Wavelet feature extraction and genetic algorithm for biomarker detection in colorectal cancer data

Biomarkers which predict patient’s survival can play an important role in medical diagnosis and treatment. How to select the significant biomarkers from hundreds of protein markers is a key step in survival analysis. In this paper a novel method is proposed to detect the prognostic biomarkers ofsurvival in colorectal cancer patients using wavelet analysis, genetic algorithm, and Bayes classifier. One dimensional discrete wavelet transform (DWT) is normally used to reduce the dimensionality of biomedical data. In this study one dimensional continuous wavelet transform (CWT) was proposed to extract the features of colorectal cancer data. One dimensional CWT has no ability to reduce dimensionality of data, but captures the missing features of DWT, and is complementary part of DWT. Genetic algorithm was performed on extracted wavelet coefficients to select the optimized features, using Bayes classifier to build its fitness function. The corresponding protein markers were located based on the position of optimized features. Kaplan-Meier curve and Cox regression model 2 were used to evaluate the performance of selected biomarkers. Experiments were conducted on colorectal cancer dataset and several significant biomarkers were detected. A new protein biomarker CD46 was found to significantly associate with survival time

On the design of an ECOC-compliant genetic algorithm

Genetic Algorithms (GA) have been previously applied to Error-Correcting Output Codes (ECOC) in state-of-the-art works in order to find a suitable coding matrix. Nevertheless, none of the presented techniques directly take into account the properties of the ECOC matrix. As a result the considered search space is unnecessarily large. In this paper, a novel Genetic strategy to optimize the ECOC coding step is presented. This novel strategy redefines the usual crossover and mutation operators in order to take into account the theoretical properties of the ECOC framework. Thus, it reduces the search space and lets the algorithm to converge faster. In addition, a novel operator that is able to enlarge the code in a smart way is introduced. The novel methodology is tested on several UCI datasets and four challenging computer vision problems. Furthermore, the analysis of the results done in terms of performance, code length and number of Support Vectors shows that the optimization process is able to find very efficient codes, in terms of the trade-off between classification performance and the number of classifiers. Finally, classification performance per dichotomizer results shows that the novel proposal is able to obtain similar or even better results while defining a more compact number of dichotomies and SVs compared to state-of-the-art approaches

A Hybrid Differential Evolution Approach to Designing Deep Convolutional Neural Networks for Image Classification

Convolutional Neural Networks (CNNs) have demonstrated their superiority in image classification, and evolutionary computation (EC) methods have recently been surging to automatically design the architectures of CNNs to save the tedious work of manually designing CNNs. In this paper, a new hybrid differential evolution (DE) algorithm with a newly added crossover operator is proposed to evolve the architectures of CNNs of any lengths, which is named DECNN. There are three new ideas in the proposed DECNN method. Firstly, an existing effective encoding scheme is refined to cater for variable-length CNN architectures; Secondly, the new mutation and crossover operators are developed for variable-length DE to optimise the hyperparameters of CNNs; Finally, the new second crossover is introduced to evolve the depth of the CNN architectures. The proposed algorithm is tested on six widely-used benchmark datasets and the results are compared to 12 state-of-the-art methods, which shows the proposed method is vigorously competitive to the state-of-the-art algorithms. Furthermore, the proposed method is also compared with a method using particle swarm optimisation with a similar encoding strategy named IPPSO, and the proposed DECNN outperforms IPPSO in terms of the accuracy.Comment: Accepted by The Australasian Joint Conference on Artificial Intelligence 201