Neural Processes Mixed-Effect Models for Deep Normative Modeling of Clinical Neuroimaging Data

Seyed Mostafa Kia, Andre F. Marquand
Proceedings of The 2nd International Conference on Medical Imaging with Deep Learning, PMLR 102:297-314, 2019.

Abstract

Normative modeling has recently been introduced as a promising approach for modeling variation of neuroimaging measures across individuals in order to derive biomarkers of psychiatric disorders. Current implementations rely on Gaussian process regression, which provides coherent estimates of uncertainty needed for the method but also suffers from drawbacks including poor scaling to large datasets and a reliance on fixed parametric kernels. In this paper, we propose a deep normative modeling framework based on neural processes (NPs) to solve these problems. To achieve this, we define a stochastic process formulation for mixed-effect models and show how NPs can be adopted for spatially structured mixed-effect modeling of neuroimaging data. This enables us to learn optimal feature representations and covariance structure for the random-effect and noise via global latent variables. In this scheme, predictive uncertainty can be approximated by sampling from the distribution of these global latent variables. On a publicly available clinical fMRI dataset, we compare the novelty detection performance of multivariate normative models estimated by the proposed NP approach to a baseline multi-task Gaussian process regression approach and show substantial improvements for certain diagnostic problems.

Cite this Paper

BibTeX
@InProceedings{pmlr-v102-kia19a, title = {Neural Processes Mixed-Effect Models for Deep Normative Modeling of Clinical Neuroimaging Data}, author = {Kia, {Seyed Mostafa} and Marquand, {Andre F.}}, booktitle = {Proceedings of The 2nd International Conference on Medical Imaging with Deep Learning}, pages = {297--314}, year = {2019}, editor = {Cardoso, M. Jorge and Feragen, Aasa and Glocker, Ben and Konukoglu, Ender and Oguz, Ipek and Unal, Gozde and Vercauteren, Tom}, volume = {102}, series = {Proceedings of Machine Learning Research}, month = {08--10 Jul}, publisher = {PMLR}, pdf = {http://proceedings.mlr.press/v102/kia19a/kia19a.pdf}, url = {https://proceedings.mlr.press/v102/kia19a.html}, abstract = {Normative modeling has recently been introduced as a promising approach for modeling variation of neuroimaging measures across individuals in order to derive biomarkers of psychiatric disorders. Current implementations rely on Gaussian process regression, which provides coherent estimates of uncertainty needed for the method but also suffers from drawbacks including poor scaling to large datasets and a reliance on fixed parametric kernels. In this paper, we propose a deep normative modeling framework based on neural processes (NPs) to solve these problems. To achieve this, we define a stochastic process formulation for mixed-effect models and show how NPs can be adopted for spatially structured mixed-effect modeling of neuroimaging data. This enables us to learn optimal feature representations and covariance structure for the random-effect and noise via global latent variables. In this scheme, predictive uncertainty can be approximated by sampling from the distribution of these global latent variables. On a publicly available clinical fMRI dataset, we compare the novelty detection performance of multivariate normative models estimated by the proposed NP approach to a baseline multi-task Gaussian process regression approach and show substantial improvements for certain diagnostic problems.} }
Endnote
%0 Conference Paper %T Neural Processes Mixed-Effect Models for Deep Normative Modeling of Clinical Neuroimaging Data %A Seyed Mostafa Kia %A Andre F. Marquand %B Proceedings of The 2nd International Conference on Medical Imaging with Deep Learning %C Proceedings of Machine Learning Research %D 2019 %E M. Jorge Cardoso %E Aasa Feragen %E Ben Glocker %E Ender Konukoglu %E Ipek Oguz %E Gozde Unal %E Tom Vercauteren %F pmlr-v102-kia19a %I PMLR %P 297--314 %U https://proceedings.mlr.press/v102/kia19a.html %V 102 %X Normative modeling has recently been introduced as a promising approach for modeling variation of neuroimaging measures across individuals in order to derive biomarkers of psychiatric disorders. Current implementations rely on Gaussian process regression, which provides coherent estimates of uncertainty needed for the method but also suffers from drawbacks including poor scaling to large datasets and a reliance on fixed parametric kernels. In this paper, we propose a deep normative modeling framework based on neural processes (NPs) to solve these problems. To achieve this, we define a stochastic process formulation for mixed-effect models and show how NPs can be adopted for spatially structured mixed-effect modeling of neuroimaging data. This enables us to learn optimal feature representations and covariance structure for the random-effect and noise via global latent variables. In this scheme, predictive uncertainty can be approximated by sampling from the distribution of these global latent variables. On a publicly available clinical fMRI dataset, we compare the novelty detection performance of multivariate normative models estimated by the proposed NP approach to a baseline multi-task Gaussian process regression approach and show substantial improvements for certain diagnostic problems.
APA
Kia, S.M. & Marquand, A.F.. (2019). Neural Processes Mixed-Effect Models for Deep Normative Modeling of Clinical Neuroimaging Data. Proceedings of The 2nd International Conference on Medical Imaging with Deep Learning, in Proceedings of Machine Learning Research 102:297-314 Available from https://proceedings.mlr.press/v102/kia19a.html.

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