Browsing by Subject "SEARCH"

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  • Mukherjee, Kingshuk; Alipanahi, Bahar; Kahveci, Tamer; Salmela, Leena; Boucher, Christina (2019)
    Motivation: Optical maps are high-resolution restriction maps (Rmaps) that give a unique numeric representation to a genome. Used in concert with sequence reads, they provide a useful tool for genome assembly and for discovering structural variations and rearrangements. Although they have been a regular feature of modern genome assembly projects, optical maps have been mainly used in post-processing step and not in the genome assembly process itself. Several methods have been proposed for pairwise alignment of single molecule optical maps-called Rmaps, or for aligning optical maps to assembled reads. However, the problem of aligning an Rmap to a graph representing the sequence data of the same genome has not been studied before. Such an alignment provides a mapping between two sets of data: optical maps and sequence data which will facilitate the usage of optical maps in the sequence assembly step itself. Results: We define the problem of aligning an Rmap to a de Bruijn graph and present the first algorithm for solving this problem which is based on a seed-and-extend approach. We demonstrate that our method is capable of aligning 73% of Rmaps generated from the Escherichia coli genome to the de Bruijn graph constructed from short reads generated from the same genome. We validate the alignments and show that our method achieves an accuracy of 99.6%. We also show that our method scales to larger genomes. In particular, we show that 76% of Rmaps can be aligned to the de Bruijn graph in the case of human data.
  • Rooijers, Koos; Kolmeder, Carolin; Juste, Catherine; Dore, Joel; de Been, Mark; Boeren, Sjef; Galan, Pilar; Beauvallet, Christian; de Vos, Willem M.; Schaap, Peter J. (2011)
  • Kindler, Oliver; Pulkkinen, Otto; Cherstvy, Andrey G.; Metzler, Ralf (2019)
    Quorum-sensing bacteria in a growing colony of cells send out signalling molecules (so-called "autoinducers") and themselves sense the autoinducer concentration in their vicinity. Once-due to increased local cell density inside a "cluster" of the growing colony-the concentration of autoinducers exceeds a threshold value, cells in this clusters get "induced" into a communal, multi-cell biofilm-forming mode in a cluster-wide burst event. We analyse quantitatively the influence of spatial disorder, the local heterogeneity of the spatial distribution of cells in the colony, and additional physical parameters such as the autoinducer signal range on the induction dynamics of the cell colony. Spatial inhomogeneity with higher local cell concentrations in clusters leads to earlier but more localised induction events, while homogeneous distributions lead to comparatively delayed but more concerted induction of the cell colony, and, thus, a behaviour close to the mean-field dynamics. We quantify the induction dynamics with quantifiers such as the time series of induction events and burst sizes, the grouping into induction families, and the mean autoinducer concentration levels. Consequences for different scenarios of biofilm growth are discussed, providing possible cues for biofilm control in both health care and biotechnology.
  • Bliem, Bernhard; Järvisalo, Matti (IEEE Computer Society, 2020)
    Proceedings-International Conference on Tools With Artificial Intelligence
    Model counting is the archetypical #P-complete problem consisting of determining the number of satisfying truth assignments of a given propositional formula. In this short paper, we empirically investigate the potential of employing graph centrality measures as a basis of search heuristics in the context of exact model counting. In particular, we integrate centrality-based heuristics into the search-based exact model counter sharpSAT. Our experiments show that employing centrality information significantly improves the empirical performance of sharpSAT, and also allows for simplifying the search heuristics compared to the current default heuristics of the model counter. In particular, we show that the VSIDS heuristic, which is an integral search heuristic employed in essentially all state-of-the-art conflict-driven clause learning Boolean satisfiability solvers, appears to be of very limited use in the context of model counting.
