Application and Extension of Weighted Quantile Sum Regression for the Development of a Clinical Risk Prediction Tool

In clinical settings, the diagnosis of medical conditions is often aided by measurement of various serum biomarkers through the use of laboratory tests. These biomarkers provide information about different aspects of a patient’s health and the overall function of different organs. In this dissertation, we develop and validate a weighted composite index that aggregates the information from a variety of health biomarkers covering multiple organ systems. The index can be used for predicting all-cause mortality and could also be used as a holistic measure of overall physiological health status. We refer to it as the Health Status Metric (HSM). Validation analysis shows that the HSM is predictive of long-term mortality risk and exhibits a robust association with concurrent chronic conditions, recent hospital utilization, and self-rated health. We develop the HSM using Weighted Quantile Sum (WQS) regression (Gennings et al., 2013; Carrico, 2013), a novel penalized regression technique that imposes nonnegativity and unit-sum constraints on the coefficients used to weight index components. In this dissertation, we develop a number of extensions to the WQS regression technique and apply them to the construction of the HSM. We introduce a new guided approach for the standardization of index components which accounts for potential nonlinear relationships with the outcome of interest. An extended version of the WQS that accommodates interaction effects among index components is also developed and implemented. In addition, we demonstrate that ensemble learning methods borrowed from the field of machine learning can be used to improve the predictive power of the WQS index. Specifically, we show that the use of techniques such as weighted bagging, the random subspace method and stacked generalization in conjunction with the WQS model can produce an index with substantially enhanced predictive accuracy. Finally, practical applications of the HSM are explored. A comparative study is performed to evaluate the feasibility and effectiveness of a number of ‘real-time’ imputation strategies in potential software applications for computing the HSM. In addition, the efficacy of the HSM as a predictor of hospital readmission is assessed in a cohort of emergency department patients

An Iterative Co-Saliency Framework for RGBD Images

As a newly emerging and significant topic in computer vision community, co-saliency detection aims at discovering the common salient objects in multiple related images. The existing methods often generate the co-saliency map through a direct forward pipeline which is based on the designed cues or initialization, but lack the refinement-cycle scheme. Moreover, they mainly focus on RGB image and ignore the depth information for RGBD images. In this paper, we propose an iterative RGBD co-saliency framework, which utilizes the existing single saliency maps as the initialization, and generates the final RGBD cosaliency map by using a refinement-cycle model. Three schemes are employed in the proposed RGBD co-saliency framework, which include the addition scheme, deletion scheme, and iteration scheme. The addition scheme is used to highlight the salient regions based on intra-image depth propagation and saliency propagation, while the deletion scheme filters the saliency regions and removes the non-common salient regions based on interimage constraint. The iteration scheme is proposed to obtain more homogeneous and consistent co-saliency map. Furthermore, a novel descriptor, named depth shape prior, is proposed in the addition scheme to introduce the depth information to enhance identification of co-salient objects. The proposed method can effectively exploit any existing 2D saliency model to work well in RGBD co-saliency scenarios. The experiments on two RGBD cosaliency datasets demonstrate the effectiveness of our proposed framework.Comment: 13 pages, 13 figures, Accepted by IEEE Transactions on Cybernetics 2017. Project URL: https://rmcong.github.io/proj_RGBD_cosal_tcyb.htm

Sélection de variables pour l’analyse des données semi-supervisées dans les systèmes d’Information décisionnels

