Identification of metabolic pathways using pathfinding approaches: a systematic review.

Metabolic pathways have become increasingly available for various microorganisms. Such pathways have spurred the development of a wide array of computational tools, in particular, mathematical pathfinding approaches. This article can facilitate the understanding of computational analysis of metabolic pathways in genomics. Moreover, stoichiometric and pathfinding approaches in metabolic pathway analysis are discussed. Three major types of studies are elaborated: stoichiometric identification models, pathway-based graph analysis and pathfinding approaches in cellular metabolism. Furthermore, evaluation of the outcomes of the pathways with mathematical benchmarking metrics is provided. This review would lead to better comprehension of metabolism behaviors in living cells, in terms of computed pathfinding approaches.

Quantitative Analysis of Cerebrospinal Fluid Pressure Gradients in Healthy Volunteers and Patients with Normal Pressure Hydrocephalus.

Magnetic resonance imaging (MRI) can depict not only anatomical information, but also physiological factors such as velocity and pressure gradient. Measurement of these physiological factors is necessary to understand the cerebrospinal fluid (CSF) environment. In this study we quantified CSF motion in various parts of the CSF space, determined changes in the CSF environment with aging, and compared CSF pressure gradient between patients with idiopathic normal pressure hydrocephalus (iNPH) and healthy elderly volunteers. Fifty-seven healthy volunteers and six iNPH patients underwent four-dimensional (4D) phase-contrast (PC) MRI. CSF motion was observed and the pressure gradient of CSF was quantified in the CSF space. In healthy volunteers, inhomogeneous CSF motion was observed whereby the pressure gradient markedly increased in the center of the skull and gradually decreased in the periphery of the skull. For example, the pressure gradient at the ventral surface of the brainstem was 6.6 times greater than that at the convexity of the cerebrum. The pressure gradient was statistically unchanged with aging. The pressure gradient of patients with iNPH was 3.2 times greater than that of healthy volunteers. The quantitative analysis of 4D-PC MRI data revealed that the pressure gradient of CSF can be used to understand the CSF environment, which is not sufficiently given by subjective impression of the anatomical image.

A newton cooperative genetic algorithm method for in silico optimization of metabolic pathway production.

This paper presents an in silico optimization method of metabolic pathway production. The metabolic pathway can be represented by a mathematical model known as the generalized mass action model, which leads to a complex nonlinear equations system. The optimization process becomes difficult when steady state and the constraints of the components in the metabolic pathway are involved. To deal with this situation, this paper presents an in silico optimization method, namely the Newton Cooperative Genetic Algorithm (NCGA). The NCGA used Newton method in dealing with the metabolic pathway, and then integrated genetic algorithm and cooperative co-evolutionary algorithm. The proposed method was experimentally applied on the benchmark metabolic pathways, and the results showed that the NCGA achieved better results compared to the existing methods.

Correlation mapping for visualizing propagation of pulsatile CSF motion in intracranial space based on magnetic resonance phase contrast velocity images: preliminary results.

Correlation time mapping based on magnetic resonance (MR) velocimetry has been applied to pulsatile cerebrospinal fluid (CSF) motion to visualize the pressure transmission between CSF at different locations and/or between CSF and arterial blood flow. Healthy volunteer experiments demonstrated that the technique exhibited transmitting pulsatile CSF motion from CSF space in the vicinity of blood vessels with short delay and relatively high correlation coefficients. Patient and healthy volunteer experiments indicated that the properties of CSF motion were different from the healthy volunteers. Resultant images in healthy volunteers implied that there were slight individual difference in the CSF driving source locations. Clinical interpretation for these preliminary results is required to apply the present technique for classifying status of hydrocephalus.

An improved differential evolution algorithm for enhancing biochemical pathways simulation and production.

This paper presents an Improved Differential Evolution (IDE) algorithm to improve the kinetic parameter estimation in simulating the glycolysis pathway and the threonine biosynthesis pathway. Experimentally derived time series kinetic data are noisy and possess many unknown parameters. These characteristics of kinetic data cause lengthy computational time to compute the optimum value of the kinetic parameters. To solve this problem, this study had been conducted to develop a hybrid method that combined the Differential Evolution algorithm (DE) and the Kalman Filter (KF) to produce IDE. Results have shown that lesser computation time (6% and 18.5% faster) and more robust to noisy data with significant reduced error rates (93% and 79% reduced error rates) compared with the Genetic Algorithm (GA) and DE, respectively, in glycolysis and threonine biosynthesis pathway simulations. IDE is reliable as it demonstrated consistent standard deviation values which were close to mean values. We foresee the applicability of IDE into other metabolic pathway simulations.

Cerebrospinal fluid image segmentation using spatial fuzzy clustering method with improved evolutionary Expectation Maximization.

Visualization of cerebrospinal fluid (CSF), that flow in the brain and spinal cord, plays an important role to detect neurodegenerative diseases such as Alzheimer's disease. This is performed by measuring the substantial changes in the CSF flow dynamics, volume and/or pressure gradient. Magnetic resonance imaging (MRI) technique has become a prominent tool to quantitatively measure these changes and image segmentation method has been widely used to distinguish the CSF flows from the brain tissues. However, this is often hampered by the presence of partial volume effect in the images. In this paper, a new hybrid evolutionary spatial fuzzy clustering method is introduced to overcome the partial volume effect in the MRI images. The proposed method incorporates Expectation Maximization (EM) method, which is improved by the evolutionary operations of the Genetic Algorithm (GA) to differentiate the CSF from the brain tissues. The proposed improvement is incorporated into a spatial-based fuzzy clustering (SFCM) method to improve segmentation of the boundary curve of the CSF and the brain tissues. The proposed method was validated using MRI images of Alzheimer's disease patient. The results presented that the proposed method is capable to filter the CSF regions from the brain tissues more effectively compared to the standard EM, FCM, and SFCM methods.

