Mathematics at the eve of a historic transition in biology

A century ago physicists and mathematicians worked in tandem and established quantum mechanism. Indeed, algebras, partial differential equations, group theory, and functional analysis underpin the foundation of quantum mechanism. Currently, biology is undergoing a historic transition from qualitative, phenomenological and descriptive to quantitative, analytical and predictive. Mathematics, again, becomes a driving force behind this new transition in biology.Comment: 5 pages, 2 figure

Computational Intelligence for Life Sciences

Computational Intelligence (CI) is a computer science discipline encompassing the theory, design, development and application of biologically and linguistically derived computational paradigms. Traditionally, the main elements of CI are Evolutionary Computation, Swarm Intelligence, Fuzzy Logic, and Neural Networks. CI aims at proposing new algorithms able to solve complex computational problems by taking inspiration from natural phenomena. In an intriguing turn of events, these nature-inspired methods have been widely adopted to investigate a plethora of problems related to nature itself. In this paper we present a variety of CI methods applied to three problems in life sciences, highlighting their effectiveness: we describe how protein folding can be faced by exploiting Genetic Programming, the inference of haplotypes can be tackled using Genetic Algorithms, and the estimation of biochemical kinetic parameters can be performed by means of Swarm Intelligence. We show that CI methods can generate very high quality solutions, providing a sound methodology to solve complex optimization problems in life sciences

Regularization and Kernelization of the Maximin Correlation Approach

Robust classification becomes challenging when each class consists of multiple subclasses. Examples include multi-font optical character recognition and automated protein function prediction. In correlation-based nearest-neighbor classification, the maximin correlation approach (MCA) provides the worst-case optimal solution by minimizing the maximum misclassification risk through an iterative procedure. Despite the optimality, the original MCA has drawbacks that have limited its wide applicability in practice. That is, the MCA tends to be sensitive to outliers, cannot effectively handle nonlinearities in datasets, and suffers from having high computational complexity. To address these limitations, we propose an improved solution, named regularized maximin correlation approach (R-MCA). We first reformulate MCA as a quadratically constrained linear programming (QCLP) problem, incorporate regularization by introducing slack variables in the primal problem of the QCLP, and derive the corresponding Lagrangian dual. The dual formulation enables us to apply the kernel trick to R-MCA so that it can better handle nonlinearities. Our experimental results demonstrate that the regularization and kernelization make the proposed R-MCA more robust and accurate for various classification tasks than the original MCA. Furthermore, when the data size or dimensionality grows, R-MCA runs substantially faster by solving either the primal or dual (whichever has a smaller variable dimension) of the QCLP.Comment: Submitted to IEEE Acces

Paradigms for computational nucleic acid design

The design of DNA and RNA sequences is critical for many endeavors, from DNA nanotechnology, to PCR‐based applications, to DNA hybridization arrays. Results in the literature rely on a wide variety of design criteria adapted to the particular requirements of each application. Using an extensively studied thermodynamic model, we perform a detailed study of several criteria for designing sequences intended to adopt a target secondary structure. We conclude that superior design methods should explicitly implement both a positive design paradigm (optimize affinity for the target structure) and a negative design paradigm (optimize specificity for the target structure). The commonly used approaches of sequence symmetry minimization and minimum free‐energy satisfaction primarily implement negative design and can be strengthened by introducing a positive design component. Surprisingly, our findings hold for a wide range of secondary structures and are robust to modest perturbation of the thermodynamic parameters used for evaluating sequence quality, suggesting the feasibility and ongoing utility of a unified approach to nucleic acid design as parameter sets are refined further. Finally, we observe that designing for thermodynamic stability does not determine folding kinetics, emphasizing the opportunity for extending design criteria to target kinetic features of the energy landscape

Systems approaches to modelling pathways and networks.

Peer reviewedPreprin

Applicability of semi-supervised learning assumptions for gene ontology terms prediction

Gene Ontology (GO) is one of the most important resources in bioinformatics, aiming to provide a unified framework for the biological annotation of genes and proteins across all species. Predicting GO terms is an essential task for bioinformatics, but the number of available labelled proteins is in several cases insufficient for training reliable machine learning classifiers. Semi-supervised learning methods arise as a powerful solution that explodes the information contained in unlabelled data in order to improve the estimations of traditional supervised approaches. However, semi-supervised learning methods have to make strong assumptions about the nature of the training data and thus, the performance of the predictor is highly dependent on these assumptions. This paper presents an analysis of the applicability of semi-supervised learning assumptions over the specific task of GO terms prediction, focused on providing judgment elements that allow choosing the most suitable tools for specific GO terms. The results show that semi-supervised approaches significantly outperform the traditional supervised methods and that the highest performances are reached when applying the cluster assumption. Besides, it is experimentally demonstrated that cluster and manifold assumptions are complimentary to each other and an analysis of which GO terms can be more prone to be correctly predicted with each assumption, is provided.Postprint (published version

Multi-objective Optimization of Biochemical System Production Using an Improve Newton Competitive Differential Evolution Method

In this paper, an improve method of multi-objective optimization for biochemical system production is presented and discussed in detail. The optimization process of biochemical system production become hard and difficult when involved a large biochemical system that contain with many components. In addition, the multi-objective problem also need to be considered. Due to that, this study proposed and improve method that comprises with Newton method, differential evolution algorithm (DE) and competitive co-evolutionary algorithm(ComCA). The aim of the proposed method is to maximize the production and simultaneously minimize the total amount of chemical concentrations involves. The operation of the proposed method starts with Newton method by dealing with biochemical system production as a nonlinear equations system. Then DE and ComCA are used to represent the variables in nonlinear equation system and tune the variables in order to find the best solution. The used of DE is to maximize the production while ComCA is to minimize the total amount of chemical concentrations involves. The effectiveness of the proposed method is evaluated using two benchmark biochemical systems and the experimental results show that the proposed method perform well compared to other works