Computational methods for the detection of facial palsy

We are developing a telemedicine application which offers automated diagnosis of facial (Bell's) palsy through a Web service. We used a test data set of 43 images of facial palsy patients and 44 normal people to develop the automatic recognition algorithm. Three different image pre-processing methods were used. Machine learning techniques (support vector machine, SVM) were used to examine the difference between the two halves of the face. If there was a sufficient difference, then the SVM recognized facial palsy. Otherwise, if the halves were roughly symmetrical, the SVM classified the image as normal. It was found that the facial palsy images had a greater Hamming Distance than the normal images, indicating greater asymmetry. The median distance in the normal group was 331 (interquartile range 277-435) and the median distance in the facial palsy group was 509 (interquartile range 334-703). This difference was significant (P

Exploiting sequence dependencies in the prediction of peroxisomal proteins

Prediction of peroxisomal matrix proteins generally depends on the presence of one of two distinct motifs at the end of the amino acid sequence. PTS1 peroxisomal proteins have a well conserved tripeptide at the C-terminal end. However, the preceding residues in the sequence arguably play a crucial role in targeting the protein to the peroxisome. Previous work in applying machine learning to the prediction of peroxisomal matrix proteins has failed W capitalize on the full extent of these dependencies. We benchmark a range of machine learning algorithms, and show that a classifier - based on the Support Vector Machine - produces more accurate results when dependencies between the conserved motif and the preceding section are exploited. We publish an updated and rigorously curated data set that results in increased prediction accuracy of most tested models.

Short-term electricity price forecasting using wavelet and SVM techniques

In deregulated electricity market, modeling and forecasting the spot price present a number of challenges. By applying wavelet and support vector machine techniques, a new time series model for short term electricity price forecasting has been developed in this paper. The model employs both historical price and other important information, such as load capacity and weather (temperature), to forecast the price of one or more time steps ahead. The developed model has been evaluated with the actual data from Australian National Electricity Market. The simulation results demonstrated that the forecast model is capable of forecasting the electricity price with a reasonable forecasting accuracy.

Suitability of dysphonia measurements for telemonitoring of Parkinson's disease

We present an assessment of the practical value of existing traditional and non-standard measures for discriminating healthy people from people with Parkinson's disease (PD) by detecting dysphonia. We introduce a new measure of dysphonia, Pitch Period Entropy (PPE), which is robust to many uncontrollable confounding effects including noisy acoustic environments and normal, healthy variations in voice frequency. We collected sustained phonations from 31 people, 23 with PD. We then selected 10 highly uncorrelated measures, and an exhaustive search of all possible combinations of these measures finds four that in combination lead to overall correct classification performance of 91.4%, using a kernel support vector machine. In conclusion, we find that non-standard methods in combination with traditional harmonics-to-noise ratios are best able to separate healthy from PD subjects. The selected non-standard methods are robust to many uncontrollable variations in acoustic environment and individual subjects, and are thus well-suited to telemonitoring applications.

On the hierarchical classification of G protein-coupled receptors

MOTIVATION: G protein-coupled receptors (GPCRs) play an important role in many physiological systems by transducing an extracellular signal into an intracellular response. Over 50% of all marketed drugs are targeted towards a GPCR. There is considerable interest in developing an algorithm that could effectively predict the function of a GPCR from its primary sequence. Such an algorithm is useful not only in identifying novel GPCR sequences but in characterizing the interrelationships between known GPCRs. RESULTS: An alignment-free approach to GPCR classification has been developed using techniques drawn from data mining and proteochemometrics. A dataset of over 8000 sequences was constructed to train the algorithm. This represents one of the largest GPCR datasets currently available. A predictive algorithm was developed based upon the simplest reasonable numerical representation of the protein's physicochemical properties. A selective top-down approach was developed, which used a hierarchical classifier to assign sequences to subdivisions within the GPCR hierarchy. The predictive performance of the algorithm was assessed against several standard data mining classifiers and further validated against Support Vector Machine-based GPCR prediction servers. The selective top-down approach achieves significantly higher accuracy than standard data mining methods in almost all cases.

