GaNDLF: the generally nuanced deep learning framework for scalable end-to-end clinical workflows

• Published in: Communications engineering Vol. 2; no. 1; p. 23
• Main Authors: Pati, Sarthak, Thakur, Siddhesh P., Hamamcı, İbrahim Ethem, Baid, Ujjwal, Baheti, Bhakti, Bhalerao, Megh, Güley, Orhun, Mouchtaris, Sofia, Lang, David, Thermos, Spyridon, Gotkowski, Karol, González, Camila, Grenko, Caleb, Getka, Alexander, Edwards, Brandon, Sheller, Micah, Wu, Junwen, Karkada, Deepthi, Panchumarthy, Ravi, Ahluwalia, Vinayak, Zou, Chunrui, Bashyam, Vishnu, Li, Yuemeng, Haghighi, Babak, Chitalia, Rhea, Abousamra, Shahira, Kurc, Tahsin M., Gastounioti, Aimilia, Er, Sezgin, Bergman, Mark, Saltz, Joel H., Fan, Yong, Shah, Prashant, Mukhopadhyay, Anirban, Tsaftaris, Sotirios A., Menze, Bjoern, Davatzikos, Christos, Kontos, Despina, Karargyris, Alexandros, Umeton, Renato, Mattson, Peter, Bakas, Spyridon
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 16.05.2023; Springer Nature B.V
• Subjects: 631/114/1564; 639/166/985; 639/705/1042; 639/705/258; 692/700/1421/1628; Algorithms; Artificial intelligence; Brain research; Cancer; Data augmentation; Deep learning; Engineering; Foot diseases; Health care; Histology; Machine learning; Medical imaging; Medical research; Medical screening; Network topologies; Open source software; Performance evaluation; Reproducibility; Software packages; User interface; Workloads
• ISSN: 2731-3395; 2731-3395
• DOI: 10.1038/s44172-023-00066-3

Deep Learning (DL) has the potential to optimize machine learning in both the scientific and clinical communities. However, greater expertise is required to develop DL algorithms, and the variability of implementations hinders their reproducibility, translation, and deployment. Here we present the community-driven Generally Nuanced Deep Learning Framework (GaNDLF), with the goal of lowering these barriers. GaNDLF makes the mechanism of DL development, training, and inference more stable, reproducible, interpretable, and scalable, without requiring an extensive technical background. GaNDLF aims to provide an end-to-end solution for all DL-related tasks in computational precision medicine. We demonstrate the ability of GaNDLF to analyze both radiology and histology images, with built-in support for k -fold cross-validation, data augmentation, multiple modalities and output classes. Our quantitative performance evaluation on numerous use cases, anatomies, and computational tasks supports GaNDLF as a robust application framework for deployment in clinical workflows. The increasing complexity of the implementation and operation of deep learning techniques hinders their reproducibility and deployment at scale, especially in healthcare. Pati and colleagues introduce a deep learning framework to analyse healthcare data without requiring extensive computational experience, facilitating the integration of artificial intelligence in clinical workflows.