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 ...

In biological research images are extensively used to monitor growth, dynamics and changes in biological specimen, such as cells or plants. Many of these images are used solely for observation or are manually annotated by an expert. In this dissertation we discuss several methods to automate the annotating and analysis of bio-images. Two large clusters of methods have been investigated and developed. A first set of methods focuses on the automatic delineation of relevant objects in bio-images, such as individual cells in microscopic images. Since these methods should be useful for many different applications, e.g. to detect and delineate different objects (cells, plants, leafs, ...) in different types of images (different types of microscopes, regular colour photographs, ...), the methods should be easy to adjust. Therefore we developed a methodology relying on probability theory, where all required parameters can easily ...

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 ...

Gliomas represent about 80% of all malignant primary brain tumors. Despite recent advancements in glioma research, patient outcome remains poor. The 5 year survival rate of the most common and most malignant subtype, i.e. glioblastoma, is about 5%. Magnetic resonance imaging (MRI) has become the imaging modality of choice in the management of brain tumor patients. Conventional MRI (cMRI) provides excellent soft tissue contrast without exposing the patient to potentially harmful ionizing radiation. Over the past decade, advanced MRI modalities, such as perfusion-weighted imaging (PWI), diffusion-weighted imaging (DWI) and magnetic resonance spectroscopic imaging (MRSI) have gained interest in the clinical field, and their added value regarding brain tumor diagnosis, treatment planning and follow-up has been recognized. Tumor segmentation involves the imaging-based delineation of a tumor and its subcompartments. In gliomas, segmentation plays an important role in treatment planning as well ...

This PhD thesis addresses the problem of measuring blood glucose from a photometric measurement setup that requires blood samples in the nano litre-range, which is several orders of magnitude less than the state of the art. The chemical reaction between the blood sample and the reagent in this setup is observed by a camera over time. Notably, the presented framework can be generalised to any image-based photometric measurement scheme in the context of modern biosensors. In this thesis a framework is developed to measure the glucose concentration from the raw images obtained by the camera. Initially, a pre-processing scheme is presented to enhance the raw images. Moreover, a reaction onset detection algorithm is developed. This eliminates unnecessary computation during the constant phase of the chemical reaction. To detect faulty glucose measurements, methods of texture analysis are identified and employed in ...

Computer vision-based analysis of human facial video provides information regarding to expression, diseases symptoms, and physiological parameters such as heartbeat rate, blood pressure and respiratory rate. It also provides a convenient source of heartbeat signal to be used in biometrics and forensics. This thesis is a collection of works done in five themes in the realm of computer vision-based facial image analysis: Monitoring elderly patients at private homes, Face quality assessment, Measurement of physiological parameters, Contact-free heartbeat biometrics, and Decision support system for healthcare. The work related to monitoring elderly patients at private homes includes a detailed survey and review of the monitoring technologies relevant to older patients living at home by discussing previous reviews and relevant taxonomies, different scenarios for home monitoring solutions for older patients, sensing and data acquisition techniques, data processing and analysis techniques, available datasets for ...

Base station cooperation is recognized as a key technology for future wireless cellular communication networks. Considering antennas of distributed base stations and those of multiple terminals within those cells as a distributed multiple-input multiple-output (MIMO) system, this technique has the potential to eliminate inter-cell interference by joint signal processing and to enhance spectral efficiency in this way. Although the theoretical gains are meanwhile well-understood, it still remains challenging to realize the full potential of such cooperative schemes in real-world systems. Among other factors, such as the limited overhead for pilot symbols and for the feedback and backhaul, these performance limitations are related to channel and synchronization impairments, such as channel estimation, feedback quantization and channel aging, as well as imperfect carrier and sampling synchronization among the base stations. Because of these impairments, joint data precoding results to be mismatched with ...

It takes more time to think of a silent scene, action or event than finding one that emanates sound. Not only speaking or playing music but almost everything that happens is accompanied with or results in one or more sounds mixed together. This makes acoustic event detection (AED) one of the most researched topics in audio signal processing nowadays and it will probably not see a decline anywhere in the near future. This is due to the thirst for understanding and digitally abstracting more and more events in life via the enormous amount of recorded audio through thousands of applications in our daily routine. But it is also a result of two intrinsic properties of audio: it doesn’t need a direct sight to be perceived and is less intrusive to record when compared to image or video. Many applications such ...

