Using Amino Acid Correlation and Community Detection Algorithms to Identify Functional Determinants in Protein Families

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Pitch detection algorithms based on zero-cross rate and autocorrelation function for musical notes

This paper discusses two pitch detection algorithms (PDA) for simple audio signals which are based on zero-cross rate (ZCR) and autocorrelation function (ACF). As it is well known, pitch detection methods based on ZCR and ACF are widely used in signal processing. This work shows some features and problems in using these methods, as well as some improvements developed to increase their performance. © 2008 IEEE.

UWB radar sensor networks: Detection algorithms design and experimental analysis

In the last years radar sensor networks for localization and tracking in indoor environment have generated more and more interest, especially for anti-intrusion security systems. These networks often use Ultra Wide Band (UWB) technology, which consists in sending very short (few nanoseconds) impulse signals. This approach guarantees high resolution and accuracy and also other advantages such as low price, low power consumption and narrow-band interference (jamming) robustness. In this thesis the overall data processing (done in MATLAB environment) is discussed, starting from experimental measures from sensor devices, ending with the 2D visualization of targets movements over time and focusing mainly on detection and localization algorithms. Moreover, two different scenarios and both single and multiple target tracking are analyzed.

An evaluation of existing incident detection algorithms.

Texas Department of Transportation, Austin

Analysis of edge detection algorithms on DIAL /

Mode of access: Internet.

Comparison of module detection algorithms in protein networks and investigation of the biological meaning of predicted modules

Background
It is generally acknowledged that a functional understanding of a biological system can only be obtained by an understanding of the collective of molecular interactions in form of biological networks. Protein networks are one particular network type of special importance, because proteins form the functional base units of every biological cell. On a mesoscopic level of protein networks, modules are of significant importance because these building blocks may be the next elementary functional level above individual proteins allowing to gain insight into fundamental organizational principles of biological cells.
Results
In this paper, we provide a comparative analysis of five popular and four novel module detection algorithms. We study these module prediction methods for simulated benchmark networks as well as 10 biological protein interaction networks (PINs). A particular focus of our analysis is placed on the biological meaning of the predicted modules by utilizing the Gene Ontology (GO) database as gold standard for the definition of biological processes. Furthermore, we investigate the robustness of the results by perturbing the PINs simulating in this way our incomplete knowledge of protein networks.
Conclusions
Overall, our study reveals that there is a large heterogeneity among the different module prediction algorithms if one zooms-in the biological level of biological processes in the form of GO terms and all methods are severely affected by a slight perturbation of the networks. However, we also find pathways that are enriched in multiple modules, which could provide important information about the hierarchical organization of the system

Interference detection in GNSS signals using Gaussianity criterion

We assess the performance of Gaussianity tests, namely the Anscombe-Glynn, Lilliefors, Cramér-von Mises, and Giannakis-Tsatsanis (G-T), with the purpose of detecting narrowband and wideband interference in GNSS signals. Simulations have shown that the G-T test outperforms the others being suitable as a benchmark for comparison with different types of interference detection algorithms. © 2014 EURASIP.

Detection of denial of service attacks

This thesis studies techniques used for detection of distributed denial of service attacks which during last decade became one of the most serious network security threats. To evaluate different detection algorithms and further improve them we need to test their performance under conditions as close to real-life situations as possible. Currently the only feasible solution for large-scale tests is the simulated environment. The thesis describes implementation of recursive non-parametric CUSUM algorithm for detection of distributed denial of service attacks in ns-2 network simulator – a standard de-facto for network simulation.

Eye Fundus Image Analysis for Automatic Detection of Diabetic Retinopathy

Diabetes is a rapidly increasing worldwide problem which is characterised by defective metabolism of glucose that causes long-term dysfunction and failure of various organs. The most common complication of diabetes is diabetic retinopathy (DR), which is one of the primary causes of blindness and visual impairment in adults. The rapid increase of diabetes pushes the limits of the current DR screening capabilities for which the digital imaging of the eye fundus (retinal imaging), and automatic or semi-automatic image analysis algorithms provide a potential solution. In this work, the use of colour in the detection of diabetic retinopathy is statistically studied using a supervised algorithm based on one-class classification and Gaussian mixture model estimation. The presented algorithm distinguishes a certain diabetic lesion type from all other possible objects in eye fundus images by only estimating the probability density function of that certain lesion type. For the training and ground truth estimation, the algorithm combines manual annotations of several experts for which the best practices were experimentally selected. By assessing the algorithm’s performance while conducting experiments with the colour space selection, both illuminance and colour correction, and background class information, the use of colour in the detection of diabetic retinopathy was quantitatively evaluated. Another contribution of this work is the benchmarking framework for eye fundus image analysis algorithms needed for the development of the automatic DR detection algorithms. The benchmarking framework provides guidelines on how to construct a benchmarking database that comprises true patient images, ground truth, and an evaluation protocol. The evaluation is based on the standard receiver operating characteristics analysis and it follows the medical practice in the decision making providing protocols for image- and pixel-based evaluations. During the work, two public medical image databases with ground truth were published: DIARETDB0 and DIARETDB1. The framework, DR databases and the final algorithm, are made public in the web to set the baseline results for automatic detection of diabetic retinopathy. Although deviating from the general context of the thesis, a simple and effective optic disc localisation method is presented. The optic disc localisation is discussed, since normal eye fundus structures are fundamental in the characterisation of DR.