Feature selection is an important task in data mining and machine learning processes. This task is well known in both supervised and unsupervised contexts. The semi-supervised feature selection is still under development and far from being mature. In general, machine learning has been well developed in order to deal with partially-labeled data. Thus, feature selection has obtained special importance in the semi-supervised context. It became more adapted with the real world applications where labeling process is costly to obtain. In this thesis, we present a literature review on semi-supervised feature selection, with regard to supervised and unsupervised contexts. The goal is to show the importance of compromising between the structure from unlabeled part of data, and the background information from their labeled part. In particular, we are interested in the so-called «small labeled-sample problem» where the difference between both data parts is very important. In order to deal with the problem of semi-supervised feature selection, we propose two groups of approaches. The first group is of «Filter» type, in which, we propose some algorithms which evaluate the relevance of features by a scoring function. In our case, this function is based on spectral-graph theory and the integration of pairwise constraints which can be extracted from the data in hand. The second group of methods is of «Embedded» type, where feature selection becomes an internal function integrated in the learning process. In order to realize embedded feature selection, we propose algorithms based on feature weighting. The proposed methods rely on constrained clustering. In this sense, we propose two visions, (1) a global vision, based on relaxed satisfaction of pairwise constraints. This is done by integrating the constraints in the objective function of the proposed clustering model; and (2) a second vision, which is local and based on strict control of constraint violation. Both approaches evaluate the relevance of features by weights which are learned during the construction of the clustering model. In addition to the main task which is feature selection, we are interested in redundancy elimination. In order to tackle this problem, we propose a novel algorithm based on combining the mutual information with maximum spanning tree-based algorithm. We construct this tree from the relevant features in order to optimize the number of these selected features at the end. Finally, all proposed methods in this thesis are analyzed and their complexities are studied. Furthermore, they are validated on high-dimensional data versus other representative methods in the literature.La sélection de variables est une tâche primordiale en fouille de données et apprentissage automatique. Il s’agit d’une problématique très bien connue par les deux communautés dans les contextes, supervisé et non-supervisé. Le contexte semi-supervisé est relativement récent et les travaux sont embryonnaires. Récemment, l’apprentissage automatique a bien été développé à partir des données partiellement labélisées. La sélection de variables est donc devenue plus importante dans le contexte semi-supervisé et plus adaptée aux applications réelles, où l’étiquetage des données est devenu plus couteux et difficile à obtenir. Dans cette thèse, nous présentons une étude centrée sur l’état de l’art du domaine de la sélection de variable en s’appuyant sur les méthodes qui opèrent en mode semi-supervisé par rapport à celles des deux contextes, supervisé et non-supervisé. Il s’agit de montrer le bon compromis entre la structure géométrique de la partie non labélisée des données et l’information supervisée de leur partie labélisée. Nous nous sommes particulièrement intéressés au «small labeled-sample problem» où l’écart est très important entre les deux parties qui constituent les données. Pour la sélection de variables dans ce contexte semi-supervisé, nous proposons deux familles d’approches en deux grandes parties. La première famille est de type «Filtre» avec une série d’algorithmes qui évaluent la pertinence d’une variable par une fonction de score. Dans notre cas, cette fonction est basée sur la théorie spectrale de graphe et l’intégration de contraintes qui peuvent être extraites à partir des données en question. La deuxième famille d’approches est de type «Embedded» où la sélection de variable est intrinsèquement liée à un modèle d’apprentissage. Pour ce faire, nous proposons des algorithmes à base de pondération de variables dans un paradigme de classification automatique sous contraintes. Deux visions sont développées à cet effet, (1) une vision globale en se basant sur la satisfaction relaxée des contraintes intégrées directement dans la fonction objective du modèle proposé ; et (2) une deuxième vision, qui est locale et basée sur le contrôle stricte de violation de ces dites contraintes. Les deux approches évaluent la pertinence des variables par des poids appris en cours de la construction du modèle de classification. En outre de cette tâche principale de sélection de variables, nous nous intéressons au traitement de la redondance. Pour traiter ce problème, nous proposons une méthode originale combinant l’information mutuelle et un algorithme de recherche d’arbre couvrant construit à partir de variables pertinentes en vue de l’optimisation de leur nombre au final. Finalement, toutes les approches développées dans le cadre de cette thèse sont étudiées en termes de leur complexité algorithmique d’une part et sont validés sur des données de très grande dimension face et des méthodes connues dans la littérature d’autre part

A weighted multiple classifier framework based on random projection.

In this paper, we propose a weighted multiple classifier framework based on random projections. Similar to the mechanism of other homogeneous ensemble methods, the base classifiers in our approach are obtained by a learning algorithm on different training sets generated by projecting the original up-space training set to lower dimensional down-spaces. We then apply a Least SquarE−based method to weigh the outputs of the base classifiers so that the contribution of each classifier to the final combined prediction is different. We choose Decision Tree as the learning algorithm in the proposed framework and conduct experiments on a number of real and synthetic datasets. The experimental results indicate that our framework is better than many of the benchmark algorithms, including three homogeneous ensemble methods (Bagging, RotBoost, and Random Subspace), several well-known algorithms (Decision Tree, Random Neural Network, Linear Discriminative Analysis, K Nearest Neighbor, L2-loss Linear Support Vector Machine, and Discriminative Restricted Boltzmann Machine), and random projection-based ensembles with fixed combining rules with regard to both classification error rates and F1 scores

Line Based Multi-Range Asymmetric Conditional Random Field For Terrestrial Laser Scanning Data Classification

Terrestrial Laser Scanning (TLS) is a ground-based, active imaging method that rapidly acquires accurate, highly dense three-dimensional point cloud of object surfaces by laser range finding. For fully utilizing its benefits, developing a robust method to classify many objects of interests from huge amounts of laser point clouds is urgently required. However, classifying massive TLS data faces many challenges, such as complex urban scene, partial data acquisition from occlusion. To make an automatic, accurate and robust TLS data classification, we present a line-based multi-range asymmetric Conditional Random Field algorithm. The first contribution is to propose a line-base TLS data classification method. In this thesis, we are interested in seven classes: building, roof, pedestrian road (PR), tree, low man-made object (LMO), vehicle road (VR), and low vegetation (LV). The line-based classification is implemented in each scan profile, which follows the line profiling nature of laser scanning mechanism.Ten conventional local classifiers are tested, including popular generative and discriminative classifiers, and experimental results validate that the line-based method can achieve satisfying classification performance. However, local classifiers implement labeling task on individual line independently of its neighborhood, the inference of which often suffers from similar local appearance across different object classes. The second contribution is to propose a multi-range asymmetric Conditional Random Field (maCRF) model, which uses object context as post-classification to improve the performance of a local generative classifier. The maCRF incorporates appearance, local smoothness constraint, and global scene layout regularity together into a probabilistic graphical model. The local smoothness enforces that lines in a local area to have the same class label, while scene layout favours an asymmetric regularity of spatial arrangement between different object classes within long-range, which is considered both in vertical (above-bellow relation) and horizontal (front-behind) directions. The asymmetric regularity allows capturing directional spatial arrangement between pairwise objects (e.g. it allows ground is lower than building, not vice-versa). The third contribution is to extend the maCRF model by adding across scan profile context, which is called Across scan profile Multi-range Asymmetric Conditional Random Field (amaCRF) model. Due to the sweeping nature of laser scanning, the sequentially acquired TLS data has strong spatial dependency, and the across scan profile context can provide more contextual information. The final contribution is to propose a sequential classification strategy. Along the sweeping direction of laser scanning, amaCRF models were sequentially constructed. By dynamically updating posterior probability of common scan profiles, contextual information propagates through adjacent scan profiles