| --- |
| |
| license: mit |
| language: |
| - en |
| tags: |
| - biomedical |
| - clinvar |
| - genomic-variants |
| - instruction-tuning |
| - text-generation |
| task_categories: |
| - text-generation |
| - tabular-classification |
| size_categories: |
| - 10K<n<100K |
| configs: |
| - config_name: tabular |
| data_files: |
| - split: train |
| path: train.csv |
| - split: validation |
| path: valid.csv |
| - split: test |
| path: test.csv |
| - config_name: instruction |
| data_files: |
| - split: train |
| path: biogpt_train.csv |
| - split: validation |
| path: biogpt_valid.csv |
| - split: test |
| path: biogpt_test.csv |
|
|
| --- |
| |
| **Year:** 2025 |
| **License:** MIT |
| **Author:** Sepideh Moafi |
|
|
| --- |
|
|
| # PathogenAgentAI Instruction Dataset |
|
|
| ## Dataset Description |
|
|
| A ClinVar-derived dataset developed as part of the **PathogenAgentAI** research software project. The dataset is released in two parallel formats: |
|
|
| - **Tabular version** (`train.csv`, `valid.csv`, `test.csv`) — structured genomic-variant data for classical ML and analysis. |
| - **BioGPT instruction version** (`biogpt_train.csv`, `biogpt_valid.csv`, `biogpt_test.csv`) — instruction-style data for fine-tuning biomedical language models. |
|
|
| ## Dataset Structure |
|
|
| ### Splits |
|
|
| | Split | Tabular file | Instruction file | |
| |---|---|---| |
| | Train | `train.csv` | `biogpt_train.csv` | |
| | Validation | `valid.csv` | `biogpt_valid.csv` | |
| | Test | `test.csv` | `biogpt_test.csv` | |
|
|
| ### Tabular Fields |
|
|
| - `GeneSymbol` (string): Gene symbol (e.g., AP5Z1, ZNF592) |
| - `ClinicalSignificance` (string): Clinical significance (e.g., Pathogenic, Likely pathogenic, Uncertain significance) |
| - `Assembly` (string): Genome assembly (e.g., GRCh38) |
| - `Chromosome` (string): Chromosome number |
| - `Start` (int64): Variant start position |
|
|
| ### Instruction Fields |
|
|
| The `biogpt_*.csv` files are formatted for instruction tuning of biomedical language models (e.g., BioGPT), derived from the same ClinVar source data. |
|
|
| ## Source Data |
|
|
| Derived from **ClinVar**, a publicly available archive of reports of the relationships among human variations and phenotypes. |
|
|
| ## Intended Use |
|
|
| - Fine-tuning biomedical language models (BioGPT and similar) |
| - Research on genomic variant interpretation |
| - Classical ML on structured variant data |
| - Reproducible biomedical AI experiments |
|
|
| **Not** intended for clinical diagnosis, treatment decisions, or direct clinical use. |
|
|
| ## Licensing |
|
|
| Released under the **MIT License**. |
|
|
| ## Citation |
|
|
| If you use this dataset in research, please cite: |
|
|
| > BioGPT-ClinVar: Parameter-Efficient Fine-Tuning of a Biomedical Foundation Model. |
| > Research Square, 2026. DOI: 10.21203/rs.3.rs-10196893/v1 |
|
|
| ## Contact |
|
|
| **Sepideh Moafi** |
| GitHub: [AIResearcher20](https://github.com/AIResearcher20) |
| Hugging Face: [Sepideh2027](https://huggingface.co/Sepideh2027) |
