A cascaded approach to normalising gene mentions in biomedical literature

Linking gene and protein names mentioned in the literature to unique identifiers in referent genomic databases is an essential step in accessing and integrating knowledge in the biomedical domain. However, it remains a challenging task due to lexical and terminological variation, and ambiguity of gene name mentions in documents. We present a generic and effective rule-based approach to link gene mentions in the literature to referent genomic databases, where pre-processing of both gene synonyms in the databases and gene mentions in text are first applied. The mapping method employs a cascaded approach, which combines exact, exact-like and token-based approximate matching by using flexible representations of a gene synonym dictionary and gene mentions generated during the pre-processing phase. We also consider multi-gene name mentions and permutation of components in gene names. A systematic evaluation of the suggested methods has identified steps that are beneficial for improving either precision or recall in gene name identification. The results of the experiments on the BioCreAtIvE2 data sets (identification of human gene names) demonstrated that our methods achieved highly encouraging results with F-measure of up to 81.20%

Mathematical control of complex systems

Copyright © 2013 ZidongWang et al.This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

Modeling the Flux-Charge Relation of Memristor with Neural Network of Smooth Hinge Functions

The memristor was proposed to characterize the flux-charge relation. We propose the generalized flux-charge relation model of memristor with neural network of smooth hinge functions. There is effective identification algorithm for the neural network of smooth hinge functions. The representation capability of this model is theoretically guaranteed. Any functional flux-charge relation of a memristor can be approximated by the model. We also give application examples to show that the given model can approximate the flux-charge relation of existing piecewise linear memristor model, window function memristor model, and a physical memristor device

A hierarchical Mamdani-type fuzzy modelling approach with new training data selection and multi-objective optimisation mechanisms: A special application for the prediction of mechanical properties of alloy steels

In this paper, a systematic data-driven fuzzy modelling methodology is proposed, which allows to construct Mamdani fuzzy models considering both accuracy (precision) and transparency (interpretability) of fuzzy systems. The new methodology employs a fast hierarchical clustering algorithm to generate an initial fuzzy model efficiently; a training data selection mechanism is developed to identify appropriate and efficient data as learning samples; a high-performance Particle Swarm Optimisation (PSO) based multi-objective optimisation mechanism is developed to further improve the fuzzy model in terms of both the structure and the parameters; and a new tolerance analysis method is proposed to derive the confidence bands relating to the final elicited models. This proposed modelling approach is evaluated using two benchmark problems and is shown to outperform other modelling approaches. Furthermore, the proposed approach is successfully applied to complex high-dimensional modelling problems for manufacturing of alloy steels, using ‘real’ industrial data. These problems concern the prediction of the mechanical properties of alloy steels by correlating them with the heat treatment process conditions as well as the weight percentages of the chemical compositions