  • The CMS collaboration; Sirunyan, A. M.; Eerola, P.; Kirschenmann, H.; Pekkanen, J.; Voutilainen, M.; Havukainen, J.; Heikkilä, J. K.; Jarvinen, T.; Karimaki, V.; Kinnunen, R.; Lampen, T.; Lassila-Perini, K.; Laurila, S.; Linden, T.; Luukka, P.; Maenpaa, T.; Siikonen, H.; Tuominen, E.; Tuominiemi, J.; Tuuva, T. (2019)
    Combined measurements of the production and decay rates of the Higgs boson, as well as its couplings to vector bosons and fermions, are presented. The analysis uses the LHC proton-proton collision data set recorded with the CMS detector in 2016 at fb-1. The combination is based on analyses targeting the five main Higgs boson production mechanisms (gluon fusion, vector boson fusion, and associated production with a W or Z boson, or a top quark-antiquark pair) and the following decay modes: H, ZZ, WW, , bb, and . Searches for invisible Higgs boson decays are also considered. The best-fit ratio of the signal yield to the standard model expectation is measured to be =1.17 +/- 0.10, assuming a Higgs boson mass of 125.09. Additional results are given for various assumptions on the scaling behavior of the production and decay modes, including generic parametrizations based on ratios of cross sections and branching fractions or couplings. The results are compatible with the standard model predictions in all parametrizations considered. In addition, constraints are placed on various two Higgs doublet models.
  • Xue, Hailian; Mäkelä, Aino Annikki; Valsta, Lauri Tapani; Vanclay, Jerome; Cao, Tianjian (2019)
    Stand management optimization has long been computationally demanding as increasingly detailed growth and yield models have been developed. Process-based growth models are useful tools for predicting forest dynamics. However, the difficulty of classic optimization algorithms limited its applications in forest planning. This study assessed alternative approaches to optimizing thinning regimes and rotation length using a process-based growth model. We considered (1) population-based algorithms proposed for stand management optimization, including differential evolution (DE), particle swarm optimization (PSO), evolution strategy (ES), and (2) derivative-free search algorithms, including the Nelder–Mead method (NM) and Osyczka’s direct and random search algorithm (DRS). We incorporated population-based algorithms into the simulation-optimization system OptiFor in which the process-based model PipeQual was the simulator. The results showed that DE was the most reliable algorithm among those tested. Meanwhile, DRS was also an effective algorithm for sparse stands with fewer decision variables. PSO resulted in some higher objective function values, however, the computational time of PSO was the longest. In general, of the population-based algorithms, DE is superior to the competing ones. The effectiveness of DE for stand management optimization is promising and manifested.
  • The CMS collaboration; Sirunyan, A. M.; Eerola, P.; Kirschenmann, H.; Pekkanen, J.; Voutilainen, M.; Havukainen, J.; Heikkilä, J. K.; Järvinen, T.; Karimäki, V.; Kinnunen, R.; Lampén, T.; Lassila-Perini, K.; Laurila, S.; Lehti, S.; Lindén, T.; Luukka, P.; Mäenpää, T.; Siikonen, H.; Tuominen, E.; Tuominiemi, J.; Tuuva, T. (2018)
    The results of a previous search by the CMS Collaboration for squarks and gluinos are reinterpreted to constrain models of leptoquark (LQ) production. The search considers jets in association with a transverse momentum imbalance, using the M-T2 variable. The analysis uses proton-proton collision data at root s = 13 TeV, recorded with the CMS detector at the LHC in 2016 and corresponding to an integrated luminosity of 35.9 fb(-1). Leptoquark pair production is considered with LQ decays to a neutrino and a top, bottom, or light quark. This reinterpretation considers higher mass values than the original CMS search to constrain both scalar and vector LQs. Limits on the cross section for LQ pair production are derived at the 95% confidence level depending on the LQ decay mode. A vector LQ decaying with a 50% branching fraction to t nu, and 50% to b tau, has been proposed as part of an explanation of anomalous flavor physics results. In such a model, using only the decays to t nu, LQ masses below 1530 GeV are excluded assuming the Yang-Mills case with coupling kappa = 1, or 1115 GeV in the minimal coupling case kappa = 0, placing the most stringent constraint to date from pair production of vector LQs.
