Modern technologies have resulted in the production of numerous high-throughput biological datasets. However, the pace of development of capable computational methods does not cope with the pace of generation of new high-throughput datasets. Amongst the most popular biological high-throughput datasets are gene expression datasets (e.g. microarray datasets). This work targets this aspect by proposing a suite of computational methods which can analyse multiple gene expression datasets collectively. The focal method in this suite is the unification of clustering results from multiple datasets using external specifications (UNCLES). This method applies clustering to multiple heterogeneous datasets which measure the expression of the same set of genes separately and then combines the resulting partitions in accordance to one of two types of external specifications; type A identifies the subsets of genes that are consistently co-expressed in all of the given datasets while type ...

The field of Life Science Engineering (LSE) is rapidly expanding and predicted to grow strongly in the next decades. It covers areas of food and medical research, plant and pests’ research, and environmental research. In each research area, engineers try to find equations that model a certain life science problem. Once found, they research different numerical techniques to solve for the unknown variables of these equations. Afterwards, solution improvement is examined by adopting more accurate conventional techniques, or developing novel algorithms. In particular, signal and image processing techniques are widely used to solve those LSE problems require pattern recognition. However, due to the continuous evolution of the life science problems and their natures, these solution techniques can not cover all aspects, and therefore demanding further enhancement and improvement. The thesis presents numerical algorithms of digital signal and image processing to ...

The discovery of novel gene regulatory processes improves the understanding of cell phenotypic responses to external stimuli for many biological applications, such as medicine, environment or biotechnologies. To this purpose, transcriptomic data are generated and analyzed from DNA microarrays or more recently RNAseq experiments. They consist in genetic expression level sequences obtained for all genes of a studied organism placed in different living conditions. From these data, gene regulation mechanisms can be recovered by revealing topological links encoded in graphs. In regulatory graphs, nodes correspond to genes. A link between two nodes is identified if a regulation relationship exists between the two corresponding genes. Such networks are called Gene Regulatory Networks (GRNs). Their construction as well as their analysis remain challenging despite the large number of available inference methods. In this thesis, we propose to address this network inference problem ...

Face recognition has been an active area of study for both computer vision and image processing communities, not only for biometrics but also for human-computer interaction applications. The purpose of the present work is to evaluate the existing 3D face recognition techniques and seek biologically motivated methods to improve them. We especially look at findings in psychophysics and cognitive science for insights. We propose a biologically motivated computational model, and focus on the earlier stages of the model, whose performance is critical for the later stages. Our emphasis is on automatic localization of facial features. We first propose a strong unsupervised learning algorithm for flexible and automatic training of Gaussian mixture models and use it in a novel feature-based algorithm for facial fiducial point localization. We also propose a novel structural correction algorithm to evaluate the quality of landmarking and ...

Nowadays, Nuclear Magnetic Resonance (NMR) is widely used in oncology as a non-invasive diagnostic tool in order to detect the presence of tumor regions in the human body. An application of NMR is Magnetic Resonance Imaging, which is applied in routine clinical practice to localize tumors and determine their size. Magnetic Resonance Imaging is able to provide an initial diagnosis, but its ability to delineate anatomical and pathological information is significantly improved by its combination with another NMR application, namely Magnetic Resonance Spectroscopy. The latter reveals information on the biochemical profile tissues, thereby allowing clinicians and radiologists to identify in a non{invasive way the different tissue types characterizing the sample under investigation, and to study the biochemical changes underlying a pathological situation. In particular, an NMR application exists which provides spatial as well as biochemical information. This application is called ...

Obstructive sleep apnea (OSA) is among the most prevalent sleep disorders, which is estimated to affect 6 %−19 % of women and 13 %−33 % of men. Besides daytime sleepiness, impaired cognitive functioning and an increased risk for accidents, OSA may lead to obesity, diabetes and cardiovascular diseases (CVD) on the long term. Its prevalence is only expected to rise, as it is linked to aging and excessive body fat. Nevertheless, many patients remain undiagnosed and untreated due to the cumbersome clinical diagnostic procedures. For this, the patient is required to sleep with an extensive set of body attached sensors. In addition, the recordings only provide a single night perspective on the patient in an uncomfortable, and often unknown, environment. Thus, large scale monitoring at home is desired with comfortable sensors, which can stay in place for several nights. To ...

Over the last decades, Magnetic Resonance Imaging (MRI) has taken a leading role in the study of human body and it is widely used in clinical diagnosis. In vivo and ex vivo Magnetic Resonance Spectroscopic (MRS) techniques can additionally provide valuable metabolic information as compared to MRI and are gaining more clinical interest. The analysis of MRS data is a complex procedure and requires several preprocessing steps aiming to improve the quality of the data and to extract the most relevant features before any classification algorithm can be successfully applied. In this thesis a new approach to quantify magnetic resonance spectroscopic imaging (MRSI) data and therefore to obtain improved metabolite estimates is proposed. Then an important part is focusing on improving the diagnosis of glial brain tumors which are characterized by an extensive heterogeneity since various intramural histopathological properties such ...

