Fully automatic localization and segmentation of 3D vertebral bodies from CT/MR images via a learning-based method

In this paper, we address the problems of fully automatic localization and segmentation of 3D vertebral bodies from CT/MR images. We propose a learning-based, unified random forest regression and classification framework to tackle these two problems. More specifically, in the first stage, the localization of 3D vertebral bodies is solved with random forest regression where we aggregate the votes from a set of randomly sampled image patches to get a probability map of the center of a target vertebral body in a given image. The resultant probability map is then further regularized by Hidden Markov Model (HMM) to eliminate potential ambiguity caused by the neighboring vertebral bodies. The output from the first stage allows us to define a region of interest (ROI) for the segmentation step, where we use random forest classification to estimate the likelihood of a voxel in the ROI being foreground or background. The estimated likelihood is combined with the prior probability, which is learned from a set of training data, to get the posterior probability of the voxel. The segmentation of the target vertebral body is then done by a binary thresholding of the estimated probability. We evaluated the present approach on two openly available datasets: 1) 3D T2-weighted spine MR images from 23 patients and 2) 3D spine CT images from 10 patients. Taking manual segmentation as the ground truth (each MR image contains at least 7 vertebral bodies from T11 to L5 and each CT image contains 5 vertebral bodies from L1 to L5), we evaluated the present approach with leave-one-out experiments. Specifically, for the T2-weighted MR images, we achieved for localization a mean error of 1.6 mm, and for segmentation a mean Dice metric of 88.7% and a mean surface distance of 1.5 mm, respectively. For the CT images we achieved for localization a mean error of 1.9 mm, and for segmentation a mean Dice metric of 91.0% and a mean surface distance of 0.9 mm, respectively.

Fool me if you can: mimicking attacks and anti-attacks in cyberspace

Botnets have become major engines for malicious activities in cyberspace nowadays. To sustain their botnets and disguise their malicious actions, botnet owners are mimicking legitimate cyber behavior to fly under the radar. This poses a critical challenge in anomaly detection. In this paper, we use web browsing on popular web sites as an example to tackle this problem. First of all, we establish a semi-Markov model for browsing behavior. Based on this model, we find that it is impossible to detect mimicking attacks based on statistics if the number of active bots of the attacking botnet is sufficiently large (no less than the number of active legitimate users). However, we also find it is hard for botnet owners to satisfy the condition to carry out a mimicking attack most of the time. With this new finding, we conclude that mimicking attacks can be discriminated from genuine flash crowds using second order statistical metrics. We define a new fine correntropy metrics and show its effectiveness compared to others. Our real world data set experiments and simulations confirm our theoretical claims. Furthermore, the findings can be widely applied to similar situations in other research fields.

Bayesian nonparametric approaches to abnormality detection in video surveillance

In data science, anomaly detection is the process of identifying the items, events or observations which do not conform to expected patterns in a dataset. As widely acknowledged in the computer vision community and security management, discovering suspicious events is the key issue for abnormal detection in video surveil-lance. The important steps in identifying such events include stream data segmentation and hidden patterns discovery. However, the crucial challenge in stream data segmenta-tion and hidden patterns discovery are the number of coherent segments in surveillance stream and the number of traffic patterns are unknown and hard to specify. Therefore, in this paper we revisit the abnormality detection problem through the lens of Bayesian nonparametric (BNP) and develop a novel usage of BNP methods for this problem. In particular, we employ the Infinite Hidden Markov Model and Bayesian Nonparamet-ric Factor Analysis for stream data segmentation and pattern discovery. In addition, we introduce an interactive system allowing users to inspect and browse suspicious events.

Prosthetic motor imaginary task classification using single channel of electroencephalography

Brain Computer Interface (BCI) is playing a very important role in human machine communications. Recent communication systems depend on the brain signals for communication. In these systems, users clearly manipulate their brain activity rather than using motor movements in order to generate signals that could be used to give commands and control any communication devices, robots or computers. In this paper, the aim was to estimate the performance of a brain computer interface (BCI) system by detecting the prosthetic motor imaginary tasks by using only a single channel of electroencephalography (EEG). The participant is asked to imagine moving his arm up or down and our system detects the movement based on the participant brain signal. Some features are extracted from the brain signal using Mel-Frequency Cepstrum Coefficient and based on these feature a Hidden Markov model is used to help in knowing if the participant imagined moving up or down. The major advantage in our method is that only one channel is needed to take the decision. Moreover, the method is online which means that it can give the decision as soon as the signal is given to the system. Hundred signals were used for testing, on average 89 % of the up down prosthetic motor imaginary tasks were detected correctly. This method can be used in many different applications such as: moving artificial prosthetic limbs and wheelchairs due to it's high speed and accuracy.