  • The CMS collaboration; Sirunyan, A. M.; Eerola, P.; Pekkanen, J.; Voutilainen, M.; Järvinen, T.; Karimäki, V.; Kinnunen, R.; Lampén, T.; Lassila-Perini, K.; Lehti, S.; Lindén, T.; Luukka, P.; Tuominen, E.; Tuominiemi, J.; Talvitie, J.; Tuuva, T. (2018)
    A first search for same-sign WW production via double-parton scattering is performed based on proton-proton collision data at a center-of-mass energy of 8TeV using dimuon and electron-muon final states. The search is based on the analysis of data corresponding to an integrated luminosity of 19.7 fb(-1). No significant excess of events is observed above the expected single-parton scattering yields. A 95% confidence level upper limit of 0.32 pb is set on the inclusive cross section for same-sign WW production via the double-parton scattering process. This upper limit is used to place a 95% confidence level lower limit of 12.2mb on the effective double-parton cross section parameter, closely related to the transverse distribution of partons in the proton. This limit on the effective cross section is consistent with previous measurements as well as with Monte Carlo event generator predictions.
  • Heikinheimo, Matti; Huitu, Katri; Keus, Venus; Koivunen, Niko (2019)
    The Froggatt-Nielsen mechanism is a well-motivated framework for generating the fermion mass hierarchy. This mechanism introduces flavons, complex scalars which are singlet under the Standard Model gauge symmetry and charged under a new global family symmetry. We make use of a leptophilic flavon to produce the charged lepton Yukawa matrix. The real part of the flavon mixes with the Higgs boson and introduces lepton flavour violating interactions which are bounded by experiment. The imaginary part of the flavon, , is a long-lived light particle, whose abundance is restricted by cosmological observations. For m<2m(e) where the decay of to charged leptons is kinematically forbidden, we identify allowed regions of m with respect to the vacuum expectation value of the flavon field where all experimental and cosmological constraints are satisfied.
  • Tiurev, Konstantin; Kuopanportti, Pekko; Möttönen, Mikko (2019)
    We theoretically demonstrate that a pair of Dirac monopoles with opposite synthetic charges can be created within a single spin-1 Bose-Einstein condensate by steering the spin degrees of freedom by external magnetic fields. Although the net synthetic magnetic charge of this configuration vanishes, both the monopole and the antimonopole are accompanied by vortex filaments carrying opposite angular momenta. Such a Dirac dipole can be realized experimentally by imprinting a spin texture with a nonlinear magnetic field generated by a pair of coils in a modified Helmholtz configuration. We also investigate the case where the initial state for the dipole-creation procedure is pierced by a quantized vortex line with a winding number kappa. It is shown that if kappa = -1, the resulting monopole and antimonopole lie along the core of a singly quantized vortex whose sign is reversed at the locations of the monopoles. For kappa = -2, the monopole and antimonopole are connected by a vortex line segment carrying two quanta of angular momentum, and hence the dipole as a whole is an isolated configuration. In addition, we simulate the long-time evolution of the dipoles in the magnetic field used to create them. For kappa = 0, each of the semi-infinite doubly quantized vortices splits into two singly quantized vortices, as in the case of a single Dirac monopole. For kappa = -1 and kappa = -2, the initial vortices deform into a vortex with a kink and a vortex ring, respectively.
  • Marchet, Camille; Boucher, Christina; Puglisi, Simon J.; Medvedev, Paul; Salson, Mikael; Chikhi, Rayan (2021)
    High-throughput sequencing data sets are usually deposited in public repositories (e.g., the European Nucleotide Archive) to ensure reproducibility. As the amount of data has reached petabyte scale, repositories do not allow one to perform online sequence searches, yet, such a feature would be highly useful to investigators. Toward this goal, in the last few years several computational approaches have been introduced to index and query large collections of data sets. Here, we propose an accessible survey of these approaches, which are generally based on representing data sets as sets of k-mers. We review their properties, introduce a classification, and present their general intuition. We summarize their performance and highlight their current strengths and limitations.
