Sequential Monte Carlo Methods for System Identification

One of the key challenges in identifying nonlinear and possibly non-Gaussian state space models (SSMs) is the intractability of estimating the system state. Sequential Monte Carlo (SMC) methods, such as the particle filter (introduced more than two decades ago), provide numerical solutions to the nonlinear state estimation problems arising in SSMs. When combined with additional identification techniques, these algorithms provide solid solutions to the nonlinear system identification problem. We describe two general strategies for creating such combinations and discuss why SMC is a natural tool for implementing these strategies.Comment: In proceedings of the 17th IFAC Symposium on System Identification (SYSID). Added cover pag

Spatial Identification Methods and Systems for RFID Tags

Disertační práce je zaměřena na metody a systémy pro měření vzdálenosti a lokalizaci RFID tagů pracujících v pásmu UHF. Úvod je věnován popisu současného stavu vědeckého poznání v oblasti RFID prostorové identifikace a stručnému shrnutí problematiky modelování a návrhu prototypů těchto systémů. Po specifikaci cílů disertace pokračuje práce popisem teorie modelování degenerovaného kanálu pro RFID komunikaci. Detailně jsou rozebrány metody měření vzdálenosti a odhadu směru příchodu signálu založené na zpracování fázové informace. Pro účely lokalizace je navrženo několik scénářů rozmístění antén. Modely degenerovaného kanálu jsou simulovány v systému MATLAB. Významná část této práce je věnována konceptu softwarově definovaného rádia (SDR) a specifikům jeho adaptace na UHF RFID, která využití běžných SDR systémů značně omezují. Diskutována je zejména problematika průniku nosné vysílače do přijímací cesty a požadavky na signál lokálního oscilátoru používaný pro směšování. Prezentovány jsou tři vyvinuté prototypy: experimentální dotazovač EXIN-1, měřicí systém založený na platformě Ettus USRP a anténní přepínací matice pro emulaci SIMO systému. Závěrečná část je zaměřena na testování a zhodnocení popisovaných lokalizačních technik, založených na měření komplexní přenosové funkce RFID kanálu. Popisuje úzkopásmové/širokopásmové měření vzdálenosti a metody odhadu směru signálu. Oba navržené scénáře rozmístění antén jsou v závěru ověřeny lokalizačním měřením v reálných podmínkách.The doctoral thesis is focused on methods and systems for ranging and localization of RFID tags operating in the UHF band. It begins with a description of the state of the art in the field of RFID positioning with short extension to the area of modeling and prototyping of such systems. After a brief specification of dissertation objectives, the thesis overviews the theory of degenerate channel modeling for RFID communication. Details are given about phase-based ranging and direction of arrival finding methods. Several antenna placement scenarios are proposed for localization purposes. The degenerate channel models are simulated in MATLAB. A significant part of the thesis is devoted to software defined radio (SDR) concept and its adaptation for UHF RFID operation, as it has its specialties which make the usage of standard SDR test equipment very disputable. Transmit carrier leakage into receiver path and requirements on local oscillator signals for mixing are discussed. The development of three experimental prototypes is also presented there: experimental interrogator EXIN-1, measurement system based on Ettus USRP platform, and antenna switching matrix for an emulation of SIMO system. The final part is focused on testing and evaluation of described positioning techniques based on complex backscatter channel transfer function measurement. Both narrowband/wideband ranging and direction of arrival methods are validated. Finally, both proposed antenna placement scenarios are evaluated with real-world measurements.

Benchmarking network propagation methods for disease gene identification

In-silico identification of potential target genes for disease is an essential aspect of drug target discovery. Recent studies suggest that successful targets can be found through by leveraging genetic, genomic and protein interaction information. Here, we systematically tested the ability of 12 varied algorithms, based on network propagation, to identify genes that have been targeted by any drug, on gene-disease data from 22 common non-cancerous diseases in OpenTargets. We considered two biological networks, six performance metrics and compared two types of input gene-disease association scores. The impact of the design factors in performance was quantified through additive explanatory models. Standard cross-validation led to over-optimistic performance estimates due to the presence of protein complexes. In order to obtain realistic estimates, we introduced two novel protein complex-aware cross-validation schemes. When seeding biological networks with known drug targets, machine learning and diffusion-based methods found around 2-4 true targets within the top 20 suggestions. Seeding the networks with genes associated to disease by genetics decreased performance below 1 true hit on average. The use of a larger network, although noisier, improved overall performance. We conclude that diffusion-based prioritisers and machine learning applied to diffusion-based features are suited for drug discovery in practice and improve over simpler neighbour-voting methods. We also demonstrate the large impact of choosing an adequate validation strategy and the definition of seed disease genesPeer ReviewedPostprint (published version

Structure identification methods for atomistic simulations of crystalline materials

We discuss existing and new computational analysis techniques to classify local atomic arrangements in large-scale atomistic computer simulations of crystalline solids. This article includes a performance comparison of typical analysis algorithms such as Common Neighbor Analysis, Centrosymmetry Analysis, Bond Angle Analysis, Bond Order Analysis, and Voronoi Analysis. In addition we propose a simple extension to the Common Neighbor Analysis method that makes it suitable for multi-phase systems. Finally, we introduce a new structure identification algorithm, the Neighbor Distance Analysis, that is designed to identify atomic structure units in grain boundaries

Methods of isolation and identification of pathogenic and potential pathogenic bacteria from skins and tannery effluents

Currently there is no standard protocol available within the leather industry to isolate and identify pathogenic bacteria from hides, skins or tannery effluent. This study was therefore carried out to identify simple but effective methods for isolation and identification of bacterial pathogens from the effluent and skins during leather processing. Identification methods based on both phenotypic and genotypic characteristics were investigated. Bacillus cereus and Pseudomonas aeruginosa were used as indicator bacteria to evaluate the isolation and identification methods. Decontaminated calfskins were inoculated with a pure culture of the above mentioned bacterial species followed by a pre-tanning and chromium tanning processes. Effluent samples were collected and skins were swabbed at the end of each processing stage. Bacterial identification was carried out based on the phenotypic characteristics; such as colony appearance on selective solid media, cell morphology following a standard Gram-staining and spore staining techniques, and biochemical reactions, e.g., the ability of a bacterial species to ferment particular sugars and ability to produce certain enzymes. Additionally, an identification system based on bacterial phenotypic characteristics, known as Biolog® system was applied. A pulsed-filed gel electrophoresis (PFGE) method for bacterial DNA fingerprinting was also evaluated and used for the identification of the inoculated bacteria. The methods described in the study were found to be effective for the identification of pathogenic bacteria from skins and effluent