Subject identification via ECG fiducial-based systems:influence of the type of QT interval correction

Electrocardiography (ECG) has been recently proposed as biometric trait for identification purposes. Intra-individual variations of ECG might affect identification performance. These variations are mainly due to Heart Rate Variability (HRV). In particular, HRV causes changes in the QT intervals along the ECG waveforms. This work is aimed at analysing the influence of seven QT interval correction methods (based on population models) on the performance of ECG-fiducial-based identification systems. In addition, we have also considered the influence of training set size, classifier, classifier ensemble as well as the number of consecutive heartbeats in a majority voting scheme. The ECG signals used in this study were collected from thirty-nine subjects within the Physionet open access database. Public domain software was used for fiducial points detection. Results suggested that QT correction is indeed required to improve the performance. However, there is no clear choice among the seven explored approaches for QT correction (identification rate between 0.97 and 0.99). MultiLayer Perceptron and Support Vector Machine seemed to have better generalization capabilities, in terms of classification performance, with respect to Decision Tree-based classifiers. No such strong influence of the training-set size and the number of consecutive heartbeats has been observed on the majority voting scheme.

Accent Recognition for Noisy Audio Signals

It is well established that accent recognition can be as accurate as up to 95% when the signals are noise-free, using feature extraction techniques such as mel-frequency cepstral coefficients and binary classifiers such as discriminant analysis, support vector machine and k-nearest neighbors. In this paper, we demonstrate that the predictive performance can be reduced by as much as 15% when the signals are noisy. Specifically, in this paper we perturb the signals with different levels of white noise, and as the noise become stronger, the out-of-sample predictive performance deteriorates from 95% to 80%, although the in-sample prediction gives overly-optimistic results. ACM Computing Classification System (1998): C.3, C.5.1, H.1.2, H.2.4., G.3.

A Comparative Analysis of Predictive Learning Algorithms on High-Dimensional Microarray Cancer Data

This research evaluates pattern recognition techniques on a subclass of big data where the dimensionality of the input space (p) is much larger than the number of observations (n). Specifically, we evaluate massive gene expression microarray cancer data where the ratio κ is less than one. We explore the statistical and computational challenges inherent in these high dimensional low sample size (HDLSS) problems and present statistical machine learning methods used to tackle and circumvent these difficulties. Regularization and kernel algorithms were explored in this research using seven datasets where κ < 1. These techniques require special attention to tuning necessitating several extensions of cross-validation to be investigated to support better predictive performance. While no single algorithm was universally the best predictor, the regularization technique produced lower test errors in five of the seven datasets studied.

Comparison of DSP-based nonlinear equalizers for intra-channel nonlinearity compensation in coherent optical OFDM

A novel versatile digital signal processing (DSP)-based equalizer using support vector machine regression (SVR) is proposed for 16-quadrature amplitude modulated (16-QAM) coherent optical orthogonal frequency-division multiplexing (CO-OFDM) and experimentally compared to traditional DSP-based deterministic fiber-induced nonlinearity equalizers (NLEs), namely the full-field digital back-propagation (DBP) and the inverse Volterra series transfer function-based NLE (V-NLE). For a 40 Gb/s 16-QAM CO-OFDM at 2000 km, SVR-NLE extends the optimum launched optical power (LOP) by 4 dB compared to V-NLE by means of reduction of fiber nonlinearity. In comparison to full-field DBP at a LOP of 6 dBm, SVR-NLE outperforms by ∼1 dB in Q-factor. In addition, SVR-NLE is the most computational efficient DSP-NLE.

Signal processing of physiological signals for automated assessment of stress in computer users

The need to provide computers with the ability to distinguish the affective state of their users is a major requirement for the practical implementation of affective computing concepts. This dissertation proposes the application of signal processing methods on physiological signals to extract from them features that can be processed by learning pattern recognition systems to provide cues about a person's affective state. In particular, combining physiological information sensed from a user's left hand in a non-invasive way with the pupil diameter information from an eye-tracking system may provide a computer with an awareness of its user's affective responses in the course of human-computer interactions. In this study an integrated hardware-software setup was developed to achieve automatic assessment of the affective status of a computer user. A computer-based "Paced Stroop Test" was designed as a stimulus to elicit emotional stress in the subject during the experiment. Four signals: the Galvanic Skin Response (GSR), the Blood Volume Pulse (BVP), the Skin Temperature (ST) and the Pupil Diameter (PD), were monitored and analyzed to differentiate affective states in the user. Several signal processing techniques were applied on the collected signals to extract their most relevant features. These features were analyzed with learning classification systems, to accomplish the affective state identification. Three learning algorithms: Naïve Bayes, Decision Tree and Support Vector Machine were applied to this identification process and their levels of classification accuracy were compared. The results achieved indicate that the physiological signals monitored do, in fact, have a strong correlation with the changes in the emotional states of the experimental subjects. These results also revealed that the inclusion of pupil diameter information significantly improved the performance of the emotion recognition system. ^

