KCO: Balancing class distribution in just-in-time software defect prediction using kernel crossover oversampling.

The performance of the defect prediction model by using balanced and imbalanced datasets makes a big impact on the discovery of future defects. Current resampling techniques only address the imbalanced datasets without taking into consideration redundancy and noise inherent to the imbalanced datasets. To address the imbalance issue, we propose Kernel Crossover Oversampling (KCO), an oversampling technique based on kernel analysis and crossover interpolation. Specifically, the proposed technique aims to generate balanced datasets by increasing data diversity in order to reduce redundancy and noise. KCO first represents multidimensional features into two-dimensional features by employing Kernel Principal Component Analysis (KPCA). KCO then divides the plotted data distribution by deploying spectral clustering to select the best region for interpolation. Lastly, KCO generates the new defect data by interpolating different data templates within the selected data clusters. According to the prediction evaluation conducted, KCO consistently produced F-scores ranging from 21% to 63% across six datasets, on average. According to the experimental results presented in this study, KCO provides more effective prediction performance than other baseline techniques. The experimental results show that KCO within project and cross project predictions especially consistently achieve higher performance of F-score results.

Artificial Bee Colony algorithm in estimating kinetic parameters for yeast fermentation pathway.

Analyzing metabolic pathways in systems biology requires accurate kinetic parameters that represent the simulated in vivo processes. Simulation of the fermentation pathway in the Saccharomyces cerevisiae kinetic model help saves much time in the optimization process. Fitting the simulated model into the experimental data is categorized under the parameter estimation problem. Parameter estimation is conducted to obtain the optimal values for parameters related to the fermentation process. This step is essential because insufficient identification of model parameters can cause erroneous conclusions. The kinetic parameters cannot be measured directly. Therefore, they must be estimated from the experimental data either in vitro or in vivo. Parameter estimation is a challenging task in the biological process due to the complexity and nonlinearity of the model. Therefore, we propose the Artificial Bee Colony algorithm (ABC) to estimate the parameters in the fermentation pathway of S. cerevisiae to obtain more accurate values. A metabolite with a total of six parameters is involved in this article. The experimental results show that ABC outperforms other estimation algorithms and gives more accurate kinetic parameter values for the simulated model. Most of the estimated kinetic parameter values obtained from the proposed algorithm are the closest to the experimental data.

An improved hybrid of particle swarm optimization and the gravitational search algorithm to produce a kinetic parameter estimation of aspartate biochemical pathways.

Mathematical modelling is fundamental to understand the dynamic behavior and regulation of the biochemical metabolisms and pathways that are found in biological systems. Pathways are used to describe complex processes that involve many parameters. It is important to have an accurate and complete set of parameters that describe the characteristics of a given model. However, measuring these parameters is typically difficult and even impossible in some cases. Furthermore, the experimental data are often incomplete and also suffer from experimental noise. These shortcomings make it challenging to identify the best-fit parameters that can represent the actual biological processes involved in biological systems. Computational approaches are required to estimate these parameters. The estimation is converted into multimodal optimization problems that require a global optimization algorithm that can avoid local solutions. These local solutions can lead to a bad fit when calibrating with a model. Although the model itself can potentially match a set of experimental data, a high-performance estimation algorithm is required to improve the quality of the solutions. This paper describes an improved hybrid of particle swarm optimization and the gravitational search algorithm (IPSOGSA) to improve the efficiency of a global optimum (the best set of kinetic parameter values) search. The findings suggest that the proposed algorithm is capable of narrowing down the search space by exploiting the feasible solution areas. Hence, the proposed algorithm is able to achieve a near-optimal set of parameters at a fast convergence speed. The proposed algorithm was tested and evaluated based on two aspartate pathways that were obtained from the BioModels Database. The results show that the proposed algorithm outperformed other standard optimization algorithms in terms of accuracy and near-optimal kinetic parameter estimation. Nevertheless, the proposed algorithm is only expected to work well in small scale systems. In addition, the results of this study can be used to estimate kinetic parameter values in the stage of model selection for different experimental conditions.