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All hits all the time: parameter-free calculation of spaced seed sensitivity

D. Y.F. Mak, G. Benson
2008 Bioinformatics  
We expect this method to greatly facilitate the study of spaced seed sensitivity and the use of alternative definitions of optimality.  ...  Only the weights assigned to those alignments change. Therefore, if we know all the hits, we can easily (and quickly) find optimal seeds.  ...  In section 6 we show results from applying our parameter free calculation to several seed classes.  ... 
doi:10.1093/bioinformatics/btn643 pmid:19095701 fatcat:q66wpw2cvfhurnmrcsvt2joouy

Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds

Laurent Noé
2017 Algorithms for Molecular Biology  
further processed in a parameter-free calculation of the sensitivity.  ...  Unfortunately, spaced seeds need to be initially designed. This task is known to be time-consuming due to the number of spaced seed candidates.  ...  The author would like to thank the second reviewer for his/ her thorough review which significantly contributed to improving the quality of the paper.  ... 
doi:10.1186/s13015-017-0092-1 pmid:28289437 pmcid:PMC5310094 fatcat:ioxohbn52bdvljst36lnyqd4di

ALL HITS ALL THE TIME: PARAMETER FREE CALCULATION OF SEED SENSITIVITY

DENISE Y.F. MAK, GARY BENSON
2007 Proceedings of the 5th Asia-Pacific Bioinformatics Conference  
We expect this method to greatly facilitate the study of seed space sensitivity, construction of multiple seed sets, and the use of alternative definitions of optimality.  ...  Only the weights assigned to those alignments change. Therefore, if we know all the hits, we can easily (and quickly) find optimal seeds.  ...  In section 5 we show results from applying our parameter free calculation to several seed classes.  ... 
doi:10.1142/9781860947995_0035 fatcat:2nqoll4o7jaorafrmmk6qb5dei

Time-aware Entity Alignment using Temporal Relational Attention

Chengjin Xu, Fenglong Su, Bo Xiong, Jens Lehmann
2022 Proceedings of the ACM Web Conference 2022  
We first map entities, relations and timestamps into an embedding space, and the initial feature of each entity is represented by fusing the embeddings of its connected relations and timestamps as well  ...  Experimental results show that our method outperforms the state-of-the-art EA methods. CCS CONCEPTS • Computing methodologies → Knowledge representation and reasoning; Temporal reasoning.  ...  ACKNOWLEDGMENTS We acknowledge the support of the following projects: SPEAKER (BMWi FKZ 01MK20011A), JOSEPH (Fraunhofer Zukunftsstiftung), the EU projects Cleopatra (GA 812997), PLATOON(GA 872592), TAILOR  ... 
doi:10.1145/3485447.3511922 fatcat:zeckpvzoqbgbxaho2cvhbs6xxy

Time Really Passes, Science Can't Deny That [chapter]

Nicolas Gisin
2017 Time in Physics  
In particular, I argue that besides the geometric time, there is creative time, when objective chance events happen. The existence of the latter follows straight from the existence of free-will.  ...  Today's science provides quite a lean picture of time as a mere geometric evolution parameter. I argue that time is much richer.  ...  Thanks are due to Chris Fuchs who introduced me to Jules Lequyer and to many participants to the workshop on Time in Physics organized at the ETH-Zurich by Sandra Rankovic, Daniela Frauchiger and Renato  ... 
doi:10.1007/978-3-319-68655-4_1 fatcat:dq3wllmnxbgntea2i3qhaejfuq

Efficient Continuous-Time Markov Chain Estimation [article]

Monir Hajiaghayi, Bonnie Kirkpatrick, Liangliang Wang, Alexandre Bouchard-Côté
2014 arXiv   pre-print
the holding times and sequences of visited states.  ...  Many problems of practical interest rely on Continuous-time Markov chains~(CTMCs) defined over combinatorial state spaces, rendering the computation of transition probabilities, and hence probabilistic  ...  where some or all the parameters of the CTMC are unknown.  ... 
arXiv:1309.3250v2 fatcat:4ggaluw4gbblflb2zn3esyx3ui

The International Pulsar Timing Array: A Galactic Scale Gravitational Wave Observatory [article]

M. A. McLaughlin
2014 arXiv   pre-print
Due to a growing number of millisecond pulsar discoveries, improved instrumentation, and growing timespans of observation, the sensitivity of our pulsar timing array experiments is expected to dramatically  ...  Here, I describe the observations and analysis necessary to accomplish this goal and present an overview of the efforts of the worldwide pulsar timing community.  ...  Acknowledgements Thank you to all of my colleagues in NANOGrav and the IPTA for many conversations that have improved this paper. The comments from the anonymous referee were also immensely helpful.  ... 
arXiv:1409.4579v2 fatcat:6f4g7plbqfdqnjn7tmb4ss7t3e

Dynamic backcalculation with different load-time histories

Stine Skov Madsen, Eyal Levenberg
2017 International Journal on Road Materials and Pavement Design  
It was found that backcalculated parameters are sensitive to the FWD pulse features.  ...  This paper focused attention to the Falling Weight Deflectometer (FWD) load-time history.  ...  In each stage the minimization process was restarted several times with new seed values to broaden the search space for a solution.  ... 
doi:10.1080/14680629.2017.1307263 fatcat:wexya5vtgrhmfok47jgj5ybhsu