A framework for monitoring and runtime recovery of web service-based applications

Service provisioning is a challenging research area for the design and implementation of autonomic service-oriented software systems. It includes automated QoS management for such systems and their applications. Monitoring, Diagnosis and Repair are three key features of QoS management. This work presents a self-healing Web service-based framework that manages QoS degradation at runtime. Our approach is based on proxies. Proxies act on meta-level communications and extend the HTTP envelope of the exchanged messages with QoS-related parameter values. QoS Data are filtered over time and analysed using statistical functions and the Hidden Markov Model. Detected QoS degradations are handled with proxies. We experienced our framework using an orchestrated electronic shop application (FoodShop).

Distributed generators as providers of reactive power support - A market approach

Traditionally, ancillary services are supplied by large conventional generators. However, with the huge penetration of distributed generators (DGs) as a result of the growing interest in satisfying energy requirements, and considering the benefits that they can bring along to the electrical system and to the environment, it appears reasonable to assume that ancillary services could also be provided by DGs in an economical and efficient way. In this paper, a settlement procedure for a reactive power market for DGs in distribution systems is proposed. Attention is directed to wind turbines connected to the network through synchronous generators with permanent magnets and doubly-fed induction generators. The generation uncertainty of this kind of DG is reduced by running a multi-objective optimization algorithm in multiple probabilistic scenarios through the Monte Carlo method and by representing the active power generated by the DGs through Markov models. The objectives to be minimized are the payments of the distribution system operator to the DGs for reactive power, the curtailment of transactions committed in an active power market previously settled, the losses in the lines of the network, and a voltage profile index. The proposed methodology was tested using a modified IEEE 37-bus distribution test system. © 1969-2012 IEEE.

Predição computacional de promotores em Xanthomonas axonopodis pv. citri

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Análise de técnicas de reconhecimento de padrões para a identificação biométrica de usuários em aplicações WEB Utilizando faces a partir de vídeos

Pós-graduação em Ciência da Computação - IBILCE

Desenvolvimento de recursos para a construção de um sistema texto-fala para o português brasileiro

Sistema Texto-Fala (TTS) é atualmente uma tecnologia madura que é utilizada em muitas aplicações. Alguns módulos de um sistema TTS são dependentes do idioma e, enquanto existem muitos recursos disponíveis para a língua inglesa, os recursos para alguns idiomas ainda são limitados. Este trabalho descreve o desenvolvimento de um sistema TTS completo para português brasileiro (PB), o qual também apresenta os recursos já disponíveis. O sistema usa a plataforma MARY e o processo de síntese da voz é baseado em cadeias escondidas de Markov (HMM). Algumas das contribuições deste trabalho consistem na implementação de silabação, determinação da sílaba tônica e conversão grafema-fonema (G2P). O trabalho também descreve as etapas para a organização dos recursos desenvolvidos e a criação de uma voz em PB junto ao MARY. Estes recursos estão disponíveis e facilita a pesquisa na normalização de texto e síntese baseada em HMM par o PB.

Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

An evolutionary approach to improve connectivity prediction in mobile wireless sensor networks

Connectivity is the basic factor for the proper operation of any wireless network. In a mobile wireless sensor network it is a challenge for applications and protocols to deal with connectivity problems, as links might get up and down frequently. In these scenarios, having knowledge of the node remaining connectivity time could both improve the performance of the protocols (e.g. handoff mechanisms) and save possible scarce nodes resources (CPU, bandwidth, and energy) by preventing unfruitful transmissions. The current paper provides a solution called Genetic Machine Learning Algorithm (GMLA) to forecast the remainder connectivity time in mobile environments. It consists in combining Classifier Systems with a Markov chain model of the RF link quality. The main advantage of using an evolutionary approach is that the Markov model parameters can be discovered on-the-fly, making it possible to cope with unknown environments and mobility patterns. Simulation results show that the proposal is a very suitable solution, as it overcomes the performance obtained by similar approaches.

