A Multi Task Learning approach to classifying the severity of Alzheimer’s disease using single-cell gene expression data
W.J.J. Dieleman (TU Delft - Electrical Engineering, Mathematics and Computer Science)
T. Verlaan – Mentor (TU Delft - Pattern Recognition and Bioinformatics)
Roy Lardenoije – Mentor (TU Delft - Pattern Recognition and Bioinformatics)
G.A. Bouland – Mentor (TU Delft - Pattern Recognition and Bioinformatics)
MJT Reinders – Graduation committee member (TU Delft - Pattern Recognition and Bioinformatics)
R. Guerra Marroquim – Graduation committee member (TU Delft - Computer Graphics and Visualisation)
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Abstract
Alzheimer's Disease (AD) is a complex heterogeneous disease and is the leading cause of dementia around the world. Treatment options remain limited and the underlying mechanisms are not yet fully understood. To get more insight on this celular level, single-cell gene expression data can be used. It has proven to be effective with machine learning for tasks like cell type classification. While prior studies have explored AD classification using scRNA-seq, this has only been a binary classification. Severity of AD is classified using multiple measures, ranging from cognitive ability scores, to neuro pathological measures. This research explores the possibility of expanding the binary prediction of AD by including these measures for AD severity. In addition, given that these measures are associated, we also investigate if Multi Task Learning (MTL) models can improve the predictions by learning multiple AD related data points. If successful, this approach can give additional analysis into key tasks, genes and/or cells (sub)types that drive the models, which would lead to more possibilities for personalized treatment options, alongside more insight into the development of AD in the brain. We used a three-layer neural network architecture alongside a translation from cellular level to individual level to make individual-level predictions. Results show that Cognitive Ability can be classified best, but overal performance is only slightly above Naive Bayes. Furthermore, MTL does not appear to have any measurable positive effect on scores compared to single task models. A link to the github repository is available at \url{https://github.com/WillemDieleman/ADseverityCSE3000}.