A digital signal processing approach for affective sensing of a computer user through pupil diameter monitoring

Recent research has indicated that the pupil diameter (PD) in humans varies with their affective states. However, this signal has not been fully investigated for affective sensing purposes in human-computer interaction systems. This may be due to the dominant separate effect of the pupillary light reflex (PLR), which shrinks the pupil when light intensity increases. In this dissertation, an adaptive interference canceller (AIC) system using the H∞ time-varying (HITV) adaptive algorithm was developed to minimize the impact of the PLR on the measured pupil diameter signal. The modified pupil diameter (MPD) signal, obtained from the AIC was expected to reflect primarily the pupillary affective responses (PAR) of the subject. Additional manipulations of the AIC output resulted in a processed MPD (PMPD) signal, from which a classification feature, PMPDmean, was extracted. This feature was used to train and test a support vector machine (SVM), for the identification of stress states in the subject from whom the pupil diameter signal was recorded, achieving an accuracy rate of 77.78%. The advantages of affective recognition through the PD signal were verified by comparatively investigating the classification of stress and relaxation states through features derived from the simultaneously recorded galvanic skin response (GSR) and blood volume pulse (BVP) signals, with and without the PD feature. The discriminating potential of each individual feature extracted from GSR, BVP and PD was studied by analysis of its receiver operating characteristic (ROC) curve. The ROC curve found for the PMPDmean feature encompassed the largest area (0.8546) of all the single-feature ROCs investigated. The encouraging results seen in affective sensing based on pupil diameter monitoring were obtained in spite of intermittent illumination increases purposely introduced during the experiments. Therefore, these results confirmed the benefits of using the AIC implementation with the HITV adaptive algorithm to isolate the PAR and the potential of using PD monitoring to sense the evolving affective states of a computer user.

Improving resource management in virtualized data centers using application performance models

The rapid growth of virtualized data centers and cloud hosting services is making the management of physical resources such as CPU, memory, and I/O bandwidth in data center servers increasingly important. Server management now involves dealing with multiple dissimilar applications with varying Service-Level-Agreements (SLAs) and multiple resource dimensions. The multiplicity and diversity of resources and applications are rendering administrative tasks more complex and challenging. This thesis aimed to develop a framework and techniques that would help substantially reduce data center management complexity.^ We specifically addressed two crucial data center operations. First, we precisely estimated capacity requirements of client virtual machines (VMs) while renting server space in cloud environment. Second, we proposed a systematic process to efficiently allocate physical resources to hosted VMs in a data center. To realize these dual objectives, accurately capturing the effects of resource allocations on application performance is vital. The benefits of accurate application performance modeling are multifold. Cloud users can size their VMs appropriately and pay only for the resources that they need; service providers can also offer a new charging model based on the VMs performance instead of their configured sizes. As a result, clients will pay exactly for the performance they are actually experiencing; on the other hand, administrators will be able to maximize their total revenue by utilizing application performance models and SLAs. ^ This thesis made the following contributions. First, we identified resource control parameters crucial for distributing physical resources and characterizing contention for virtualized applications in a shared hosting environment. Second, we explored several modeling techniques and confirmed the suitability of two machine learning tools, Artificial Neural Network and Support Vector Machine, to accurately model the performance of virtualized applications. Moreover, we suggested and evaluated modeling optimizations necessary to improve prediction accuracy when using these modeling tools. Third, we presented an approach to optimal VM sizing by employing the performance models we created. Finally, we proposed a revenue-driven resource allocation algorithm which maximizes the SLA-generated revenue for a data center.^

Reverse Engineering of Modified Genes by Bayesian Network Analysis Defines Molecular Determinants Critical to the Development of Glioblastoma

