Huseyin Seker

A fuzzy logic based-method for prognostic decision making in breast and prostate cancers

Accurate and reliable decision making in oncological prognosis can help in the planning of suitable surgery and therapy, and generally, improve patient management through the different stages of the disease. In recent years, several prognostic markers have been used as indicators of disease progression in oncology. However, the rapid increase in the discovery of novel prognostic markers resulting from the development in medical technology, has dictated the need for developing reliable methods for extracting clinically significant markers where complex and nonlinear interactions between these markers naturally exist. The aim of this paper is to investigate the fuzzy k-nearest neighbor (FK-NN) classifier as a fuzzy logic method that provides a certainty degree for prognostic decision and assessment of the markers, and to compare it with: 1) logistic regression as a statistical method and 2) multilayer feedforward backpropagation neural networks an artificial neural-network tool, the latter two techniques having been widely used for oncological prognosis. In order to achieve this aim, breast and prostate cancer data sets are considered as benchmarks for this analysis. The overall results obtained indicate that the FK-NN-based method yields the highest predictive accuracy, and that it has produced a more reliable prognostic marker model than both the statistical and artificial neural-network-based methods.

FPGA implementation of K-means algorithm for bioinformatics application: An accelerated approach to clustering Microarray data

The Microarray is a technique used by biologists to perform many genome experiments simultaneously, which produces very large datasets. Analysis of these datasets is a challenge for scientists especially as the number of genome databases is increasing rapidly every year. K-means clustering is an unsupervised data mining technique used widely by bioinformaticians to analyze Microarray data. However, K-means can take between a few seconds to several days to process Microarray data depending on the size of these datasets. This puts a limit on the complexity of biological problems which can be asked by bioinfomaticians, and hence may result in an incomplete solution to the problem. In order to overcome such problems, we propose a highly parallel hardware design to accelerate the K-means clustering of Microarray data by implementing the K-means algorithm in Field Programmable Gate Arrays (FPGA). Our implementation is particularly suitable for server solution as it allows for processing many different datasets simultaneously. We have designed, and implemented five k-mean cores on Xilinx Virtex4 XC4VLX25 FPGA, and tested them on a sample of real Yeast Microarray data. Our design achieved about 51.7× speed-up when compared to a software model while being 206.8× more energy efficient.

Compensatory fuzzy neural networks-based intelligent detection of abnormal neonatal cerebral Doppler ultrasound waveforms

Compensatory fuzzy neural networks (CFNN) without normalization, which can be trained with a backpropagation learning algorithm, are proposed as a pattern recognition technique for the intelligent detection of Doppler ultrasound waveforms of abnormal neonatal cerebral hemodynamics. Doppler ultrasound signals were recorded from the anterior cerebral arteries of 40 normal full-term babies and 14 mature babies with intracranial pathology. The features of normal and abnormal groups as inputs to the pattern recognition algorithms were extracted from the maximum-velocity waveforms by using principal component analysis. The proposed technique is compared with the CFNN with normalization and other pattern recognition techniques applied to Doppler ultrasound signals from various arteries. The results show that the proposed method is superior to the other techniques, and can be a powerful way to analyze Doppler ultrasound signals from various arteries.

Highly Parameterized K-means Clustering on FPGAs: Comparative Results with GPPs and GPUs

K-means clustering has been widely used in processing large datasets in many fields of studies. Advancement in many data collection techniques has been generating enormous amount of data, leaving scientists with the challenging task of processing them. Using General Purpose Processors or GPPs to process large datasets may take a long time, therefore many acceleration methods have been proposed in the literature to speed-up the processing of such large datasets. In this work, we propose a parameterized Field Programmable Gate Array (FPGA) implementation of the Kmeans algorithm and compare it with previous FPGA implementation as well as recent implementations on Graphics Processing Units (GPUs) and with GPPs. The proposed FPGA implementation has shown higher performance in terms of speed-up over previous FPGA GPU and GPP implementations, and is more energy efficient.

A fuzzy measurement-based assessment of breast cancer prognostic markers

The paper aims to assess breast cancer prognostic markers and to determine an optimum subset that can yield high prediction accuracy for an individual breast cancer patients prognosis by means of a fuzzy measurement derived from the fuzzy k-nearest neighbour algorithm (FK-NN). The analyses are carried out for both nodal involvement and five-year survival. The data set used for the analysis of breast cancer prognosis consists of seven input markers (histology type, grade, DNA ploidy, S-Phase Fraction (SPF), G/sub 0/G/sub 1//G/sub 2/M ratio, minimum and maximum nuclear pleomorphism indices (NPI)) and two corresponding outputs to be predicted (negative or positive nodal status in the case of nodal involvement assessment, and whether the patient is alive or dead within 5 years of diagnosis for survival analysis). The highest predictive accuracy is 78% with the fuzzy measurement of 0.7254 for nodal involvement assessment, and 88% with the fuzzy measurement of 0.8183 for survival analysis. The best results are obtained from the subset (Histology type, Grade, DNA. Ploidy, SPF (%), G/sub 0/G/sub 1//G/sub 2/M Ratio) for survival prediction and the subset (Grade, SPF, minimum NPI) for nodal involvement analysis.

