A memetic algorithm for gene selection and molecular classification of cancer

Choosing a small subset of genes that enables a good classification of diseases on the basis of microarray data is a difficult optimization problem. This paper presents a memetic algorithm, called MAGS, to deal with gene selection for supervised classification of microarray data. MAGS is based on an embedded approach for attribute selection where a classifier tightly interacts with the selection process. The strength of MAGS relies on the synergy created by combining a problem specific crossover operator and a dedicated local search procedure, both being guided by relevant information from a SVM classifier. Computational experiments on 8 well-known microarray datasets show that our memetic algorithm is very competitive compared with some recently published studies

Dimensionality reduction by minimizing nearest-neighbor classification error

There is a great interest in dimensionality reduction techniques for tackling the problem of high-dimensional pattern classification. This paper addresses the topic of supervised learning of a linear dimension reduction mapping suitable for classification problems. The proposed optimization procedure is based on minimizing an estimation of the nearest neighbor classifier error probability, and it learns a linear projection and a small set of prototypes that support the class boundaries. The learned classifier has the property of being very computationally efficient, making the classification much faster than state-of-the-art classifiers, such as SVMs, while having competitive recognition accuracy. The approach has been assessed through a series of experiments, showing a uniformly good behavior, and competitive compared with some recently proposed supervised dimensionality reduction techniques. © 2010 Elsevier B.V. All rights reserved.Work partially supported by the Spanish projects TIN2008-04571 and Consolider Ingenio 2010: MIPRCV (CSD2007-00018).Villegas, M.; Paredes Palacios, R. (2011). Dimensionality reduction by minimizing nearest-neighbor classification error. Pattern Recognition Letters. 32(4):633-639. https://doi.org/10.1016/j.patrec.2010.12.002S63363932

Boosting for tumor classification with gene expression data

Motivation: Microarray experiments generate large datasets with expression values for thousands of genes but not more than a few dozens of samples. Accurate supervised classification of tissue samples in such high-dimensional problems is difficult but often crucial for successful diagnosis and treatment. A promising way to meet this challenge is by using boosting in conjunction with decision trees. Results: We demonstrate that the generic boosting algorithm needs some modification to become an accurate classifier in the context of gene expression data. In particular, we present a feature preselection method, a more robust boosting procedure and a new approach for multi-categorical problems. This allows for slight to drastic increase in performance and yields competitive results on several publicly available datasets. Availability: Software for the modified boosting algorithms as well as for decision trees is available for free in R at http://stat.ethz.ch/~dettling/boosting.html Contact: [email protected] * To whom correspondence should be addresse

Implicitly Constrained Semi-Supervised Least Squares Classification

We introduce a novel semi-supervised version of the least squares classifier. This implicitly constrained least squares (ICLS) classifier minimizes the squared loss on the labeled data among the set of parameters implied by all possible labelings of the unlabeled data. Unlike other discriminative semi-supervised methods, our approach does not introduce explicit additional assumptions into the objective function, but leverages implicit assumptions already present in the choice of the supervised least squares classifier. We show this approach can be formulated as a quadratic programming problem and its solution can be found using a simple gradient descent procedure. We prove that, in a certain way, our method never leads to performance worse than the supervised classifier. Experimental results corroborate this theoretical result in the multidimensional case on benchmark datasets, also in terms of the error rate.Comment: 12 pages, 2 figures, 1 table. The Fourteenth International Symposium on Intelligent Data Analysis (2015), Saint-Etienne, Franc

Semi-supervised Tuning from Temporal Coherence

Recent works demonstrated the usefulness of temporal coherence to regularize supervised training or to learn invariant features with deep architectures. In particular, enforcing smooth output changes while presenting temporally-closed frames from video sequences, proved to be an effective strategy. In this paper we prove the efficacy of temporal coherence for semi-supervised incremental tuning. We show that a deep architecture, just mildly trained in a supervised manner, can progressively improve its classification accuracy, if exposed to video sequences of unlabeled data. The extent to which, in some cases, a semi-supervised tuning allows to improve classification accuracy (approaching the supervised one) is somewhat surprising. A number of control experiments pointed out the fundamental role of temporal coherence.Comment: Under review as a conference paper at ICLR 201

Projected Estimators for Robust Semi-supervised Classification

For semi-supervised techniques to be applied safely in practice we at least want methods to outperform their supervised counterparts. We study this question for classification using the well-known quadratic surrogate loss function. Using a projection of the supervised estimate onto a set of constraints imposed by the unlabeled data, we find we can safely improve over the supervised solution in terms of this quadratic loss. Unlike other approaches to semi-supervised learning, the procedure does not rely on assumptions that are not intrinsic to the classifier at hand. It is theoretically demonstrated that, measured on the labeled and unlabeled training data, this semi-supervised procedure never gives a lower quadratic loss than the supervised alternative. To our knowledge this is the first approach that offers such strong, albeit conservative, guarantees for improvement over the supervised solution. The characteristics of our approach are explicated using benchmark datasets to further understand the similarities and differences between the quadratic loss criterion used in the theoretical results and the classification accuracy often considered in practice.Comment: 13 pages, 2 figures, 1 tabl