GREMA: modelling of emulated gene regulatory networks with confidence levels based on evolutionary intelligence to cope with the underdetermined problem.

Motivation: Non-linear ordinary differential equation (ODE) models that contain numerous parameters are suitable for inferring an emulated gene regulatory network (eGRN). However, the number of experimental measurements is usually far smaller than the number of parameters of the eGRN model that leads to an underdetermined problem. There is no unique solution to the inference problem for an eGRN using insufficient measurements.

Prediction and analysis of protein solubility using a novel scoring card method with dipeptide composition.

Background: Existing methods for predicting protein solubility on overexpression in Escherichia coli advance performance by using ensemble classifiers such as two-stage support vector machine (SVM) based classifiers and a number of feature types such as physicochemical properties, amino acid and dipeptide composition, accompanied with feature selection. It is desirable to develop a simple and easily interpretable method for predicting protein solubility, compared to existing complex SVM-based methods.

Results: This study proposes a novel scoring card method (SCM) by using dipeptide composition only to estimate solubility scores of sequences for predicting protein solubility.

FRKAS: knowledge acquisition using a fuzzy rule base approach to insight of DNA-binding domains/proteins.

Numerous prediction methods of DNA-binding domains/proteins were proposed by identifying informative features and designing effective classifiers. These researches reveal that the DNA-protein binding mechanism is complicated and existing accurate predictors such as support vector machine (SVM) with position specific scoring matrices (PSSMs) are regarded as black-box methods which are not easily interpretable for biologists. In this study, we propose an ensemble fuzzy rule base classifier consisting of a set of interpretable fuzzy rule classifiers (iFRCs) using informative physicochemical properties as features.

Predicting and analyzing DNA-binding domains using a systematic approach to identifying a set of informative physicochemical and biochemical properties.

Background: Existing methods of predicting DNA-binding proteins used valuable features of physicochemical properties to design support vector machine (SVM) based classifiers. Generally, selection of physicochemical properties and determination of their corresponding feature vectors rely mainly on known properties of binding mechanism and experience of designers. However, there exists a troublesome problem for designers that some different physicochemical properties have similar vectors of representing 20 amino acids and some closely related physicochemical properties have dissimilar vectors.

Prediction of non-classical secreted proteins using informative physicochemical properties.

The prediction of non-classical secreted proteins is a significant problem for drug discovery and development of disease diagnosis. The characteristic of non-classical secreted proteins is they are leaderless proteins without signal peptides in N-terminal. This characteristic makes the prediction of non-classical proteins more difficult and complicated than the classical secreted proteins.

Design of accurate classifiers with a compact fuzzy-rule base using an evolutionary scatter partition of feature space.

An evolutionary approach to designing accurate classifiers with a compact fuzzy-rule base using a scatter partition of feature space is proposed, in which all the elements of the fuzzy classifier design problem have been moved in parameters of a complex optimization problem. An intelligent genetic algorithm (IGA) is used to effectively solve the design problem of fuzzy classifiers with many tuning parameters. The merits of the proposed method are threefold: 1) the proposed method has high search ability to efficiently find fuzzy rule-based systems with high fitness values, 2) obtained fuzzy rules have high interpretability, and 3) obtained compact classifiers have high classification accuracy on unseen test patterns.