  • Mesihää, Samuel; Ketola, Raimo A.; Pelander, Anna; Rasanen, Ilpo; Ojanpera, Ilkka (2017)
    Gas chromatography coupled to atmospheric pressure chemical ionization quadrupole time-of-flight mass spectrometry (GC-APCI-QTOFMS) was evaluated for the identification of new psychoactive substances (NPS). An in-house high mass resolution GC-APCI-QTOFMS test library was developed for 29 nitrogen-containing drugs belonging mostly to synthetic stimulants. The library was based on 12 intra-day measurements of each compound at three different collision energies, 10, 20 and 40 eV. The in-house library mass spectra were compared to mass spectra from a commercial library constructed by liquid chromatography-electrospray ionization (LC-ESI) QTOFMS. The reversed library search scores between the in-house GC-APCI library and the commercial LC-ESI library were compared once a week during a 5-week period by using data measured by GC-APCI-QTOFMS. The protonated molecule was found for all drugs in the full scan mode, and the drugs were successfully identified by both libraries in the targeted MS/MS mode. The GC-APCI library score averaged over all collision energies was as high as 94.4/100 with a high repeatability, while the LC-ESI library score was also high (89.7/100) with a repeatability only slightly worse. These results highlight the merits of GC-APCI-QTOFMS in the analysis of NPS even in situations where the reference standards are not immediately available, taking advantage of the accurate mass measurement of the protonated molecule and product ions, and comparison to existing soft-ionization mass spectral libraries.
  • Jacucci, Giulio; Daee, Pedram; Vuong, Tung; Andolina, Salvatore; Klouche, Khalil; Sjöberg, Mats; Ruotsalo, Tuukka; Kaski, Samuel (2021)
    Recommender systems can support everyday digital tasks by retrieving and recommending useful information contextually. This is becoming increasingly relevant in services and operating systems. Previous research often focuses on specific recommendation tasks with data captured from interactions with an individual application. The quality of recommendations is also often evaluated addressing only computational measures of accuracy, without investigating the usefulness of recommendations in realistic tasks. The aim of this work is to synthesize the research in this area through a novel approach by (1) demonstrating comprehensive digital activity monitoring, (2) introducing entity-based computing and interaction, and (3) investigating the previously overlooked usefulness of entity recommendations and their actual impact on user behavior in real tasks. The methodology exploits context from screen frames recorded every 2 seconds to recommend information entities related to the current task. We embodied this methodology in an interactive system and investigated the relevance and influence of the recommended entities in a study with participants resuming their realworld tasks after a 14-day monitoring phase. Results show that the recommendations allowed participants to find more relevant entities than in a control without the system. In addition, the recommended entities were also used in the actual tasks. In the discussion, we reflect on a research agenda for entity recommendation in context, revisiting comprehensive monitoring to include the physical world, considering entities as actionable recommendations, capturing drifting intent and routines, and considering explainability and transparency of recommendations, ethics, and ownership of data.
  • Roman, Veronica L.; Merlin, Christophe; Virta, Marko P. J.; Bellanger, Xavier (2021)
    EpicPCR (Emulsion, Paired Isolation and Concatenation PCR) is a recent single-cell genomic method based on a fusion-PCR allowing us to link a functional sequence of interest to a 16S rRNA gene fragment and use the mass sequencing of the resulting amplicons for taxonomic assignment of the functional sequence-carrying bacteria. Although it is interesting because it presents the highest efficiency for assigning a bacterial host to a marker, epicPCR remains a complex multistage procedure with technical difficulties that may easily impair the approach depth and quality. Here, we described how to adapt epicPCR to new gene targets and environmental matrices while identifying the natural host range of SXT/R391 integrative and conjugative elements in water microbial communities from the Meurthe River (France). We notably show that adding a supplementary PCR step allowed us to increase the amplicon yield and thus the number of reads obtained after sequencing. A comparison of operational taxonomic unit (OTU) identification approaches when using biological and technical replicates demonstrated that, although OTUs can be validated when obtained from three out of three technical replicates, up to now, results obtained from two or three biological replicates give a similar and even a better confidence level in OTU identification, while allowing us to detect poorly represented SXT/R391 hosts in microbial communities.
