Differentiation of multiple sclerosis lesions and low-grade brain tumors on MRS data: machine learning approaches.

Some multiple sclerosis (MS) lesions may have great similarities with neoplastic brain lesions in magnetic resonance (MR) imaging and thus wrong diagnoses may occur. In this study, differentiation of MS and low-grade brain tumors was performed with computer-aided diagnosis (CAD) methods by magnetic resonance spectroscopy (MRS) data. MRS data belonging to 51 MS and 39 low-grade brain tumor patients were obtained. The feature extraction from MRS data was performed by the help of peak integration (PI) and full spectra (FS) methods and the most significant features were identified. For the classification step, artificial neural network (ANN), support vector machine (SVM), and linear discriminant analysis (LDA) methods were used and the differentiation between MS and brain tumor was performed automatically. Examining the results, one can conclude that data which belong to MS and low-grade brain tumor cases were automatically differentiated from each other with the help of ANN with 100% accuracy, 100% sensitivity, and 100% specificity. Using of MR spectroscopy and artificial intelligence methods may be useful as a complementary imaging technique to MR imaging in the differentiation of MS lesions and low-grade brain tumors.

Differentiation of relapsing-remitting and secondary progressive multiple sclerosis: a magnetic resonance spectroscopy study based on machine learning.

INTRODUCTION: Magnetic resonance imaging (MRI) is the most important tool for diagnosis and follow-up in multiple sclerosis (MS). The discrimination of relapsing-remitting MS (RRMS) from secondary progressive MS (SPMS) is clinically difficult, and developing the proposal presented in this study would contribute to the process. OBJECTIVE: This study aimed to ensure the automatic classification of healthy controls, RRMS, and SPMS by using MR spectroscopy and machine learning methods. METHODS: MR spectroscopy (MRS) was performed on a total of 91 participants, distributed into healthy controls (n=30), RRMS (n=36), and SPMS (n=25). Firstly, MRS metabolites were identified using signal processing techniques. Secondly, feature extraction was performed based on MRS Spectra. N-acetylaspartate (NAA) was the most significant metabolite in differentiating MS types. Lastly, binary classifications (healthy controls-RRMS and RRMS-SPMS) were carried out according to features obtained by the Support Vector Machine algorithm. RESULTS: RRMS cases were differentiated from healthy controls with 85% accuracy, 90.91% sensitivity, and 77.78% specificity. RRMS and SPMS were classified with 83.33% accuracy, 81.81% sensitivity, and 85.71% specificity. CONCLUSIONS: A combined analysis of MRS and computer-aided diagnosis may be useful as a complementary imaging technique to determine MS types.

Differentiation of relapsing-remitting and secondary progressive multiple sclerosis: a magnetic resonance spectroscopy study based on machine learning / Diferenciação de esclerose múltipla recorrente-remitente e progressiva secundária: um estudo de ressonância magnética com espectroscopia baseado em aprendizado de máquina

ABSTRACT Introduction: Magnetic resonance imaging (MRI) is the most important tool for diagnosis and follow-up in multiple sclerosis (MS). The discrimination of relapsing-remitting MS (RRMS) from secondary progressive MS (SPMS) is clinically difficult, and developing the proposal presented in this study would contribute to the process. Objective: This study aimed to ensure the automatic classification of healthy controls, RRMS, and SPMS by using MR spectroscopy and machine learning methods. Methods: MR spectroscopy (MRS) was performed on a total of 91 participants, distributed into healthy controls (n=30), RRMS (n=36), and SPMS (n=25). Firstly, MRS metabolites were identified using signal processing techniques. Secondly, feature extraction was performed based on MRS Spectra. N-acetylaspartate (NAA) was the most significant metabolite in differentiating MS types. Lastly, binary classifications (healthy controls-RRMS and RRMS-SPMS) were carried out according to features obtained by the Support Vector Machine algorithm. Results: RRMS cases were differentiated from healthy controls with 85% accuracy, 90.91% sensitivity, and 77.78% specificity. RRMS and SPMS were classified with 83.33% accuracy, 81.81% sensitivity, and 85.71% specificity. Conclusions: A combined analysis of MRS and computer-aided diagnosis may be useful as a complementary imaging technique to determine MS types.

