Search for TeV Scale Physics in Heavy Flavour Decays

The subject of heavy flavour decays as probes for physics beyond the TeV scale is covered from the experimental perspective. Emphasis is placed on the more traditional Beyond the Standard Model topics that have potential for impact in the short term, with the physics explained. We do unabashedly promote our own phemonenology work.Comment: 10 pages, 9 figures (now fixed); Submitted for the SUSY07 proceeding

Approximation Schemes for Subset Sum Ratio Problems

We consider the Subset Sum Ratio Problem ($SSR$), in which given a set of integers the goal is to find two subsets such that the ratio of their sums is as close to~1 as possible, and introduce a family of variations that capture additional meaningful requirements. Our main contribution is a generic framework that yields fully polynomial time approximation schemes (FPTAS) for problems in this family that meet certain conditions. We use our framework to design explicit FPTASs for two such problems, namely Two-Set Subset-Sum Ratio and Factor-$r$ Subset-Sum Ratio, with running time $\mathcal{O}(n^4/\varepsilon)$, which coincides with the best known running time for the original $SSR$ problem [15]

The application of artificial intelligence techniques to a sequencing problem in the biological domain

SIGLEAvailable from British Library Document Supply Centre- DSC:DXN002816 / BLDSC - British Library Document Supply CentreGBUnited Kingdo

05441 Abstracts Collection -- Managing and Mining Genome Information: Frontiers in Bioinformatics

From 30.10.05 to 04.11.05, the Dagstuhl Seminar 05441 ``Managing and Mining Genome Information: Frontiers in Bioinformatics\u27\u27 was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

Applying Formal Methods to Networking: Theory, Techniques and Applications

Despite its great importance, modern network infrastructure is remarkable for the lack of rigor in its engineering. The Internet which began as a research experiment was never designed to handle the users and applications it hosts today. The lack of formalization of the Internet architecture meant limited abstractions and modularity, especially for the control and management planes, thus requiring for every new need a new protocol built from scratch. This led to an unwieldy ossified Internet architecture resistant to any attempts at formal verification, and an Internet culture where expediency and pragmatism are favored over formal correctness. Fortunately, recent work in the space of clean slate Internet design---especially, the software defined networking (SDN) paradigm---offers the Internet community another chance to develop the right kind of architecture and abstractions. This has also led to a great resurgence in interest of applying formal methods to specification, verification, and synthesis of networking protocols and applications. In this paper, we present a self-contained tutorial of the formidable amount of work that has been done in formal methods, and present a survey of its applications to networking.Comment: 30 pages, submitted to IEEE Communications Surveys and Tutorial

Äriprotsessimudelite ühildamine

Väitekirja elektrooniline versioon ei sisalda publikatsioone.Ettevõtted, kellel on aastatepikkune kogemus äriprotsesside haldamises, omavad sageli protsesside repositooriumeid, mis võivad endas sisaldada sadu või isegi tuhandeid äriprotsessimudeleid. Need mudelid pärinevad erinevatest allikatest ja need on loonud ning neid on muutnud erinevad osapooled, kellel on erinevad modelleerimise oskused ning praktikad. üheks sagedaseks praktikaks on uute mudelite loomine, kasutades olemasolevaid mudeleid, kopeerides neist fragmente ning neid seejärel muutes. See omakorda loob olukorra, kus protsessimudelite repositoorium sisaldab mudeleid, milles on identseid mudeli fragmente, mis viitavad samale alamprotsessile. Kui sellised fragmendid jätta konsolideerimata, siis võib see põhjustada repositooriumis ebakõlasid -- üks ja sama alamprotsess võib olla erinevates protsessides erinevalt kirjeldatud. Sageli on ettevõtetel mudelid, millel on sarnased eesmärgid, kuid mis on mõeldud erinevate klientide, toodete, äriüksuste või geograafiliste regioonide jaoks. Näiteks on äriprotsessid kodukindlustuse ja autokindlustuse jaoks sama ärilise eesmärgiga. Loomulikult sisaldavad nende protsesside mudelid mitmeid identseid alamfragmente (nagu näiteks poliisi andmete kontrollimine), samas on need protsessid mitmes punktis erinevad. Nende protsesside eraldi haldamine on ebaefektiivne ning tekitab liiasusi. Doktoritöös otsisime vastust küsimusele: kuidas identifitseerida protsessimudelite repositooriumis korduvaid mudelite fragmente, ning üldisemalt -- kuidas leida ning konsolideerida sarnasusi suurtes äriprotsessimudelite repositooriumites? Doktoritöös on sisse toodud kaks üksteist täiendavat meetodit äriprotsessimudelite konsolideerimiseks, täpsemalt protsessimudelite ühildamine üheks mudeliks ning mudelifragmentide ekstraktimine. Esimene neist võtab sisendiks kaks või enam protsessimudelit ning konstrueerib neist ühe konsolideeritud protsessimudeli, mis sisaldab kõikide sisendmudelite käitumist. Selline lähenemine võimaldab analüütikutel hallata korraga tervet perekonda sarnaseid mudeleid ning neid muuta sünkroniseeritud viisil. Teine lähenemine, alamprotsesside ekstraktimine, sisaldab endas sagedasti esinevate fragmentide identifitseerimist (protsessimudelites kloonide leidmist) ning nende kapseldamist alamprotsessideks

Analysing and quantitatively modelling nucleosome binding preferences

The main emphasis of my work as a PhD student was the analysis and prediction of nucleosome positioning, focusing on the role sequence features play. Part I gives a broad overview of nucleosomes, before defining important technical terms. It continues by describing and reviewing experiments that measure nucleosome positioning and bioinformatic methods that learn the sequence preferences of nucleosomes to predict their positioning. Part II describes a collaboration project with the Gaul-lab, where I analyzed MNase-Seq measurements of nucleosomes in Drosophila. The original intention was to investigate the extent to which experimental biases influence the measurements. We extended the analysis to categorize and explore fragile, average and resistant nucleosome populations. I focused on the relation between nucleosome fragility and the sequence landscape, especially at promoters and enhancers. Analyzing the partial unwrapping of nucleosomes genome-wide, I found that the G+C ratio is a determinant of asymmetric unwrapping. I excluded an analysis of histone modifications from this work, which was part of this collaboration, due to its low relevance to the rest of the presented work. Part III describes my main project of developing a probabilistic nucleosome-position prediction method. I developed a maximum likelihood approach to learn a biophysical model of nucleosome binding. By including the low positional resolution of MNase-Seq and the sequence bias of CC-Seq into the likelihood, I could separate them from the nucleosome binding preferences and learn highly correlated nucleosome binding energy models. My analysis shows that nucleosomes have a position-specific binding preference and might be uninfluenced by G+C content or even disfavor it – contrary to the Consensus in literature. Part IV describes further analysis I did during my time as a PhD student that are not part of any planned publications. The main topics are: ancillary elements of my main project, unsuccessful attempts to correct experimental biases, analysis of the quality of experimental measurements, and adapting my probabilistic nucleosome-position prediction method to work with occupancy measurements. Lastly, I give a general outlook that reflects on my results and discusses next steps, like ways to improve my method further. I excluded two collaboration projects I participated in from this thesis, because they are still ongoing: a systematic analysis of how the core promoter sequence influences gene expression in Drosophila and the development of an experiment to measure nucleosome occupancy more precisely