Fuzzy rules for describing subgroups from Influenza A virus using a multi-objective evolutionary algorithm

Abstract Extraction of biologically-meaningful knowledge is one of the important and challenging tasks in bioinformatics, in particular computational analysis of DNA and protein sequences, in order to identify biological function(s) and behaviour(s) of newly-extracted sequences. Computational intelligence techniques in corporation with sequence-driven features have been applied to tackle the problem and help classify different functional classes of the sequences. In order to study this problem, subgroup discovery algorithms together with a signal processing-based feature extraction method are applied, where the sequences are represented as a signal. The applicability of this method has been studied through four different Neuraminidase genes of Influenza A subtypes, H1N1, H2N2, H3N2 and H5N1. The results yielded not only higher predictive accuracy over these four classes of the proteins but also interpretable rule-based representation of the descriptive model with a significantly reduced feature set driven by means of the signal processing method. Subgroup discovery technique based on evolutionary fuzzy systems is expected to open new areas of research in bioinformatics and further help identify and understand more focused therapeutic protein targets.

EMG signal classification using conic section function neural networks

The aim of this work is to classify EMG signals using a new neural network architecture to control multifunction prostheses. The control of these prostheses can be made using myoelectric signals taken from a single pair of surface electrodes. This case has been demonstrated specifically for use by above elbow amputees. The ability to separate different muscle contraction characters depends on myoelectric signal information. Therefore, the classification of these signals is investigated. The proposed neural network algorithm here makes the user learn better and faster.

Quantitative prediction of peptide binding affinity by using hybrid fuzzy support vector regression

Graphical abstractDisplay Omitted HighlightsHigh-dimensional biological data sets are modelled with a regression based fuzzy system.An SVR based fuzzy model is proposed to find degree of peptide binding to MHC molecules.SVR is enhanced by adding the fuzziness concept.TSK fuzzy system is benefited from SVR-based training.The proposed models suggest that the predictive ability and performance are increased. Support vector machines have a wide use for the prediction problems in life sciences. It has been shown to offer more generalisation ability in input-output mapping. However, the performance of predictive models is often negatively influenced due to the complex, high-dimensional, and non-linear nature of the post-genome data. Soft computing methods can be used to model such non-linear systems. Fuzzy systems are one of the widely used methods of soft computing that model uncertainties. It is formed of interpretable rules aiding one to gain insight into applied model. This study is therefore concerned to provide more interpretable and efficient biological model with the development of a hybrid method that integrates the fuzzy system and support vector regression. In order to demonstrate the robustness of this new hybrid method, it is applied to the prediction of peptide binding affinity being one of the most challenging problems in the post-genomic era due to diversity in peptide families and complexity and high-dimensionality in the characteristic features of the peptides. Having used four different case studies, this hybrid predictive model has yielded the highest predictive power in all the four cases and achieved an improvement of as much as 34% compared to the results presented in the literature. Availability: Matlab scripts are available at https://github.com/sekerbigdatalab/tsksvr.

An adaptive implementation of a dynamically reconfigurable K-nearest neighbour classifier on FPGA

K-nearest neighbour (KNN) is a supervised classification technique that is widely used in many fields of study to classify unknown queries based on some known information about the dataset. KNN is known to be robust and simple to implement when dealing with data of small size. However it performs slowly when data are large and have high dimensions. Therefore, KNN classifiers can benefit from the parallelism offered by Field Programmable Gate Arrays (FPGAs) to accelerate the algorithm. In addition, the KNN classifier is sensitive to the user defined parameter (K) which is the number of nearest neighbours. This parameter is known to affect the performance of the classifier; thus users would want the classifier to be easily adaptable to different values of K. In this work, we propose two adaptive FPGA architectures of the KNN classifier, and compare the implementations of each one of them with an equivalent implementation running on a general purpose processor (GPP). The proposed hardware implementations outperformed GPP by 76× for the first architecture and 68× for the second. In addition, we propose a novel dynamic partial reconfiguration (DPR) architecture of the KNN classifier, which allows for an efficient dynamic partial reconfiguration of a classifier implementation on FPGA for different Ks. This DPR implementation offers 5× speed-up in the reconfiguration time of a KNN classifier on FPGA.

Predicting Clinical Outcomes for Newborns Using Two Artificial Intelligence Approaches

Two different approaches, based on artificial neural networks (ANN) and fuzzy logic, were used to predict a number of outcomes of newborns: How they would be delivered, their 5 minute Apgar score, and neonatal mortality. The goal was to assess whether the methods would be comparable or whether they would perform differently for different outcomes. The results were comparable for Correct Classification Rate (CCR) and Specificity (true negative cases). Sensitivity (true positive cases) was slightly higher for the back-propagation feed-forward ANN than using the Fuzzy-Logic Classifier (FLC). Since this is one single database and a very large one, it is possible that the FLC would perform better than the ANN for very small databases, as shown by some of the co-authors in the past. The next step will be to test a small database with both methods to assess strengths and weaknesses with the intent to use both if needed with some medical data in the future.