RESUMO Introdução: A ressonância magnética é a ferramenta mais importante para o diagnóstico e acompanhamento na EM. A transição da EM recorrente-remitente (EMRR) para a EM progressiva secundária (EMPS) é clinicamente difícil e seria importante desenvolver a proposta apresentada neste estudo a fim de contribuir com o processo. Objetivo: o objetivo deste estudo foi garantir a classificação automática de grupo controle saudável, EMRR e EMPS usando a RM com espectroscopia e métodos de aprendizado de máquina. Métodos: Os exames de RM com espectroscopia foram realizados em um total de 91 amostras com grupo controle saudável (n=30), EMRR (n=36) e EMPS (n=25). Em primeiro lugar, os metabólitos da RM com espectroscopia foram identificados usando técnicas de processamento de sinal. Em segundo lugar, a extração de recursos foi realizada a partir do MRS Spectra. O NAA foi determinado como o metabólito mais significativo na diferenciação dos tipos de MS. Por fim, as classificações binárias (Healthy Control Group-RRMS e RRMS-SPMS) foram realizadas de acordo com as características obtidas por meio do algoritmo Support Vector Machine. Resultados: Os casos de EMRR e do grupo de controle saudável foram diferenciados entre si com 85% de acerto, 90,91% de sensibilidade e 77,78% de especificidade, respectivamente. A EMRR e a EMPS foram classificadas com 83,33% de acurácia, 81,81% de sensibilidade e 85,71% de especificidade, respectivamente. Conclusões: Uma análise combinada de RM com espectroscopia e abordagem de diagnóstico auxiliado por computador pode ser útil como uma técnica de imagem complementar na determinação dos tipos de EM.

Facial expression recognition for monitoring neurological disorders based on convolutional neural network.

Facial expressions are a significant part of non-verbal communication. Recognizing facial expressions of people with neurological disorders is essential because these people may have lost a significant amount of their verbal communication ability. Such an assessment requires time consuming examination involving medical personnel, which can be quite challenging and expensive. Automated facial expression recognition systems that are low-cost and noninvasive can help experts detect neurological disorders. In this study, an automated facial expression recognition system is developed using a novel deep learning approach. The architecture consists of four-stage networks. The first, second and third networks segment the facial components which are essential for facial expression recognition. Owing to the three networks, an iconize facial image is obtained. The fourth network classifies facial expressions using raw facial images and iconize facial images. This four-stage method combines holistic facial information with local part-based features to achieve more robust facial expression recognition. Preliminary experimental results achieved 94.44% accuracy for facial expression recognition on RaFD database. The proposed system produced 5% improvement than the facial expression recognition system by using raw images. This study presents a quantitative, objective and non-invasive facial expression recognition system to help in the monitoring and diagnosis of neurological disorders influencing facial expressions.

A new sequence based encoding for prediction of host-pathogen protein interactions.

Pathogen-host interactions are very important to figure out the infection process at the molecular level, where pathogen proteins physically bind to human proteins to manipulate critical biological processes in the host cell. Data scarcity and data unavailability are two major problems for computational approaches in the prediction of pathogen-host interactions. Developing a computational method to predict pathogen-host interactions with high accuracy, based on protein sequences alone, is of great importance because it can eliminate these problems. In this study, we propose a novel and robust sequence based feature extraction method, named Location Based Encoding, to predict pathogen-host interactions with machine learning based algorithms. In this context, we use Bacillus Anthracis and Yersinia Pestis data sets as the pathogen organisms and human proteins as the host model to compare our method with sequence based protein encoding methods, which are widely used in the literature, namely amino acid composition, amino acid pair, and conjoint triad. We use these encoding methods with decision trees (Random Forest, j48), statistical (Bayesian Networks, Naive Bayes), and instance based (kNN) classifiers to predict pathogen-host interactions. We conduct different experiments to evaluate the effectiveness of our method. We obtain the best results among all the experiments with RF classifier in terms of F1, accuracy, MCC, and AUC.

PROSES: A Web Server for Sequence-Based Protein Encoding.

Recently, the number of the amino acid sequences shared in online databases is growing rapidly in huge amounts. By using sequence-derived features, machine learning algorithms are successfully applied to prediction of protein functional classes, protein-protein interactions, subcellular location, and peptides of specific properties in many studies. Protein Sequence Encoding System (PROSES) is a web server designed as freely and easily accessible for all researchers who want to use computational methods on protein sequence data. That is, PROSES provides users to encode their protein sequences easily without writing any programming code.