Time-resolved studies with FELs

Artem Rudenko, Daniel Rolles
2015 Journal of Electron Spectroscopy and Related Phenomena  
In this paper, we focus on time-resolved studies of gas-phase molecules, which lie at the crossroad between atomic, molecular and optical physics and ultrafast photochemistry.  ...  We describe the current status of the field and discuss typical experimental configurations used for pump-probe experiments with FELs.  ...  We acknowledge the Max Planck Society for funding the development and operation of the CAMP instrument within the ASG at CFEL.  ... 
doi:10.1016/j.elspec.2015.07.010 fatcat:ic5jt4zuljbknpcpotoqf7kwcy

Pump-Probe Time-Resolved Serial Femtosecond Crystallography at X-Ray Free Electron Lasers

Suraj Pandey, Ishwor Poudyal, Tek Narsingh Malla
2020 Crystals  
With time-resolved crystallography (TRX), it is possible to follow the reaction dynamics in biological macromolecules by investigating the structure of transient states along the reaction coordinate.  ...  Here, we review the recent developments, opportunities, and challenges of pump-probe TRX at XFELs.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/cryst10070628 fatcat:vaz6p77bp5bxvmhpyaz5vwa5jy

First Detection Of Low Energy Electron Neutrinos In Liquid Argon Time Projection Chambers

Corey Adams, Bonnie Fleming, Ornella Palamara
2016 Zenodo  
Liquid argon time projection chambers are the forefront of neutrino detection technology, and the detector of choice for both short and long baseline neutrino oscillation experiments.  ...  This work presents the first experimental observation and study of electron neutrinos in the 1-10 GeV range, the essential oscillation energy regime for the above experiments.  ...  The free ionization density along the track can be sampled by the hit amplitude to the track pitch length ratio (Q f ree /δx), which allows calculating the value of the R factor.  ... 
doi:10.5281/zenodo.1158052 fatcat:woqbjexy6bg2feqg37jdpqaeq4

Technical Design Study for the PANDA Time Projection Chamber [article]

M. Ball , B. Ketzer, S. Uhl, F. Cusanno, J. Frühauf, J. Kunkel, L. Schmitt, D. Kaiser, P. Müllner Technische Universität München, Germany, GSI Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany (+7 others)
2012 arXiv   pre-print
This document illustrates the technical layout and the expected performance of a Time Projection Chamber as the central tracking system of the PANDA experiment.  ...  The detector is based on a continuously operating TPC with Gas Electron Multiplier (GEM) amplification.  ...  density of the p i in the parameter space.  ... 
arXiv:1207.0013v1 fatcat:62poxk7lifgj3b3mz2zhfmwlnq

rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison

Lars Hahn, Chris-André Leimeister, Rachid Ounit, Stefano Lonardi, Burkhard Morgenstern, Andreas Prlic
2016 PLoS Computational Biology  
In our Spaced Words approach to alignment-free sequence comparison, pattern sets calculated with rasbhari led to more accurate estimates of phylogenetic distances than the randomly generated pattern sets  ...  Here too, the sensitivity of the results could be improved, compared to the default patterns of the program.  ...  Acknowledgments We would like to thank Laurent Noé for helpful discussions and for pointing out the similarity between the overlap complexity and the variance of the number of spaced-word matches.  ... 
doi:10.1371/journal.pcbi.1005107 pmid:27760124 pmcid:PMC5070788 fatcat:wi7dcyps4jfjzb6gams4swt6ji

Real-Time Community Detection in Large Social Networks on a Laptop [article]

Benjamin Paul Chamberlain, Josh Levy-Kramer, Clive Humby, Marc Peter Deisenroth
2016 arXiv   pre-print
We achieve single machine real-time performance by compressing the neighbourhood of each vertex using minhash signatures and facilitate rapid queries through Locality Sensitive Hashing.  ...  The key idea is that the aggregate actions of large numbers of users can be compressed into a data structure that encapsulates user similarities while being robust to noise and queryable in real-time.  ...  Acknowledgements This work was partly funded by a Royal Commission for the Exhibition of 1851 Industrial Fellowship.  ... 
arXiv:1601.03958v2 fatcat:ngr47upgn5aa3amraurfmjblja

A Timing-Aware Probabilistic Model for Single-Event-Upset Analysis

T. Rejimon, S. Bhanja
2006 IEEE Transactions on Very Large Scale Integration (vlsi) Systems  
To model the effect of timing, we consider signals at their possible arrival times as the random variables of interest.  ...  We propose a probabilistic framework to the study the effect of inputs, circuits structure and gate delays on Single-Event-Upset sensitivities of nodes in logic circuits as a single joint probability distribution  ...  Time-space transformed circuit of benchmark c17, modeling all SEUs.  ... 
doi:10.1109/tvlsi.2006.884165 fatcat:43enh4yptfalvmriyf6l4enj2m
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