The thriving development of wireless communications calls for innovative and advanced signal processing techniques targeting at an enhanced performance in terms of reliability, throughput, robustness, efficiency, flexibility, etc.. This thesis addresses such a compelling demand and presents new and intriguing progress towards fulfilling it. We mainly concentrate on two advanced multi-dimensional signal processing challenges for wireless systems that have attracted tremendous research attention in recent years, multi-carrier Multiple-Input Multiple-Output (MIMO) systems and multi-dimensional harmonic retrieval. As the key technologies of wireless communications, the numerous benefits of MIMO and multi-carrier modulation, e.g., boosting the data rate and improving the link reliability, have long been identified and have ignited great research interest. In particular, the Orthogonal Frequency Division Multiplexing (OFDM)-based multi-user MIMO downlink with Space-Division Multiple Access (SDMA) combines the twofold advantages of MIMO and multi-carrier modulation. It is the essential element ...

This Thesis is focused on the use of automatic speaker recognition systems for forensic identification, in what is called forensic automatic speaker recognition. More generally, forensic identification aims at individualization, defined as the certainty of distinguishing an object or person from any other in a given population. This objective is followed by the analysis of the forensic evidence, understood as the comparison between two samples of material, such as glass, blood, speech, etc. An automatic speaker recognition system can be used in order to perform such comparison between some recovered speech material of questioned origin (e.g., an incriminating wire-tapping) and some control speech material coming from a suspect (e.g., recordings acquired in police facilities). However, the evaluation of such evidence is not a trivial issue at all. In fact, the debate about the presentation of forensic evidence in a court ...

The main objective of the thesis is the development of efficient multipath mitigation techniques for navigation systems. By efficient mitigation we refer to the use of asymptotic efficient estimators, and also to the minimization of their computational burden. In this thesis, the efficient estimators are derived from the Maximum Likelihood Principle in several important scenarios. The computational burden is reduced in two ways. One is through data compression techniques that yield receiver implementations of small complexity and small data sizes. The other consists of the efficient implementation of Newton-type methods for the computation of the Maximum Likelihood estimators. The first part of the thesis is dedicated to present the fundamentals of synchronization in a navigation receiver, and to the state of the art in multipath mitigation. Afterward, several results concerning the interpolation of a band limited signal in a finite ...

In this thesis we investigate centralized and distributed variants of sparse Bayesian learning (SBL), an effective probabilistic regression method used in machine learning. Since inference in an SBL model is not tractable in closed form, approximations are needed. We focus on the variational Bayesian approximation, as opposed to others used in the literature, for three reasons: First, it is a flexible general framework for approximate Bayesian inference that estimates probability densities including point estimates as a special case. Second, it has guaranteed convergence properties. And third, it is a deterministic approximation concept that is even applicable for high dimensional problems where non-deterministic sampling methods may be prohibitive. We resolve some inconsistencies in the literature involved in other SBL approximation techniques with regard to a proper Bayesian treatment and the incorporation of a very desired property, namely scale invariance. More specifically, ...

Despite decades of exponential growth in computational power, humans continue to find new problems that eclipse available computational resources. This unrelenting pursuit for computational power has brought about supercomputers consisting of millions of individual computing units. Writing programs that would efficiently utilize the computational power of such complex machines has turned out to be a major challenge. As of today, most \ac{HPC} applications continue to be based on the distributed memory programming paradigm, through the use of \ac{MPI}. One of the principal drivers behind the research in this dissertation was the coupling of multi-scale and multi-physics iPIC3D space weather simulation with in-situ raytraced visualization for real-time simulation steering. This application was developed by the Leuven Intel ExaScale Lab as a research prototype for the type of HPC applications projected to run on exascale machines of the 2018-2020 timeframe. Due to ...

Reverberation consists of a complex acoustic phenomenon that occurs inside rooms. Many audio signal processing methods, addressing source localization, signal enhancement and other tasks, often assume absence of reverberation. Consequently, reverberant environments are considered challenging as state-ofthe-art methods can perform poorly. The acoustics of a room can be described using a variety of mathematical models, among which, physical models are the most complete and accurate. The use of physical models in audio signal processing methods is often non-trivial since it can lead to ill-posed inverse problems. These inverse problems require proper regularization to achieve meaningful results and involve the solution of computationally intensive large-scale optimization problems. Recently, however, sparse regularization has been applied successfully to inverse problems arising in different scientific areas. The increased computational power of modern computers and the development of new efficient optimization algorithms makes it possible ...

Wireless communications have gone through an exponential growth in the last several years and it is forecast that this growth will be sustained for the coming decades. This ever-increasing demand for radio resources is now facing one of its main limitations: inter-user interference, arising from the fact of multiple users accessing the propagation medium simultaneously which limits the total amount of data that can be reliably communicated through the wireless links. Traditionally, interference has been dealt with by allocating disjoint channel resources to distinct users. However, the advent of a novel interference coordination technique known as interference alignment (IA) brought to the forefront the promise of a much larger spectral efficiency. This dissertation revolves around the idea of linear interference alignment for a network consisting of several mutually interfering transmitter-receiver pairs, which is com-monly known as interference channel. In particular, ...