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 ...

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 ...

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 ...

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 ...

This dissertation develops false discovery rate (FDR) controlling machine learning algorithms for large-scale high-dimensional data. Ensuring the reproducibility of discoveries based on high-dimensional data is pivotal in numerous applications. The developed algorithms perform fast variable selection tasks in large-scale high-dimensional settings where the number of variables may be much larger than the number of samples. This includes large-scale data with up to millions of variables such as genome-wide association studies (GWAS). Theoretical finite sample FDR-control guarantees based on martingale theory have been established proving the trustworthiness of the developed methods. The practical open-source R software packages TRexSelector and tlars, which implement the proposed algorithms, have been published on the Comprehensive R Archive Network (CRAN). Extensive numerical experiments and real-world problems in biomedical and financial engineering demonstrate the performance in challenging use-cases. The first three main parts of this dissertation present ...

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 ...

Automatic ear recognition systems have seen increased interest over recent years due to multiple desirable characteristics. Ear images used in such systems can typically be extracted from profile head shots or video footage. The acquisition procedure is contactless and non-intrusive, and it also does not depend on the cooperation of the subjects. In this regard, ear recognition technology shares similarities with other image-based biometric modalities. Another appealing property of ear biometrics is its distinctiveness. Recent studies even empirically validated existing conjectures that certain features of the ear are distinct for identical twins. This fact has significant implications for security-related applications and puts ear images on a par with epigenetic biometric modalities, such as the iris. Ear images can also supplement other biometric modalities in automatic recognition systems and provide identity cues when other information is unreliable or even unavailable. In ...

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 ...

For a large class of non-delay-critical applications (e.g., buffered video streaming or data transfer from cloud services to local devices), end-to-end throughput becomes the most crucial key performance indicator (KPI). In cellular networks, the achievable end-user throughput (the maximum throughput a user will get when attempting to download as much data as possible) is a spatiotemporal function, and its estimation poses a challenging and as-yet unsolved problem. The ability to accurately predict achievable throughput in a given location and time interval would, for example, allow mobile operators to further optimize their networks and design more personalized offers for the customers, or allow end-users with mobile broadband modems to make more informed decisions when selecting a provider. This work investigates the impact of individual parameters on the end-user achievable throughput in cellular networks and analyzes the feasibility and limitations of constructing ...

Multiple-input multiple-output (MIMO) technology promises significant capacity improvements in order to more efficiently utilise the radio frequency spectrum. To achieve its anticipated multiplexing gain as well as meet the requirements for high data rate services, proposed broadband systems are based on OFDM or similar block based techniques, which are afflicted by poor design freedom at low redundancy, and are known to suffer badly from co-channel interference (CCI) in the presence of synchronisation errors. Non-block based approaches are scarce and use mostly decision feedback equalisation (DFE) or V-BLAST approaches adopted for the broadband case, as well as Tomlinson-Harashima precoding (THP). These methods do not require a guard interval and can therefore potentially achieve a higher spectral efficiency. The drawback of these schemes is the large effort in determining the optimum detection order in both space and time, often motivating the adoption ...

This thesis shows research performed into the topic of speaker diarization for meeting rooms. It looks into the algorithms and the implementation of an offline speaker segmentation and clustering system for a meeting recording where usually more than one microphone is available. The main research and system implementation has been done while visiting the International Computes Science Institute (ICSI, Berkeley, California) for a period of two years. Speaker diarization is a well studied topic on the domain of broadcast news recordings. Most of the proposed systems involve some sort of hierarchical clustering of the data into clusters, where the optimum number of speakers of their identities are unknown a priory. A very commonly used method is called bottom-up clustering, where multiple initial clusters are iteratively merged until the optimum number of clusters is reached, according to some stopping criterion. Such ...