Evolutionary Computation and QSAR Research

[Abstract] The successful high throughput screening of molecule libraries for a specific biological property is one of the main improvements in drug discovery. The virtual molecular filtering and screening relies greatly on quantitative structure-activity relationship (QSAR) analysis, a mathematical model that correlates the activity of a molecule with molecular descriptors. QSAR models have the potential to reduce the costly failure of drug candidates in advanced (clinical) stages by filtering combinatorial libraries, eliminating candidates with a predicted toxic effect and poor pharmacokinetic profiles, and reducing the number of experiments. To obtain a predictive and reliable QSAR model, scientists use methods from various fields such as molecular modeling, pattern recognition, machine learning or artificial intelligence. QSAR modeling relies on three main steps: molecular structure codification into molecular descriptors, selection of relevant variables in the context of the analyzed activity, and search of the optimal mathematical model that correlates the molecular descriptors with a specific activity. Since a variety of techniques from statistics and artificial intelligence can aid variable selection and model building steps, this review focuses on the evolutionary computation methods supporting these tasks. Thus, this review explains the basic of the genetic algorithms and genetic programming as evolutionary computation approaches, the selection methods for high-dimensional data in QSAR, the methods to build QSAR models, the current evolutionary feature selection methods and applications in QSAR and the future trend on the joint or multi-task feature selection methods.Instituto de Salud Carlos III, PIO52048Instituto de Salud Carlos III, RD07/0067/0005Ministerio de Industria, Comercio y Turismo; TSI-020110-2009-53)Galicia. Consellería de Economía e Industria; 10SIN105004P

Towards Biological Inspiration in the Development of Complex Systems

Greater understanding of biology in modem times has enabled significant breakthroughs in improving healthcare, quality of life, and eliminating many diseases and congenital illnesses. Simultaneously there is a move towards emulating nature and copying many of the wonders uncovered in biology, resulting in "biologically inspired" systems. Significant results have been reported in a wide range of areas, with systems inspired by nature enabling exploration, communication, and advances that were never dreamed possible just a few years ago. We warn, that as in many other fields of endeavor, we should be inspired by nature and biology, not engage in mimicry. We describe some results of biological inspiration that augur promise in terms of improving the safety and security of systems, and in developing self-managing systems, that we hope will ultimately lead to self-governing systems

Designing Artificial Neural Network Using Particle Swarm Optimization: A Survey

Neural network modeling has become a special interest for many engineers and scientists to be utilized in different types of data as time series, regression, and classification and have been used to solve complicated practical problems in different areas, such as medicine, engineering, manufacturing, military, business. To utilize a prediction model that is based upon artificial neural network (ANN), some challenges should be addressed that optimal designing and training of ANN are major ones. ANN can be defined as an optimization task because it has many hyper parameters and weights that can be optimized. Metaheuristic algorithms such as swarm intelligence-based methods are a category of optimization methods that aim to find an optimal structure of ANN and to train the network by optimizing the weights. One of the commonly used swarm intelligence-based algorithms is particle swarm optimization (PSO) that can be used for optimizing ANN. In this study, we review the conducted research works on optimizing the ANNs using PSO. All studies are reviewed from two different perspectives: optimization of weights and optimization of structure and hyper parameters

99% (Biological) Inspiration …

Greater understanding of biology in modern times has enabled significant breakthroughs in improving healthcare, quality of life, and eliminating many diseases and congenital illnesses. Simultaneously there is a move towards emulating nature and copying many of the wonders uncovered in biology, resulting in “biologically inspired” systems. Significant results have been reported in a wide range of areas, with systems inspired by nature enabling exploration, communication, and advances that were never dreamed possible just a few years ago. We warn, that as in many other fields of endeavor, we should be inspired by nature and biology, not engage in mimicry. We describe some results of biological inspiration that augur promise in terms of improving the safety and security of systems, and in developing self-managing systems, that we hope will ultimately lead to self-governing systems.1st IFIP International Conference on Biologically Inspired Cooperative Computing - Biological Inspiration: Just a dream?Red de Universidades con Carreras en Informática (RedUNCI

Gravity Data Interpretation Using Different New Algorithms: A Comparative Study

Gravity data interpretation is useful in exploring regions that have different geological structures, which contain minerals, ores and oil deposits. There are different numerical methods for the model parameters (depth (z), origin location (xo), shape parameter (q) and amplitude coefficient (A)) evaluation of a covered structure such as gradient method, particle swarm optimization technique and Werner deconvolution method. In this study, application of these methods is utilized to appraise the model parametric quantity of the covered structures. The application of these methods was demonstrated by different engineered data without and with various range of noise (5%, 10%) and applied for a real example from Egypt. The result values of each method were compared together and with those published and drilling information

Prognosis Prediction for Class III Malocclusion Treatment by Feature Wrapping Method

Objective: To use the feature wrapping (FW) method to identify which cephalometric markers show the highest classification accuracy in prognosis prediction for Class III malocclusion and to compare the prediction accuracy between the FW method and conventional statistical methods such as discriminant analysis (DA). Materials and Methods: The sample set consisted of 38 patients (15 boys and 23 girls, mean age 8.53 ± 1.36 years) who were diagnosed with Class III malocclusion and received both first-phase (orthopedic) and second-phase (fixed orthodontic) treatments. Lateral cephalograms were taken before (T0) and after first-phase treatment (T1) and after second-phase treatment and retention (T2). Based on the measurements taken at the T2 stage, the patients were allocated into good (n = 20) or poor (n = 18) prognosis groups. Forty-six cephalometric variables on T0 lateral cephalograms were analyzed by the FW method to identify key determinants for discriminating between the two groups. Sequential forward search (SFS) algorism and support vector machine (SVM) were used in conjunction with the FW method to improve classification accuracy. To compare the prediction accuracy of the FW method with conventional statistical methods, DA was performed for the same data set. Results: AB to mandibular plane angle (°) and A to N-perpendicular (mm) were selected as the most accurate cephalometric predictors by both the FW and DA methods. However, classification accuracy was higher with the FW method (97.2%) compared with DA (92.1%), because the FW method with SFS and SVM has a more precise classification algorithm. Conclusions: The FW method, which uses a learning algorithm, might be an effective alternative to DA for prognosis prediction

Machine learning assisted optimization with applications to diesel engine optimization with the particle swarm optimization algorithm

A novel approach to incorporating Machine Learning into optimization routines is presented. An approach which combines the benefits of ML, optimization, and meta-model searching is developed and tested on a multi-modal test problem; a modified Rastragin\u27s function. An enhanced Particle Swarm Optimization method was derived from the initial testing. Optimization of a diesel engine was carried out using the modified algorithm demonstrating an improvement of 83% compared with the unmodified PSO algorithm. Additionally, an approach to enhancing the training of ML models by leveraging Virtual Sensing as an alternative to standard multi-layer neural networks is presented. Substantial gains were made in the prediction of Particulate matter, reducing the MMSE by 50% and improving the correlation R^2 from 0.84 to 0.98. Improvements were made in models of PM, NOx, HC, CO, and Fuel Consumption using the method, while training times and convergence reliability were simultaneously improved over the traditional approach