Estimation of Parkinson's disease severity using speech features and extreme gradient boosting.

In recent years, there is an increasing interest in building e-health systems. The systems built to deliver the health services with the use of internet and communication technologies aim to reduce the costs arising from outpatient visits of patients. Some of the related recent studies propose machine learning-based telediagnosis and telemonitoring systems for Parkinson's disease (PD). Motivated from the studies showing the potential of speech disorders in PD telemonitoring systems, in this study, we aim to estimate the severity of PD from voice recordings of the patients using motor Unified Parkinson's Disease Rating Scale (UPDRS) as the evaluation metric. For this purpose, we apply various speech processing algorithms to the voice signals of the patients and then use these features as input to a two-stage estimation model. The first step is to apply a wrapper-based feature selection algorithm, called Boruta, and select the most informative speech features. The second step is to feed the selected set of features to a decision tree-based boosting algorithm, extreme gradient boosting, which has been recently applied successfully in many machine learning tasks due to its generalization ability and speed. The feature selection analysis showed that the vibration pattern of the vocal fold is an important indicator of PD severity. Besides, we also investigate the effectiveness of using age and years passed since diagnosis as covariates together with speech features. The lowest mean absolute error with 3.87 was obtained by combining these covariates and speech features with prediction level fusion. Graphical Abstract Framework for the proposed UPDRS estimation model.

Analyzing the effectiveness of vocal features in early telediagnosis of Parkinson's disease.

The recently proposed Parkinson's Disease (PD) telediagnosis systems based on detecting dysphonia achieve very high classification rates in discriminating healthy subjects from PD patients. However, in these studies the data used to construct the classification model contain the speech recordings of both early and late PD patients with different severities of speech impairments resulting in unrealistic results. In a more realistic scenario, an early telediagnosis system is expected to be used in suspicious cases by healthy subjects or early PD patients with mild speech impairment. In this paper, considering the critical importance of early diagnosis in the treatment of the disease, we evaluate the ability of vocal features in early telediagnosis of Parkinson's Disease (PD) using machine learning techniques with a two-step approach. In the first step, using only patient data, we aim to determine the patient group with relatively greater severity of speech impairments using Unified Parkinson's Disease Rating Scale (UPDRS) score as an index of disease progression. For this purpose, we use three supervised and two unsupervised learning techniques. In the second step, we exclude the samples of this group of patients from the dataset, create a new dataset consisting of the samples of PD patients having less severity of speech impairments and healthy subjects, and use three classifiers with various settings to address this binary classification problem. In this classification problem, the highest accuracy of 96.4% and Matthew's Correlation Coefficient of 0.77 is obtained using support vector machines with third-degree polynomial kernel showing that vocal features can be used to build a decision support system for early telediagnosis of PD.

Analysis of shared miRNAs of different species using ensemble CCA and genetic distance.

MicroRNA is a type of single stranded RNA molecule and has an important role for gene expression. Although there have been a number of computational methodologies in bioinformatics research for miRNA classification and target prediction tasks, analysis of shared miRNAs among different species has not yet been addressed. In this article, we analyzed miRNAs that have the same name and function but have different sequences and belong to different (but closely related) species which are constructed from the online miRBase database. We used sequence-driven features and performed the standard and the ensemble versions of Canonical Correlation Analysis (CCA). However, due to its sensitivity to noise and outliers, we extended it using an ensemble approach. Using linear combinations of dimer features, the proposed Ensemble CCA (ECCA) method has identified higher test-set-correlations than CCA. Moreover, our analysis reveals that the Redundancy Index of ECCA applied to a pair of species has correlation with their genetic distance.

Combining multiple clusterings for protein structure prediction.

Computational annotation and prediction of protein structure is very important in the post-genome era due to existence of many different proteins, most of which are yet to be verified. Mutual information based feature selection methods can be used in selecting such minimal yet predictive subsets of features. However, as protein features are organised into natural partitions, individual feature selection that ignores the presence of these views, dismantles them, and treats their variables intermixed along with those of others at best results in a complex un-interpretable predictive system for such multi-view datasets. In this paper, instead of selecting a subset of individual features, each feature subset is passed through a clustering step so that it is represented in discrete form using the cluster indices; this makes mutual information based methods applicable to view-selection. We present our experimental results on a multi-view protein dataset that are used to predict protein structure.

Collection and analysis of a Parkinson speech dataset with multiple types of sound recordings.

There has been an increased interest in speech pattern analysis applications of Parkinsonism for building predictive telediagnosis and telemonitoring models. For this purpose, we have collected a wide variety of voice samples, including sustained vowels, words, and sentences compiled from a set of speaking exercises for people with Parkinson's disease. There are two main issues in learning from such a dataset that consists of multiple speech recordings per subject: 1) How predictive these various types, e.g., sustained vowels versus words, of voice samples are in Parkinson's disease (PD) diagnosis? 2) How well the central tendency and dispersion metrics serve as representatives of all sample recordings of a subject? In this paper, investigating our Parkinson dataset using well-known machine learning tools, as reported in the literature, sustained vowels are found to carry more PD-discriminative information. We have also found that rather than using each voice recording of each subject as an independent data sample, representing the samples of a subject with central tendency and dispersion metrics improves generalization of the predictive model.

Feature extraction using time-frequency/scale analysis and ensemble of feature sets for crackle detection.

Pulmonary crackles are used as indicators for the diagnosis of different pulmonary disorders. Crackles are very common adventitious sounds which have transient characteristic. From the characteristics of crackles such as timing and number of occurrences, the type and the severity of the pulmonary diseases can be obtained. In this study, a novel method is proposed for crackle detection. In this method, various feature sets are extracted using time-frequency and time-scale analysis. The extracted feature sets are fed into support vector machines both individually and as an ensemble of networks. Besides, as a preprocessing stage in order to improve the success of the model, frequency bands containing no-information are removed using dual tree complex wavelet transform, which is a shift invariant transform with limited redundancy and an improved version of discrete wavelet transform. The comparative results of individual feature sets and ensemble of sets with pre-processed and non pre-processed data are proposed.

Telediagnosis of Parkinson's disease using measurements of dysphonia.

Parkinson's disease (PD) is a neurological illness which impairs motor skills, speech, and other functions such as mood, behavior, thinking, and sensation. It causes vocal impairment for approximately 90% of the patients. As the symptoms of PD occur gradually and mostly targeting the elderly people for whom physical visits to the clinic are inconvenient and costly, telemonitoring of the disease using measurements of dysphonia (vocal features) has a vital role in its early diagnosis. Such dysphonia features extracted from the voice come in variety and most of them are interrelated. The purpose of this study is twofold: (1) to select a minimal subset of features with maximal joint relevance to the PD-score, a binary score indicating whether or not the sample belongs to a person with PD; and (2) to build a predictive model with minimal bias (i.e. to maximize the generalization of the predictions so as to perform well with unseen test examples). For these tasks, we apply the mutual information measure with the permutation test for assessing the relevance and the statistical significance of the relations between the features and the PD-score, rank the features according to the maximum-relevance-minimum-redundancy (mRMR) criterion, use a Support Vector Machine (SVM) for building a classification model and test it with a more suitable cross-validation scheme that we called leave-one-individual-out that fits with the dataset in hand better than the conventional bootstrapping or leave-one-out validation methods.