An improved swarm optimization for parameter estimation and biological model selection.

One of the key aspects of computational systems biology is the investigation on the dynamic biological processes within cells. Computational models are often required to elucidate the mechanisms and principles driving the processes because of the nonlinearity and complexity. The models usually incorporate a set of parameters that signify the physical properties of the actual biological systems. In most cases, these parameters are estimated by fitting the model outputs with the corresponding experimental data. However, this is a challenging task because the available experimental data are frequently noisy and incomplete. In this paper, a new hybrid optimization method is proposed to estimate these parameters from the noisy and incomplete experimental data. The proposed method, called Swarm-based Chemical Reaction Optimization, integrates the evolutionary searching strategy employed by the Chemical Reaction Optimization, into the neighbouring searching strategy of the Firefly Algorithm method. The effectiveness of the method was evaluated using a simulated nonlinear model and two biological models: synthetic transcriptional oscillators, and extracellular protease production models. The results showed that the accuracy and computational speed of the proposed method were better than the existing Differential Evolution, Firefly Algorithm and Chemical Reaction Optimization methods. The reliability of the estimated parameters was statistically validated, which suggests that the model outputs produced by these parameters were valid even when noisy and incomplete experimental data were used. Additionally, Akaike Information Criterion was employed to evaluate the model selection, which highlighted the capability of the proposed method in choosing a plausible model based on the experimental data. In conclusion, this paper presents the effectiveness of the proposed method for parameter estimation and model selection problems using noisy and incomplete experimental data. This study is hoped to provide a new insight in developing more accurate and reliable biological models based on limited and low quality experimental data.

An enhancement of binary particle swarm optimization for gene selection in classifying cancer classes.

BACKGROUND: Gene expression data could likely be a momentous help in the progress of proficient cancer diagnoses and classification platforms. Lately, many researchers analyze gene expression data using diverse computational intelligence methods, for selecting a small subset of informative genes from the data for cancer classification. Many computational methods face difficulties in selecting small subsets due to the small number of samples compared to the huge number of genes (high-dimension), irrelevant genes, and noisy genes. METHODS: We propose an enhanced binary particle swarm optimization to perform the selection of small subsets of informative genes which is significant for cancer classification. Particle speed, rule, and modified sigmoid function are introduced in this proposed method to increase the probability of the bits in a particle's position to be zero. The method was empirically applied to a suite of ten well-known benchmark gene expression data sets. RESULTS: The performance of the proposed method proved to be superior to other previous related works, including the conventional version of binary particle swarm optimization (BPSO) in terms of classification accuracy and the number of selected genes. The proposed method also requires lower computational time compared to BPSO.

An evolutionary firefly algorithm for the estimation of nonlinear biological model parameters.

The development of accurate computational models of biological processes is fundamental to computational systems biology. These models are usually represented by mathematical expressions that rely heavily on the system parameters. The measurement of these parameters is often difficult. Therefore, they are commonly estimated by fitting the predicted model to the experimental data using optimization methods. The complexity and nonlinearity of the biological processes pose a significant challenge, however, to the development of accurate and fast optimization methods. We introduce a new hybrid optimization method incorporating the Firefly Algorithm and the evolutionary operation of the Differential Evolution method. The proposed method improves solutions by neighbourhood search using evolutionary procedures. Testing our method on models for the arginine catabolism and the negative feedback loop of the p53 signalling pathway, we found that it estimated the parameters with high accuracy and within a reasonable computation time compared to well-known approaches, including Particle Swarm Optimization, Nelder-Mead, and Firefly Algorithm. We have also verified the reliability of the parameters estimated by the method using an a posteriori practical identifiability test.

An improved hybrid of SVM and SCAD for pathway analysis.

Pathway analysis has lead to a new era in genomic research by providing further biological process information compared to traditional single gene analysis. Beside the advantage, pathway analysis provides some challenges to the researchers, one of which is the quality of pathway data itself. The pathway data usually defined from biological context free, when it comes to a specific biological context (e.g. lung cancer disease), typically only several genes within pathways are responsible for the corresponding cellular process. It also can be that some pathways may be included with uninformative genes or perhaps informative genes were excluded. Moreover, many algorithms in pathway analysis neglect these limitations by treating all the genes within pathways as significant. In previous study, a hybrid of support vector machines and smoothly clipped absolute deviation with groups-specific tuning parameters (gSVM-SCAD) was proposed in order to identify and select the informative genes before the pathway evaluation process. However, gSVM-SCAD had showed a limitation in terms of the performance of classification accuracy. In order to deal with this limitation, we made an enhancement to the tuning parameter method for gSVM-SCAD by applying the B-Type generalized approximate cross validation (BGACV). Experimental analyses using one simulated data and two gene expression data have shown that the proposed method obtains significant results in identifying biologically significant genes and pathways, and in classification accuracy.