Modular framework for outlier detection

Outlier detection is an important form of data analysis because outliers in several cases contain the interesting and important pieces of information. In the recent years, many different outlier detection algorithms have been devised for finding different kinds of outliers in varying contexts and environments. Some effort has been put to study how to effectively combine different outlier detection methods. The combination of outlier detection algorithms as an ensemble was studied in this thesis by designing a modular framework for outlier detection, which combines arbitrary outlier detection techniques. This work resulted in an example implementation of the framework. Outlier detection capability of the ensemble method was validated using datasets and methods found in outlier detection research. The framework achieved better results than the individual outlier algorithms. Future research includes how to handle large datasets effectively and the possibilities for real-time outlier monitoring.

Face Detection and Facial Feature Localization for multi-pose faces and complex backgroundimages

The objective of this thesis work, is to propose an algorithm to detect the faces in a digital image with complex background. A lot of work has already been done in the area of face detection, but drawback of some face detection algorithms is the lack of ability to detect faces with closed eyes and open mouth. Thus facial features form an important basis for detection. The current thesis work focuses on detection of faces based on facial objects. The procedure is composed of three different phases: segmentation phase, filtering phase and localization phase. In segmentation phase, the algorithm utilizes color segmentation to isolate human skin color based on its chrominance properties. In filtering phase, Minkowski addition based object removal (Morphological operations) has been used to remove the non-skin regions. In the last phase, Image Processing and Computer Vision methods have been used to find the existence of facial components in the skin regions.This method is effective on detecting a face region with closed eyes, open mouth and a half profile face. The experiment’s results demonstrated that the detection accuracy is around 85.4% and the detection speed is faster when compared to neural network method and other techniques.

Automatic system for thermal damage detection in manufacturing process with Internet monitoring

This work involved the development of a smart system dedicated to surface burning detection in the grinding process through constant monitoring of the process by acoustic emission and electrical power signals. A program in Visual Basic® for Windows® was developed, which collects the signals through an analog-digital converter and further processes them using burning detection algorithms already known. Three other parameters are proposed here and a comparative study carried out. When burning occurs, the newly developed software program sends a control signal warning the operator or interrupting the process, and delivers process information via the Internet. Parallel to this, the user can also interfere in the process via Internet, changing parameters and/or monitoring the grinding process. The findings of a comparative study of the various parameters are also discussed here. Copyright © 2006 by ABCM.

Intrusion detection system using optimum-path forest

Intrusion detection systems that make use of artificial intelligence techniques in order to improve effectiveness have been actively pursued in the last decade. Neural networks and Support Vector Machines have been also extensively applied to this task. However, their complexity to learn new attacks has become very expensive, making them inviable for a real time retraining. In this research, we introduce a new pattern classifier named Optimum-Path Forest (OPF) to this task, which has demonstrated to be similar to the state-of-the-art pattern recognition techniques, but extremely more efficient for training patterns. Experiments on public datasets showed that OPF classifier may be a suitable tool to detect intrusions on computer networks, as well as allow the algorithm to learn new attacks faster than the other techniques. © 2011 IEEE.

Detection and Tracking of Dynamic Objects. A MultiRobot approach to Critical Infrastructures Surveillance.

Despite that Critical Infrastructures (CIs) security and surveillance are a growing concern for many countries and companies, Multi Robot Systems (MRSs) have not been yet broadly used in this type of facilities. This dissertation presents a novel study of the challenges arisen by the implementation of this type of systems and proposes solutions to specific problems. First, a comprehensive analysis of different types of CIs has been carried out, emphasizing the influence of the different characteristics of the facilities in the design of a security and surveillance MRS. One of the most important needs for the surveillance of a CI is the detection of intruders. From a technical point of view this problem can be abstracted as equivalent to the Detection and Tracking of Mobile Objects (DATMO). This dissertation proposes algorithms to solve this specific problem in a CI environment. Using 3D range images of the environment as input data, two detection algorithms for ground robots have been developed. These detection algorithms provide a list of moving objects in the robot detection area. Direct image differentiation and computer vision techniques are used when the robot is static. Alternatively, multi-layer ground reconstructions are compared to detect the dynamic objects when the robot is moving. Since CIs usually spread over large areas, it is very useful to incorporate aerial vehicles in the surveillance MRS. Therefore, a moving object detection algorithm for aerial vehicles has been also developed. This algorithm compares the real optical flow obtained from a down-face oriented camera with an artificial optical flow computed using a RANSAC based homography matrix. Two tracking algorithms have been developed to follow the moving objects trajectories. These algorithms can efficiently handle occlusions and crossings, as well as exchange information among robots. The multirobot tracking can be applied to any type of communication structure: centralized, decentralized or a combination of both. Even more, the developed tracking algorithms are independent of the detection algorithms and could be potentially used with other detection procedures or even with static sensors, such as cameras. In addition, using the 3D point clouds available to the robots, a relative localization algorithm has been developed to improve the position estimation of a given robot with observations from other robots. All the developed algorithms have been extensively tested in different simulated CIs using the Webots robotics simulator. Furthermore, the algorithms have also been validated with real robots operating in real scenarios. In conclusion, this dissertation presents a multirobot approach to Critical Infrastructure Surveillance, mainly focusing on Detecting and Tracking Dynamic Objects.