  • Hofmann, F.; Sanders, J. S.; Clerc, N.; Nandra, K.; Ridl, J.; Dennerl, K.; Ramos-Ceja, M.; Finoguenov, A.; Reiprich, T. H. (2017)
    Context. The eROSITA mission will provide the largest sample of galaxy clusters detected in X-ray to date (one hundred thousand expected). This sample will be used to constrain cosmological models by measuring cluster masses. An important mass proxy is the electron temperature of the hot plasma detected in X-rays. Aims. We want to understand the detection properties and possible bias in temperatures due to unresolved substructures in the cluster halos. Methods. We simulated a large number of galaxy cluster spectra with known temperature substructures and compared the results from analysing eROSITA simulated observations to earlier results from Chandra. Results. We were able to constrain a bias in cluster temperatures and its impact on cluster masses, as well as cosmological parameters derived from the survey. We found temperatures in the eROSITA survey to be biased low by about five per cent due to unresolved temperature substructures (compared to emission-weighted average temperatures from the Chandra maps). This bias would have a significant impact on the eROSITA cosmology constraints if not accounted for in the calibration. Conclusions. We isolated the bias effect that substructures in galaxy clusters have on temperature measurements and their impact on derived cosmological parameters in the eROSITA cluster survey.
  • The CMS collaboration; Sirunyan, A. M.; Eerola, P.; Kirschenmann, H.; Pekkanen, J.; Voutilainen, M.; Havukainen, J.; Heikkilä, J. K.; Järvinen, T.; Karimäki, V.; Kinnunen, R.; Lampén, T.; Lassila-Perini, K.; Laurila, S.; Lehti, S.; Lindén, T.; Luukka, P.; Mäenpää, T.; Siikonen, H.; Tuominen, E.; Tuominiemi, J.; Tuuva, T. (2018)
    Results of a search for the standard model Higgs boson produced in association with a top quark pair (t (t) over barH) in final states with electrons, muons, and hadronically decaying tau leptons are presented. The analyzed data set corresponds to an integrated luminosity of 35.9 fb(-1) recorded in proton-proton collisions at root s = 13 TeV by the CMS experiment in 2016. The sensitivity of the search is improved by using matrix element and machine learning methods to separate the signal from backgrounds. The measured signal rate amounts to 1.23(-0.43)(+0.45) times the production rate expected in the standard model, with an observed (expected) significance of 3.2 sigma (2.8 sigma), which represents evidence for t (t) over barH production in those final states. An upper limit on the signal rate of 2.1 times the standard model production rate is set at 95% confidence level.
  • The CMS collaboration; Sirunyan, A. M.; Tumasyan, A.; Eerola, P.; Forthomme, Laurent; Kirschenmann, H.; Österberg, K.; Voutilainen, M.; Brücken, Erik; Garcia, F.; Havukainen, J.; Karimäki, V.; Kim, Minsuk; Kinnunen, R.; Lampén, T.; Lassila-Perini, K.; Lehti, S.; Lindén, T.; Siikonen, H.; Tuominen, E.; Tuominiemi, J.; Luukka, P.; Tuuva, T. (2021)
    Evidence for Higgs boson decay to a pair of muons is presented. This result combines searches in four exclusive categories targeting the production of the Higgs boson via gluon fusion, via vector boson fusion, in association with a vector boson, and in association with a top quark-antiquark pair. The analysis is performed using proton-proton collision data at root s = 13 TeV, corresponding to an integrated luminosity of 137 fb(-1), recorded by the CMS experiment at the CERN LHC. An excess of events over the back- ground expectation is observed in data with a significance of 3.0 standard deviations, where the expectation for the standard model (SM) Higgs boson with mass of 125.38 GeV is 2.5. The combination of this result with that from data recorded at root s = 7 and 8 TeV, corresponding to integrated luminosities of 5.1 and 19.7 fb(-1), respectively, increases both the expected and observed significances by 1%. The measured signal strength, relative to the SM prediction, is 1.19(-0.39)(+0.40)(stat)(-0.14)(+0.15). This result constitutes the first evidence for the decay of the Higgs boson to second generation fermions and is the most precise measurement of the Higgs boson coupling to muons reported to date.
