Cargando…

Continual learning approaches for single cell RNA sequencing data

Single-cell RNA sequencing data is among the most interesting and impactful data of today and the sizes of the available datasets are increasing drastically. There is a substantial need for learning from large datasets, causing nontrivial challenges, especially in hardware. Loading even a single dat...

Descripción completa

Detalles Bibliográficos
Autores principales: Saygili, Gorkem, OzgodeYigin, Busra
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10504339/
https://www.ncbi.nlm.nih.gov/pubmed/37714869
http://dx.doi.org/10.1038/s41598-023-42482-7
Descripción
Sumario:Single-cell RNA sequencing data is among the most interesting and impactful data of today and the sizes of the available datasets are increasing drastically. There is a substantial need for learning from large datasets, causing nontrivial challenges, especially in hardware. Loading even a single dataset into the memory of an ordinary, off-the-shelf computer can be infeasible, and using computing servers might not always be an option. This paper presents continual learning as a solution to such hardware bottlenecks. The findings of cell-type classification demonstrate that XGBoost and Catboost algorithms, when implemented in a continual learning framework, exhibit superior performance compared to the best-performing static classifier. We achieved up to 10% higher median F1 scores than the state-of-the-art on the most challenging datasets. On the other hand, these algorithms can suffer from variations in data characteristics across diverse datasets, pointing out indications of the catastrophic forgetting problem.