Using Neural Networks for Relation Extraction from Biomedical Literature

Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedical literature. Several relation extraction approaches have been proposed to identify relations between concepts in biomedical literature, namely, using neural networks algorithms. The use of multichannel architectures composed of multiple data representations, as in deep neural networks, is leading to state-of-the-art results. The right combination of data representations can eventually lead us to even higher evaluation scores in relation extraction tasks. Thus, biomedical ontologies play a fundamental role by providing semantic and ancestry information about an entity. The incorporation of biomedical ontologies has already been proved to enhance previous state-of-the-art results.Comment: Artificial Neural Networks book (Springer) - Chapter 1

Self learning neuro-fuzzy modeling using hybrid genetic probabilistic approach for engine air/fuel ratio prediction

Machine Learning is concerned in constructing models which can learn and make predictions based on data. Rule extraction from real world data that are usually tainted with noise, ambiguity, and uncertainty, automatically requires feature selection. Neuro-Fuzzy system (NFS) which is known with its prediction performance has the difficulty in determining the proper number of rules and the number of membership functions for each rule. An enhanced hybrid Genetic Algorithm based Fuzzy Bayesian classifier (GA-FBC) was proposed to help the NFS in the rule extraction. Feature selection was performed in the rule level overcoming the problems of the FBC which depends on the frequency of the features leading to ignore the patterns of small classes. As dealing with a real world problem such as the Air/Fuel Ratio (AFR) prediction, a multi-objective problem is adopted. The GA-FBC uses mutual information entropy, which considers the relevance between feature attributes and class attributes. A fitness function is proposed to deal with multi-objective problem without weight using a new composition method. The model was compared to other learning algorithms for NFS such as Fuzzy c-means (FCM) and grid partition algorithm. Predictive accuracy and the complexity of the Fuzzy Rule Base System (FRBS) including number of rules and number of terms in each rule were taken as terms of evaluation. It was also compared to the original GA-FBC depending on the frequency not on Mutual Information (MI). Experimental results using Air/Fuel Ratio (AFR) data sets show that the new model participates in decreasing the average number of attributes in the rule and sometimes in increasing the average performance compared to other models. This work facilitates in achieving a self-generating FRBS from real data. The GA-FBC can be used as a new direction in machine learning research. This research contributes in controlling automobile emissions in helping the reduction of one of the most causes of pollution to produce greener environment

A Supervised Learning Approach to Acronym Identification

This paper addresses the task of finding acronym-definition pairs in text. Most of the previous work on the topic is about systems that involve manually generated rules or regular expressions. In this paper, we present a supervised learning approach to the acronym identification task. Our approach reduces the search space of the supervised learning system by putting some weak constraints on the kinds of acronym-definition pairs that can be identified. We obtain results comparable to hand-crafted systems that use stronger constraints. We describe our method for reducing the search space, the features used by our supervised learning system, and our experiments with various learning schemes

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

HYEI: A New Hybrid Evolutionary Imperialist Competitive Algorithm for Fuzzy Knowledge Discovery

In recent years, imperialist competitive algorithm (ICA), genetic algorithm (GA), and hybrid fuzzy classification systems have been successfully and effectively employed for classification tasks of data mining. Due to overcoming the gaps related to ineffectiveness of current algorithms for analysing high-dimension independent datasets, a new hybrid approach, named HYEI, is presented to discover generic rule-based systems in this paper. This proposed approach consists of three stages and combines an evolutionary-based fuzzy system with two ICA procedures to generate high-quality fuzzy-classification rules. Initially, the best feature subset is selected by using the embedded ICA feature selection, and then these features are used to generate basic fuzzy-classification rules. Finally, all rules are optimized by using an ICA algorithm to reduce their length or to eliminate some of them. The performance of HYEI has been evaluated by using several benchmark datasets from the UCI machine learning repository. The classification accuracy attained by the proposed algorithm has the highest classification accuracy in 6 out of the 7 dataset problems and is comparative to the classification accuracy of the 5 other test problems, as compared to the best results previously published

Extracting protein-protein interactions from text using rich feature vectors and feature selection

Because of the intrinsic complexity of natural language, automatically extracting accurate information from text remains a challenge. We have applied rich featurevectors derived from dependency graphs to predict protein-protein interactions using machine learning techniques. We present the first extensive analysis of applyingfeature selection in this domain, and show that it can produce more cost-effective models. For the first time, our technique was also evaluated on several large-scalecross-dataset experiments, which offers a more realistic view on model performance. During benchmarking, we encountered several fundamental problems hindering comparability with other methods. We present a set of practical guidelines to set up ameaningful evaluation. Finally, we have analysed the feature sets from our experiments before and after feature selection, and evaluated the contribution of both lexical and syntacticinformation to our method. The gained insight will be useful to develop better performing methods in this domain