  • The CMS collaboration; Sirunyan, A. M.; Eerola, P.; Kirschenmann, H.; Pekkanen, J.; Voutilainen, M.; Havukainen, J.; Heikkilä, J. K.; Järvinen, T.; Karimäki, V.; Kinnunen, R.; Lampén, T.; Lassila-Perini, K.; Laurila, S.; Lehti, S.; Lindén, T.; Luukka, P.; Siikonen, H.; Tuominen, E.; Tuominiemi, J.; Tuuva, T. (2018)
    A search for the standard model (SM) Higgs boson (H) decaying to b(b)over-bar when produced in association with an electroweak vector boson is reported for the following processes: Z(vv)H, W(mu v)H, W(ev)H, Z(mu mu)H, and Z(ee)H. The search is performed in data samples corresponding to an integrated luminosity of 35.9 f( -1) at root s = 13 TeV recorded by the CMS experiment at the LHC during Run 2 in 2016. An excess of events is observed in data compared to the expectation in the absence of a H -> b(b)over-bar, signal. The significance of this excess is 3.3 standard deviations, where the expectation from SM Higgs boson production is 2.8. The signal strength corresponding to this excess, relative to that of the SM Higgs boson production, is 1.2 +/- 0.4. When combined with the Run 1 measurement of the same processes, the signal significance is 3.8 standard deviations with 3.8 expected. The corresponding signal strength, relative to that of the SM Higgs boson, is 1.06(-0.29)(+0.31). (C) 2018 The Author(s). Published by Elsevier B.V.
  • The CMS collaboration; Sirunyan, A. M.; Eerola, P.; Forthomme, L.; Kirschenmann, H.; Österberg, K.; Voutilainen, M.; Garcia, F.; Havukainen, J.; Heikkilä, J. K.; Järvinen, T.; Karimäki, V.; Kinnunen, R.; Lampen, T.; Lassila-Perini, K.; Laurila, S.; Lehti, S.; Linden, T.; Luukka, P.; Mäenpää, T.; Siikonen, H.; Tuominen, E.; Tuominiemi, J.; Tuuva, T. (2020)
    A search forWWproduction from double-parton scattering processes using same-charge electron-muon and dimuon events is reported, based on proton-proton collision data collected at a center-of-mass energy of 13 TeV. The analyzed data set corresponds to an integrated luminosity of 77.4 fb-1, collected using the CMS detector at the LHC in 2016 and 2017. Multivariate classifiers are used to discriminate between the signal and the dominant background processes. A maximum likelihood fit is performed to extract the signal cross section. This leads to the first evidence for WW production via double-parton scattering, with a significance of 3.9 standard deviations. The measured inclusive cross section is 1.41 +/- 0.28 (stat) +/- 0.28 (syst) pb.
  • Huitu, Katri; Kärkkäinen, Timo J.; Mondal, Subhadeep; Rai, Santosh Kumar (2018)
    We consider a neutrinophilic Higgs scenario where the Standard Model is extended by one additional Higgs doublet and three generations of singlet right-handed Majorana neutrinos. Light neutrino masses are generated through mixing with the heavy neutrinos via the Type-I seesaw mechanism when the neutrinophilic Higgs gets a vacuum expectation value (VEV). The Dirac neutrino Yukawa coupling in this scenario can be sizable compared to those in the canonical Type-I seesaw mechanism owing to the small neutrinophilic Higgs VEV giving rise to interesting phenomenological consequences. We have explored various signal regions likely to provide a hint of such a scenario at the LHC as well as at future e(+)e(-) colliders. We have also highlighted the consequences of light neutrino mass hierarchies in collider phenomenology that can complement the findings of neutrino oscillation experiments.