GitHub repository for the code accompanying my MSc in Computational Biology thesis. The project is being carried out at the School of Informatics of the Complutense University of Madrid (UCM).
The main objective of this project is to construct and analyze a network of cognitive domains in Mild Cognitive Impairment (MCI) and Alzheimer's patients using a graph theory approach to study whether there are some rearrangements of the network due to the progression of dementia. This network will be constructed from raw scores from neuropsychological tests covering several cognitive domains (memory, language, executive function, motor and visuospatial skills, attention, and orientation). Patient's scores will be normalized to those of healthy elderly controls, which are cognitive normal subjects.
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Python version 3.9.12
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R version 4.2.3
| File name | Description |
|---|---|
GT_analysis.ipynb |
Construction and analysis of cognitive networks with the nodes being different cognitive tests |
GT_analysis_domains.ipynb |
Construction and analysis of cognitive networks with the nodes being cognitive domains |
GT_analysis_genetics.ipynb |
Construction and analysis of cognitive networks for various genetic profiles clusters |
results_visualization.R |
Exploratory data analysis and results visualizations |
For this work, the demographical and neuropsychological data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) was employed. These datasets are available at the ADNI website upon formal request. A complete listing of ADNI investigators can be found in the following link.
The original Tableau dashboard can be found in the following link.
In particular, the ADNI datasets used in the study are the following:
- Neuropsychological Battery [ADNI1,GO,2,3]
- Montreal Cognitive Assessment (MoCA) [ADNIGO,2,3]
- Mini-Mental State Examination (MMSE) [ADNI1,GO,2,3]
- Alzheimer's Disease Assessment Scale (ADAS) [ADNIGO,2,3]
- ADNIMERGE - Key ADNI tables merged into one table - Dictionary [ADNI1,GO,2,3]
In addition, we have created some metadata files associating cognitive tests with cognitive tests. These files can be found in the NC_Tests folder of the current repository.
Data used for the GT_analysis.ipnyb comes from the implementation of an unsupervised machine learning developed by another research project of the Department of Computer Architecture and Automation of the Complutense University of Madrid (UCM) and it is currently no open access.
Ana Solbas Casajús
MSc in Computational Biology, Technical University of Madrid (UPM)