In the modern world, we are increasingly surrounded by computation devices with communication links and one or more microphones. Such devices are, for example, smartphones, tablets, laptops or hearing aids. These devices can work together as nodes in an acoustic sensor network (ASN). Such networks are a growing platform that opens the possibility for many practical applications. ASN based speech enhancement, source localization, and event detection can be applied for teleconferencing, camera control, automation, or assisted living. For this kind of applications, the awareness of auditory objects and their spatial positioning are key properties. In order to provide these two kinds of information, novel methods have been developed in this thesis. Information on the type of auditory objects is provided by a novel real-time sound classification method. Information on the position of human speakers is provided by a novel localization ...

Wireless Sensor Networks (WSNs) aim for accurate data gathering and representation of one or multiple physical variables from the environment, by means of sensor reading and wireless data packets transmission to a Data Fusion Center (DFC). There is no comprehensive common set of requirements for all WSN, as they are application dependent. Moreover, due to specific node capabilities or energy consumption constraints several tradeoffs have to be considered during the design, and particularly, the price of the sensor nodes is a determining factor. The distinction between small and large scale WSNs does not only refers to the quantity of sensor nodes, but also establishes the main design challenges in each case. For example, the node organization is a key issue in large scale WSNs, where many inexpensive nodes have to properly work in a coordinated manner. Regarding the amount of ...

Advances in compression techniques, decreasing cost of storage, and high-speed transmission have facilitated the way videos are created, stored and distributed. As a consequence, videos are now being used in many applications areas. The increase in the amount of video data deployed and used in today's applications reveals not only the importance as multimedia data type, but also led to the requirement of efficient management of video data. This management paved the way for new research areas, such as indexing and retrieval of video with respect to their spatio-temporal, visual and semantic contents. This thesis presents work towards a unified framework for semi-automated video indexing and interactive retrieval. To create an efficient index, a set of representative key frames are selected which capture and encapsulate the entire video content. This is achieved by, firstly, segmenting the video into its constituent ...

The present doctoral thesis aims towards the development of new long-term, multi-channel, audio-visual processing techniques for the analysis of bioacoustics phenomena. The effort is focused on the study of the physiology of the gastrointestinal system, aiming at the support of medical research for the discovery of gastrointestinal motility patterns and the diagnosis of functional disorders. The term "processing" in this case is quite broad, incorporating the procedures of signal processing, content description, manipulation and analysis, that are applied to all the recorded bioacoustics signals, the auxiliary audio-visual surveillance information (for the monitoring of experiments and the subjects' status), and the extracted audio-video sequences describing the abdominal sound-field alterations. The thesis outline is as follows. The main objective of the thesis, which is the technological support of medical research, is presented in the first chapter. A quick problem definition is initially ...

The goal of the dissertation is to investigate and propose new methods for automatic Kikuchi lines detection. New subdivision of microscopic investigation called Orientation Microscopy is already well known in scanning electron microscope (SEM). Spatial resolution in SEM causes the limitation for investigation of fine grained and highly deformed materials. Needs for investigation in nanoscale contribute to development of an appropriate method for transmission electron microscope (TEM). Automated acquisition and indexing Kikuchi diffraction pattern, necessary for creation of orientation maps in TEM, cause more difficulties than in SEM. In order to solve the problem, the author developed and tested three methods for automatic Kikuchi lines detection. The first method is based on directional image filtration and scanning the entire image with a specially designed mask. This method yields good results but is relatively slow. The second method make use of ...

The subject of this PhD thesis is the efficient and robust processing and analysis of the audio recordings that are derived from a call center. The thesis is comprised of two parts. The first part is dedicated to dialogue/non-dialogue detection and to speaker segmentation. The systems that are developed are prerequisite for detecting (i) the audio segments that actually contain a dialogue between the system and the call center customer and (ii) the change points between the system and the customer. This way the volume of the audio recordings that need to be processed is significantly reduced, while the system is automated. To detect the presence of a dialogue several systems are developed. This is the first effort found in the international literature that the audio channel is exclusively exploited. Also, it is the first time that the speaker utterance ...

The main research area of this Ph.D. thesis is video sequence processing and analysis for description and indexing of visual content. Its objective is to contribute in the development of a computational system with the capabilities of object-based segmentation of audiovisual material, automatic content description, summarization for preview and browsing, as well as content-based retrieval. The thesis consists of four parts. The first introduces video sequence analysis, segmentation and object extraction based on color, motion, and depth field. A fusion technique is proposed that combines individual cue segmentations and allows for reliable identification of semantic objects. The second part refers to automatic description and annotation of the visual content by means of feature vectors, summarization, implemented by optimal selection of a limited set of key frames and shots, and content-based search and retrieval. In the third part, the problem of ...

Cryptography and biometrics have been identified as two of the most important aspects of digital security environment. For various types of security problems the merging between cryptography and biometrics has led to the development of Bio crypt technology. The new technology suffers from several limitations and this thesis, addresses the biometric information quality and the security weakness of cryptography. In many applications fingerprint has been chosen as a core of bio crypt combined technology due to it’s maturity in terms of availability, uniqueness, permanence, feasibility, ease of use and acceptance. Fingerprint has been studied from the point of view of information strength to suitability to the cryptographic requirement. The factors relating to generating and constructing combined bio crypt key such as biometric image validity, quality assessment and distinct feature extraction are studied to avoid corruptness of the source biometric images. ...