Clusterwise Independent Component Analysis (C-ICA): using fMRI resting state networks to cluster subjects and find neurofunctional subtypes

Background: FMRI resting state networks (RSNs) are used to characterize brain disorders. They also show extensive heterogeneity across patients. Identifying systematic differences between RSNs in patients, i.e. discovering neurofunctional subtypes, may further increase our understanding of disease heterogeneity. Currently, no methodology is available to estimate neurofunctional subtypes and their associated RSNs simultaneously.New method: We present an unsupervised learning method for fMRI data, called Clusterwise Independent Component Analysis (C-ICA). This enables the clustering of patients into neurofunctional subtypes based on differences in shared ICA-derived RSNs. The parameters are estimated simultaneously, which leads to an improved estimation of subtypes and their associated RSNs.Results: In five simulation studies, the C-ICA model is successfully validated using both artificially and realistically simulated data (N = 30-40). The successful performance of the C-ICA model is also illustrated on an empirical data set consisting of Alzheimer's disease patients and elderly control subjects (N = 250). C-ICA is able to uncover a meaningful clustering that partially matches (balanced accuracy = .72) the diagnostic labels and identifies differences in RSNs between the Alzheimer and control cluster. Comparison with other methods: Both in the simulation study and the empirical application, C-ICA yields better results compared to competing clustering methods (i.e., a two step clustering procedure based on single subject ICA's and a Group ICA plus dual regression variant thereof) that do not simultaneously estimate a clustering and associated RSNs. Indeed, the overall mean adjusted Rand Index, a measure for cluster recovery, equals 0.65 for C-ICA and ranges from 0.27 to 0.46 for competing methods.Conclusions: The successful performance of C-ICA indicates that it is a promising method to extract neuro-functional subtypes from multi-subject resting state-fMRI data. This method can be applied on fMRI scans of patient groups to study (neurofunctional) subtypes, which may eventually further increase understanding of disease heterogeneity.Multivariate analysis of psychological dat

Résolution exacte du problème de partitionnement de données avec minimisation de variance sous contraintes de cardinalité par programmation par contraintes

Le partitionnement de données représente une procédure destinée à regrouper un ensemble d’observations dans plusieurs sous ensembles homogènes et/ou bien séparés. L’idée derrière une telle activité est de simplifier l’extraction d’information utile en étudiant les groupes résultants plutôt que les observations elles-mêmes. Cela dit, plusieurs situations appellent à ce que la solution générée respecte un ensemble de contraintes données. En particulier, on exige parfois que les groupes résultants comportent un nombre prédéfini d’éléments. On parle de partitionnement avec contraintes de cardinalité. On présente alors, dans ce travail, une approche de résolution exacte pour le partitionnement de données avec minimisation de la variance sous contraintes de cardinalité. En utilisant le paradigme de la Programmation par Contraintes, on propose d’abord un modèle adéquat du problème selon celui-ci. Ensuite, on suggère à la fois une stratégie de recherche rehaussée ainsi que deux algorithmes de filtrage. Ces outils ainsi développés tirent avantage de la structure particulière du problème afin de naviguer l’espace de recherche de façon efficace, à la recherche d’une solution globalement optimale. Des expérimentations pratiques montrent que notre approche procure un avantage important par rapport aux autres méthodes exactes existantes lors de la résolution de plusieurs exemplaires du problème.----------ABSTRACT: Data clustering is a procedure designed to group a set of observations into subsets that are homogeneous and/or well separated. The idea behind such an endeavor is to simplify extraction of useful information by studying the resulting groups instead of directly dealing with the observations themselves. However, many situations mandate that the answer conform to a set of constraints. Particularly one that involves the target number of elements each group must possess. This is known as cardinality constrained clustering. In this work we present an exact approach to solve the cardinality constrained Euclidian minimum sum-of-squares clustering. Based on the Constraint Programming paradigm, we first present an adequate model for this problem in the aforementioned framework. We then suggest both an upgraded search heuristic as well as two filtering algorithms. We take advantage of the structure of the problem in designing these tools to efficiently navigate the search space, looking for a globally optimal solution. Computational experiments show that our approach provides a substantial boost to the resolution of several instances of the problem in comparison to existing exact methods