A avaliação da efetividade de um modelo de intervenção breve (método BASICS) para o uso de risco de álcool em estudantes do ensino médio

Pós-graduação em Saúde Coletiva - FMB

A complex chromosomal rearrangement involving chromosomes 2, 5, and X in autism spectrum disorder

Here, we describe a female patient with autism spectrum disorder and dysmorphic features that harbors a complex genetic alteration, involving a de novo balanced translocation t(2;X)(q11;q24), a 5q11 segmental trisomy and a maternally inherited isodisomy on chromosome 5. All the possibly damaging genetic effects of such alterations are discussed. In light of recent findings on ASD genetic causes, the hypothesis that all these alterations might be acting in orchestration and contributing to the phenotype is also considered. (C) 2012 Wiley Periodicals, Inc.

Studying the influence of a secondary variable in Collocated Cokriging estimates

In this paper the influence of a secondary variable as a function of the correlation with the primary variable for collocated cokriging is examined. For this study five exhaustive data sets were generated in computer, from which samples with 60 and 104 data points were drawn using the stratified random sampling method. These exhaustive data sets were generated departing from a pair of primary and secondary variables showing a good correlation. Then successive sets were generated by adding an amount of white noise in such a way that the correlation gets poorer. Using these samples, it was possible to find out how primary and secondary information is used to estimate an unsampled location according to the correlation level.

Design and implementation of bioinformatics tools for large scale genome annotation

The continuous increase of genome sequencing projects produced a huge amount of data in the last 10 years: currently more than 600 prokaryotic and 80 eukaryotic genomes are fully sequenced and publically available. However the sole sequencing process of a genome is able to determine just raw nucleotide sequences. This is only the first step of the genome annotation process that will deal with the issue of assigning biological information to each sequence. The annotation process is done at each different level of the biological information processing mechanism, from DNA to protein, and cannot be accomplished only by in vitro analysis procedures resulting extremely expensive and time consuming when applied at a this large scale level. Thus, in silico methods need to be used to accomplish the task. The aim of this work was the implementation of predictive computational methods to allow a fast, reliable, and automated annotation of genomes and proteins starting from aminoacidic sequences. The first part of the work was focused on the implementation of a new machine learning based method for the prediction of the subcellular localization of soluble eukaryotic proteins. The method is called BaCelLo, and was developed in 2006. The main peculiarity of the method is to be independent from biases present in the training dataset, which causes the over‐prediction of the most represented examples in all the other available predictors developed so far. This important result was achieved by a modification, made by myself, to the standard Support Vector Machine (SVM) algorithm with the creation of the so called Balanced SVM. BaCelLo is able to predict the most important subcellular localizations in eukaryotic cells and three, kingdom‐specific, predictors were implemented. In two extensive comparisons, carried out in 2006 and 2008, BaCelLo reported to outperform all the currently available state‐of‐the‐art methods for this prediction task. BaCelLo was subsequently used to completely annotate 5 eukaryotic genomes, by integrating it in a pipeline of predictors developed at the Bologna Biocomputing group by Dr. Pier Luigi Martelli and Dr. Piero Fariselli. An online database, called eSLDB, was developed by integrating, for each aminoacidic sequence extracted from the genome, the predicted subcellular localization merged with experimental and similarity‐based annotations. In the second part of the work a new, machine learning based, method was implemented for the prediction of GPI‐anchored proteins. Basically the method is able to efficiently predict from the raw aminoacidic sequence both the presence of the GPI‐anchor (by means of an SVM), and the position in the sequence of the post‐translational modification event, the so called ω‐site (by means of an Hidden Markov Model (HMM)). The method is called GPIPE and reported to greatly enhance the prediction performances of GPI‐anchored proteins over all the previously developed methods. GPIPE was able to predict up to 88% of the experimentally annotated GPI‐anchored proteins by maintaining a rate of false positive prediction as low as 0.1%. GPIPE was used to completely annotate 81 eukaryotic genomes, and more than 15000 putative GPI‐anchored proteins were predicted, 561 of which are found in H. sapiens. In average 1% of a proteome is predicted as GPI‐anchored. A statistical analysis was performed onto the composition of the regions surrounding the ω‐site that allowed the definition of specific aminoacidic abundances in the different considered regions. Furthermore the hypothesis that compositional biases are present among the four major eukaryotic kingdoms, proposed in literature, was tested and rejected. All the developed predictors and databases are freely available at: BaCelLo http://gpcr.biocomp.unibo.it/bacello eSLDB http://gpcr.biocomp.unibo.it/esldb GPIPE http://gpcr.biocomp.unibo.it/gpipe