mlni 0.1.4

Machine Learning in NeuroImaging for various tasks, e.g., regression, classification and clustering.

MLNI

Machine Learning in NeuroImaging

Documentation

MLNI

MLNI is a python package that performs various tasks using neuroimaging data: i) binary classification for disease diagnosis, following good practice proposed in AD-ML; ii) regression prediction, such as age prediction; and iii) semi-supervised clustering with HYDRA.

:warning: The documentation of this software is currently under development

Citing this work

If you use this software for clustering:

Varol, E., Sotiras, A., Davatzikos, C., 2017. HYDRA: Revealing heterogeneity of imaging and genetic patterns through a multiple max-margin discriminative analysis framework. Neuroimage, 145, pp.346-364. doi:10.1016/j.neuroimage.2016.02.041 - Paper in PDF

If you use this software for classification or regression:

Wen, J., Samper-González, J., Bottani, S., Routier, A., Burgos, N., Jacquemont, T., Fontanella, S., Durrleman, S., Epelbaum, S., Bertrand, A. and Colliot, O., 2020. Reproducible evaluation of diffusion MRI features for automatic classification of patients with Alzheimer’s disease. Neuroinformatics, pp.1-22. doi:10.1007/s12021-020-09469-5 - Paper in PDF

J. Samper-Gonzalez, N. Burgos, S. Bottani, S. Fontanella, P. Lu, A. Marcoux, A. Routier, J. Guillon, M. Bacci, J. Wen, A. Bertrand, H. Bertin, M.-O. Habert, S. Durrleman, T. Evgeniou and O. Colliot, Reproducible evaluation of classification methods in Alzheimer’s disease: Framework and application to MRI and PET data. NeuroImage, 183:504–521, 2018 doi:10.1016/j.neuroimage.2018.08.042 - Paper in PDF - Supplementary material

Publication using MLNI

Wen, J., Varol, E., Davatzikos, C., 2020. Multi-scale feature reduction and semi-supervised learning for parsing neuroanatomical heterogeneity. Organization for Human Brain Mapping. - Link

Wen, J., Varol, E., Davatzikos, C., 2021. Multi-scale semi-supervised clustering of brain images: deriving disease subtypes. MedIA. - Link

Wen, J., Fu, C.H., Tosun, Davatzikos, C. 2022. Characterizing Heterogeneity in Neuroimaging, Cognition, Clinical Symptoms, and Genetics Among Patients With Late-Life Depression. JAMA Psychiatry - Link

Lalousis, P.A., Schmaal, L., Wood, S.J., Reniers, R.L., Barnes, N.M., Chisholm, K., Griffiths, S.L., Stainton, A., Wen, J., Hwang, G. and Davatzikos, C., 2022. Neurobiologically Based Stratification of Recent Onset Depression and Psychosis: Identification of Two Distinct Transdiagnostic Phenotypes. Biological Psychiatry. - Link