad0d79071c
+size 72839

dataset_infos.json

@@ -1 +0,0 @@
-{"damlab--HIV_PI": {"description": "This dataset was constructed the Stanford HIV Drug Resistance Database. \nhttps://hivdb.stanford.edu/pages/genopheno.dataset.html\nThe sequences were interpolated from the protease high-quality dataset.\nSequences with >4-fold increased resistance relative to wild-type was labeled as True.\n", "citation": "@InProceedings{huggingface:dataset,\ntitle = {HIV Protease Drug Resistance Prediction Dataset},\nauthor={Will Dampier\n},\nyear={2021}\n}\n", "homepage": "", "license": "", "features": {"sequence": {"dtype": "string", "id": null, "_type": "Value"}, "id": {"dtype": "string", "id": null, "_type": "Value"}, "FPV": {"dtype": "bool", "id": null, "_type": "Value"}, "IDV": {"dtype": "bool", "id": null, "_type": "Value"}, "NFV": {"dtype": "bool", "id": null, "_type": "Value"}, "SQV": {"dtype": "bool", "id": null, "_type": "Value"}, "fold": {"dtype": "int32", "id": null, "_type": "Value"}}, "post_processed": null, "supervised_keys": null, "task_templates": null, "builder_name": null, "config_name": null, "version": null, "splits": {"train": {"name": "train", "num_bytes": 205318, "num_examples": 1733, "dataset_name": "HIV_PI"}}, "download_checksums": null, "download_size": 69238, "post_processing_size": null, "dataset_size": 205318, "size_in_bytes": 274556}}