Branching strategies for mixed-integer programs containing logical constraints and decomposable structure

Decision-making optimisation problems can include discrete selections, e.g. selecting a route, arranging non-overlapping items or designing a network of items. Branch-and-bound (B&B), a widely applied divide-and-conquer framework, often solves such problems by considering a continuous approximation, e.g. replacing discrete variable domains by a continuous superset. Such approximations weaken the logical relations, e.g. for discrete variables corresponding to Boolean variables. Branching in B&B reintroduces logical relations by dividing the search space. This thesis studies designing B&B branching strategies, i.e. how to divide the search space, for optimisation problems that contain both a logical and a continuous structure. We begin our study with a large-scale, industrially-relevant optimisation problem where the objective consists of machine-learnt gradient-boosted trees (GBTs) and convex penalty functions. GBT functions contain if-then queries which introduces a logical structure to this problem. We propose decomposition-based rigorous bounding strategies and an iterative heuristic that can be embedded into a B&B algorithm. We approach branching with two strategies: a pseudocost initialisation and strong branching that target the structure of GBT and convex penalty aspects of the optimisation objective, respectively. Computational tests show that our B&B approach outperforms state-of-the-art solvers in deriving rigorous bounds on optimality. Our second project investigates how satisfiability modulo theories (SMT) derived unsatisfiable cores may be utilised in a B&B context. Unsatisfiable cores are subsets of constraints that explain an infeasible result. We study two-dimensional bin packing (2BP) and develop a B&B algorithm that branches on SMT unsatisfiable cores. We use the unsatisfiable cores to derive cuts that break 2BP symmetries. Computational results show that our B&B algorithm solves 20% more instances when compared with commercial solvers on the tested instances. Finally, we study convex generalized disjunctive programming (GDP), a framework that supports logical variables and operators. Convex GDP includes disjunctions of mathematical constraints, which motivate branching by partitioning the disjunctions. We investigate separation by branching, i.e. eliminating solutions that prevent rigorous bound improvement, and propose a greedy algorithm for building the branches. We propose three scoring methods for selecting the next branching disjunction. We also analyse how to leverage infeasibility to expedite the B&B search. Computational results show that our scoring methods can reduce the number of explored B&B nodes by an order of magnitude when compared with scoring methods proposed in literature. Our infeasibility analysis further reduces the number of explored nodes.Open Acces

A comparison of the CAR and DAGAR spatial random effects models with an application to diabetics rate estimation in Belgium

When hierarchically modelling an epidemiological phenomenon on a finite collection of sites in space, one must always take a latent spatial effect into account in order to capture the correlation structure that links the phenomenon to the territory. In this work, we compare two autoregressive spatial models that can be used for this purpose: the classical CAR model and the more recent DAGAR model. Differently from the former, the latter has a desirable property: its ρ parameter can be naturally interpreted as the average neighbor pair correlation and, in addition, this parameter can be directly estimated when the effect is modelled using a DAGAR rather than a CAR structure. As an application, we model the diabetics rate in Belgium in 2014 and show the adequacy of these models in predicting the response variable when no covariates are available

A Statistical Approach to the Alignment of fMRI Data

Multi-subject functional Magnetic Resonance Image studies are critical. The anatomical and functional structure varies across subjects, so the image alignment is necessary. We define a probabilistic model to describe functional alignment. Imposing a prior distribution, as the matrix Fisher Von Mises distribution, of the orthogonal transformation parameter, the anatomical information is embedded in the estimation of the parameters, i.e., penalizing the combination of spatially distant voxels. Real applications show an improvement in the classification and interpretability of the results compared to various functional alignment methods