GaNDLF: A Generally Nuanced Deep Learning Framework for Scalable End-to-End Clinical Workflows in Medical Imaging

Pati, Sarthak; Thakur, Siddhesh P.; Bhalerao, Megh; Thermos, Spyridon; Baid, Ujjwal; Gotkowski, Karol; Gonzalez, Camila; Guley, Orhun; Hamamci, Ibrahim Ethem; Er, Sezgin; Grenko, Caleb; Edwards, Brandon; Sheller, Micah; Agraz, Jose; Baheti, Bhakti; Bashyam, Vishnu; Sharma, Parth; Haghighi, Babak; Gastounioti, Aimilia; Bergman, Mark; Mukhopadhyay, Anirban; Tsaftaris, Sotirios A.; Menze, Bjoern; Kontos, Despina; Davatzikos, Christos; Bakas, Spyridon

Deep Learning (DL) has greatly highlighted the potential impact of optimized machine learning in both the scientific and clinical communities. The advent of open-source DL libraries from major industrial entities, such as TensorFlow (Google), PyTorch (Facebook), and MXNet (Apache), further contributes to DL promises on the democratization of computational analytics. However, increased technical and specialized background is required to develop DL algorithms, and the variability of implementation details hinders their reproducibility. Towards lowering the barrier and making the mechanism of DL development, training, and inference more stable, reproducible, and scalable, without requiring an extensive technical background, this manuscript proposes the Generally Nuanced Deep Learning Framework (GaNDLF). With built-in support for $k$-fold cross-validation, data augmentation, multiple modalities and output classes, and multi-GPU training, as well as the ability to work with both radiographic and histologic imaging, GaNDLF aims to provide an end-to-end solution for all DL-related tasks, to tackle problems in medical imaging and provide a robust application framework for deployment in clinical workflows.