In this study we have identified key genes that are critical in development of astrocytic tumors. Meta-analysis of microarray studies which compared normal tissue to astrocytoma revealed a set of 646 differentially expressed genes in the majority of astrocytoma. Reverse engineering of these 646 genes using Bayesian network analysis produced a gene network for each grade of astrocytoma (Grade I–IV), and ‘key genes’ within each grade were identified. Genes found to be most influential to development of the highest grade of astrocytoma, Glioblastoma multiforme were: COL4A1, EGFR, BTF3, MPP2, RAB31, CDK4, CD99, ANXA2, TOP2A, and SERBP1. All of these genes were up-regulated, except MPP2 (down regulated). These 10 genes were able to predict tumor status with 96–100% confidence when using logistic regression, cross validation, and the support vector machine analysis. Markov genes interact with NFkβ, ERK, MAPK, VEGF, growth hormone and collagen to produce a network whose top biological functions are cancer, neurological disease, and cellular movement. Three of the 10 genes - EGFR, COL4A1, and CDK4, in particular, seemed to be potential ‘hubs of activity’. Modified expression of these 10 Markov Blanket genes increases lifetime risk of developing glioblastoma compared to the normal population. The glioblastoma risk estimates were dramatically increased with joint effects of 4 or more than 4 Markov Blanket genes. Joint interaction effects of 4, 5, 6, 7, 8, 9 or 10 Markov Blanket genes produced 9, 13, 20.9, 26.7, 52.8, 53.2, 78.1 or 85.9%, respectively, increase in lifetime risk of developing glioblastoma compared to normal population. In summary, it appears that modified expression of several ‘key genes’ may be required for the development of glioblastoma. Further studies are needed to validate these ‘key genes’ as useful tools for early detection and novel therapeutic options for these tumors.

A Digital Signal Processing Approach for Affective Sensing of a Computer User through Pupil Diameter Monitoring

Recent research has indicated that the pupil diameter (PD) in humans varies with their affective states. However, this signal has not been fully investigated for affective sensing purposes in human-computer interaction systems. This may be due to the dominant separate effect of the pupillary light reflex (PLR), which shrinks the pupil when light intensity increases. In this dissertation, an adaptive interference canceller (AIC) system using the H∞ time-varying (HITV) adaptive algorithm was developed to minimize the impact of the PLR on the measured pupil diameter signal. The modified pupil diameter (MPD) signal, obtained from the AIC was expected to reflect primarily the pupillary affective responses (PAR) of the subject. Additional manipulations of the AIC output resulted in a processed MPD (PMPD) signal, from which a classification feature, PMPDmean, was extracted. This feature was used to train and test a support vector machine (SVM), for the identification of stress states in the subject from whom the pupil diameter signal was recorded, achieving an accuracy rate of 77.78%. The advantages of affective recognition through the PD signal were verified by comparatively investigating the classification of stress and relaxation states through features derived from the simultaneously recorded galvanic skin response (GSR) and blood volume pulse (BVP) signals, with and without the PD feature. The discriminating potential of each individual feature extracted from GSR, BVP and PD was studied by analysis of its receiver operating characteristic (ROC) curve. The ROC curve found for the PMPDmean feature encompassed the largest area (0.8546) of all the single-feature ROCs investigated. The encouraging results seen in affective sensing based on pupil diameter monitoring were obtained in spite of intermittent illumination increases purposely introduced during the experiments. Therefore, these results confirmed the benefits of using the AIC implementation with the HITV adaptive algorithm to isolate the PAR and the potential of using PD monitoring to sense the evolving affective states of a computer user.

LCD-OpenPACS: sistema integrado de telerradiologia com auxílio ao diagnóstico de nódulos pulmonares em exames de tomografia computadorizada

Lung cancer is one of the most common types of cancer and has the highest mortality rate. Patient survival is highly correlated with early detection. Computed Tomography technology services the early detection of lung cancer tremendously by offering aminimally invasive medical diagnostic tool. However, the large amount of data per examination makes the interpretation difficult. This leads to omission of nodules by human radiologist. This thesis presents a development of a computer-aided diagnosis system (CADe) tool for the detection of lung nodules in Computed Tomography study. The system, called LCD-OpenPACS (Lung Cancer Detection - OpenPACS) should be integrated into the OpenPACS system and have all the requirements for use in the workflow of health facilities belonging to the SUS (Brazilian health system). The LCD-OpenPACS made use of image processing techniques (Region Growing and Watershed), feature extraction (Histogram of Gradient Oriented), dimensionality reduction (Principal Component Analysis) and classifier (Support Vector Machine). System was tested on 220 cases, totaling 296 pulmonary nodules, with sensitivity of 94.4% and 7.04 false positives per case. The total time for processing was approximately 10 minutes per case. The system has detected pulmonary nodules (solitary, juxtavascular, ground-glass opacity and juxtapleural) between 3 mm and 30 mm.