PLS dimension reduction for classification of microarray data

PLS dimension reduction is known to give good prediction accuracy in the context of classification with high-dimensional microarray data. In this paper, PLS is compared with some of the best state-of-the-art classification methods. In addition, a simple procedure to choose the number of components is suggested. The connection between PLS dimension reduction and gene selection is examined and a property of the first PLS component for binary classification is proven. PLS can also be used as a visualization tool for high-dimensional data in the classification framework. The whole study is based on 9 real microarray cancer data sets

Heterogeneous Kohonen networks

A large number of practical problems involves elements that are described as a mixture of qualitative and quantitative infomation, and whose description is probably incomplete. The self-organizing map is an effective tool for visualization of high-dimensional continuous data. In this work, we extend the network and training algorithm to cope with heterogeneous information, as well as missing values. The classification performance on a collection of benchmarking data sets is compared in different configurations. Various visualization methods are suggested to aid users interpret post-training results.Peer ReviewedPostprint (author's final draft

Multi-Objective Genetic Programming for Feature Extraction and Data Visualization

Feature extraction transforms high dimensional data into a new subspace of lower dimensionalitywhile keeping the classification accuracy. Traditional algorithms do not consider the multi-objective nature of this task. Data transformations should improve the classification performance on the new subspace, as well as to facilitate data visualization, which has attracted increasing attention in recent years. Moreover, new challenges arising in data mining, such as the need to deal with imbalanced data sets call for new algorithms capable of handling this type of data. This paper presents a Pareto-basedmulti-objective genetic programming algorithm for feature extraction and data visualization. The algorithm is designed to obtain data transformations that optimize the classification and visualization performance both on balanced and imbalanced data. Six classification and visualization measures are identified as objectives to be optimized by the multi-objective algorithm. The algorithm is evaluated and compared to 11 well-known feature extraction methods, and to the performance on the original high dimensional data. Experimental results on 22 balanced and 20 imbalanced data sets show that it performs very well on both types of data, which is its significant advantage over existing feature extraction algorithms

Projections as visual aids for classification system design.

Dimensionality reduction is a compelling alternative for high-dimensional data visualization. This method provides insight into high-dimensional feature spaces by mapping relationships between observations (high-dimensional vectors) to low (two or three) dimensional spaces. These low-dimensional representations support tasks such as outlier and group detection based on direct visualization. Supervised learning, a subfield of machine learning, is also concerned with observations. A key task in supervised learning consists of assigning class labels to observations based on generalization from previous experience. Effective development of such classification systems depends on many choices, including features descriptors, learning algorithms, and hyperparameters. These choices are not trivial, and there is no simple recipe to improve classification systems that perform poorly. In this context, we first propose the use of visual representations based on dimensionality reduction (projections) for predictive feedback on classification efficacy. Second, we propose a projection-based visual analytics methodology, and supportive tooling, that can be used to improve classification systems through feature selection. We evaluate our proposal through experiments involving four datasets and three representative learning algorithms

Maximum Entropy Linear Manifold for Learning Discriminative Low-dimensional Representation

Representation learning is currently a very hot topic in modern machine learning, mostly due to the great success of the deep learning methods. In particular low-dimensional representation which discriminates classes can not only enhance the classification procedure, but also make it faster, while contrary to the high-dimensional embeddings can be efficiently used for visual based exploratory data analysis. In this paper we propose Maximum Entropy Linear Manifold (MELM), a multidimensional generalization of Multithreshold Entropy Linear Classifier model which is able to find a low-dimensional linear data projection maximizing discriminativeness of projected classes. As a result we obtain a linear embedding which can be used for classification, class aware dimensionality reduction and data visualization. MELM provides highly discriminative 2D projections of the data which can be used as a method for constructing robust classifiers. We provide both empirical evaluation as well as some interesting theoretical properties of our objective function such us scale and affine transformation invariance, connections with PCA and bounding of the expected balanced accuracy error.Comment: submitted to ECMLPKDD 201

High Dimensional Classification with combined Adaptive Sparse PLS and Logistic Regression

Motivation: The high dimensionality of genomic data calls for the development of specific classification methodologies, especially to prevent over-optimistic predictions. This challenge can be tackled by compression and variable selection, which combined constitute a powerful framework for classification, as well as data visualization and interpretation. However, current proposed combinations lead to instable and non convergent methods due to inappropriate computational frameworks. We hereby propose a stable and convergent approach for classification in high dimensional based on sparse Partial Least Squares (sparse PLS). Results: We start by proposing a new solution for the sparse PLS problem that is based on proximal operators for the case of univariate responses. Then we develop an adaptive version of the sparse PLS for classification, which combines iterative optimization of logistic regression and sparse PLS to ensure convergence and stability. Our results are confirmed on synthetic and experimental data. In particular we show how crucial convergence and stability can be when cross-validation is involved for calibration purposes. Using gene expression data we explore the prediction of breast cancer relapse. We also propose a multicategorial version of our method on the prediction of cell-types based on single-cell expression data. Availability: Our approach is implemented in the plsgenomics R-package.Comment: 9 pages, 3 figures, 4 tables + Supplementary Materials 8 pages, 3 figures, 10 table