Optimization of Computer Aided Detection systems: an evolutionary approach

Computer Aided Diagnosis (CAD) systems are designed to aid the radiologist in interpreting medical images. They are usually based on lesion detection and segmentation algorithms whose performance depends on a large number of parameters. While time consuming and sub-optimal, manual adjustment is still widely used to adjust parameter values. Genetic or evolutionary algorithms (GA) are effective optimization methods that mimic biological evolution. Genetic algorithms have been shown to efficiently manage complex search spaces, and can be applied to all kinds of objective functions, including discontinuous, nondifferentiable, or highly nonlinear ones. In this study, we have adopted an evolutionary approach to the problem of parameter optimization. We show that the genetic algorithm is able to effectively converge to a better solution than manual optimization on a case study for digital breast tomosynthesis CAD. Parameter optimization was framed as a constrained optimization problem, where the function to be maximized was defined as weighted sum of sensitivity, false positive rate and segmentation accuracy. A modified Dice coefficient was defined to assess the segmentation quality of individual lesions. Finally, all viable solutions evaluated by the GA were studied by means of exploratory data analysis techniques, such as association rules, to gain useful insight on the strength of the influence of each parameter on overall algorithm performance. We showed that this combination was able to identify multiple ranges of viable solutions with good segmentation accuracy

A graph-based representation of Gene Expression profiles in DNA microarrays

This paper proposes a new and very flexible data model, called gene expression graph (GEG), for genes expression analysis and classification. Three features differentiate GEGs from other available microarray data representation structures: (i) the memory occupation of a GEG is independent of the number of samples used to built it; (ii) a GEG more clearly expresses relationships among expressed and non expressed genes in both healthy and diseased tissues experiments; (iii) GEGs allow to easily implement very efficient classifiers. The paper also presents a simple classifier for sample-based classification to show the flexibility and user-friendliness of the proposed data structur

Feature selection and categorization to design reliable fault detection systems.

International audienceIn this work, we will develop a fault detection system which is identified as a classification task. The classes are the nominal or malfunctioning state. To develop a decision system it is important to select among the data collected by the supervision system, only those carrying relevant information related to the decision task. There are two objectives presented in this paper, the first one is to use data mining techniques to improve fault detection tasks. For this purpose, feature selection algorithms are applied before a classifier to select which measures are needed for a fault detection system. The second objective is to use STRASS (STrong Relevant Algorithm of Subset Selection), which gives a useful feature categorization: strong relevant features, weak relevant and/or redundant ones. This feature categorization permits to design reliable fault detection system. The algorithm is tested on real benchmarks in medical diagnosis and fault detection. Our results indicate that a small number of measures can accomplish and perform the classification task and shown our algorithm ability to detect the correlated features. Furthermore, the proposed feature selection and categorization permits to design reliable and efficient fault detection system

Differential gene expression graphs: A data structure for classification in DNA microarrays

This paper proposes an innovative data structure to be used as a backbone in designing microarray phenotype sample classifiers. The data structure is based on graphs and it is built from a differential analysis of the expression levels of healthy and diseased tissue samples in a microarray dataset. The proposed data structure is built in such a way that, by construction, it shows a number of properties that are perfectly suited to address several problems like feature extraction, clustering, and classificatio

Optimization techniques in respiratory control system models

One of the most complex physiological systems whose modeling is still an open study is the respiratory control system where different models have been proposed based on the criterion of minimizing the work of breathing (WOB). The aim of this study is twofold: to compare two known models of the respiratory control system which set the breathing pattern based on quantifying the respiratory work; and to assess the influence of using direct-search or evolutionary optimization algorithms on adjustment of model parameters. This study was carried out using experimental data from a group of healthy volunteers under CO2 incremental inhalation, which were used to adjust the model parameters and to evaluate how much the equations of WOB follow a real breathing pattern. This breathing pattern was characterized by the following variables: tidal volume, inspiratory and expiratory time duration and total minute ventilation. Different optimization algorithms were considered to determine the most appropriate model from physiological viewpoint. Algorithms were used for a double optimization: firstly, to minimize the WOB and secondly to adjust model parameters. The performance of optimization algorithms was also evaluated in terms of convergence rate, solution accuracy and precision. Results showed strong differences in the performance of optimization algorithms according to constraints and topological features of the function to be optimized. In breathing pattern optimization, the sequential quadratic programming technique (SQP) showed the best performance and convergence speed when respiratory work was low. In addition, SQP allowed to implement multiple non-linear constraints through mathematical expressions in the easiest way. Regarding parameter adjustment of the model to experimental data, the evolutionary strategy with covariance matrix and adaptation (CMA-ES) provided the best quality solutions with fast convergence and the best accuracy and precision in both models. CMAES reached the best adjustment because of its good performance on noise and multi-peaked fitness functions. Although one of the studied models has been much more commonly used to simulate respiratory response to CO2 inhalation, results showed that an alternative model has a more appropriate cost function to minimize WOB from a physiological viewpoint according to experimental data.Postprint (author's final draft