This directory contains example input files for fine-tuning examples in the Geneformer model repository. Please note that the fine-tuning examples are meant to be generally applicable and the input datasets and labels will vary dependent on the downstream task. Example input files for a few of the downstream tasks demonstrated in the manuscript are located in this directory, but these only represent a few example fine-tuning applications.
Please note that GPU resources are required for efficient usage of Geneformer. Additionally, we strongly recommend tuning hyperparameters for each downstream fine-tuning application as this can significantly boost predictive potential in the downstream task (e.g. max learning rate, learning schedule, number of layers to freeze, etc.).