B-flavor tagging at Belle II Akopov, N.; Banerjee, Sw; Bauer, M. ...
The European physical journal. C, Particles and fields,
04/2022, Volume:
82, Issue:
4
Journal Article
Peer reviewed
Open access
We report on new flavor tagging algorithms developed to determine the quark-flavor content of bottom (
) mesons at Belle II. The algorithms provide essential inputs for measurements of quark-flavor ...mixing and charge-parity violation. We validate and evaluate the performance of the algorithms using hadronic
decays with flavor-specific final states reconstructed in a data set corresponding to an integrated luminosity of 62.8 fb
-
1
, collected at the
resonance with the Belle II detector at the SuperKEKB collider. We measure the total effective tagging efficiency to be
ε
eff
=
(
30.0
±
1.2
(
stat
)
±
0.4
(
syst
)
)
%
for a category-based algorithm and
ε
eff
=
(
28.8
±
1.2
(
stat
)
±
0.4
(
syst
)
)
%
for a deep-learning-based algorithm.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Department of Microbiology, University of Iowa, Iowa City, IA 52242, USA
Correspondence George V. Stauffer george-stauffer{at}uiowa.edu
In Escherichia coli , the gcvB gene encodes a small ...non-translated RNA that regulates several genes involved in transport of amino acids and peptides (including sstT , oppA and dppA ). Microarray analysis identified cycA as an additional regulatory target of GcvB. The cycA gene encodes a permease for the transport of glycine, D -alanine, D -serine and D -cycloserine. RT-PCR confirmed that GcvB and the Hfq protein negatively regulate cycA mRNA in cells grown in Luria–Bertani broth. In addition, deletion of the gcvB gene resulted in increased sensitivity to D -cycloserine, consistent with increased expression of cycA . A cycA : : lacZ translational fusion confirmed that GcvB negatively regulates cycA expression in Luria–Bertani broth and that Hfq is required for the GcvB effect. GcvB had no effect on cycA : : lacZ expression in glucose minimal medium supplemented with glycine. However, Hfq still negatively regulated the fusion in the absence of GcvB. A set of transcriptional fusions of cycA to lacZ identified a sequence in cycA necessary for regulation by GcvB. Analysis of GcvB identified a region complementary to this region of cycA mRNA. However, mutations predicted to disrupt base-pairing between cycA mRNA and GcvB did not alter expression of cycA : : lacZ . A model for GcvB function in cell physiology is discussed.
Abbreviations: DEPC, diethylpyrocarbonate; sRNA, small non-translated regulatory RNA; WT, wild-type
A supplementary table listing genes shown to be significantly regulated in the WT versus the gcvB strain by microarray analysis is available with the online version of this paper.
Today's analyses for high-energy physics (HEP) experiments involve processing a large amount of data with highly specialized algorithms. The contemporary workflow from recorded data to final results ...is based on the execution of small scripts - often written in Python or ROOT macros which call complex compiled algorithms in the background - to perform fitting procedures and generate plots. During recent years interactive programming environments, such as Jupyter, became popular. Jupyter allows to develop Python-based applications, so-called notebooks, which bundle code, documentation and results, e.g. plots. Advantages over classical script-based approaches is the feature to recompute only parts of the analysis code, which allows for fast and iterative development, and a web-based user frontend, which can be hosted centrally and only requires a browser on the user side. In our novel approach, Python and Jupyter are tightly integrated into the Belle II Analysis Software Framework (basf2), currently being developed for the Belle II experiment in Japan. This allows to develop code in Jupyter notebooks for every aspect of the event simulation, reconstruction and analysis chain. These interactive notebooks can be hosted as a centralized web service via jupyterhub with docker and used by all scientists of the Belle II Collaboration. Because of its generality and encapsulation, the setup can easily be scaled to large installations.
Punzi-loss Abudinén, F.; Bertemes, M.; Bilokin, S. ...
The European physical journal. C, Particles and fields,
2022/2, Volume:
82, Issue:
2
Journal Article
Peer reviewed
Open access
We present the novel implementation of a non-differentiable metric approximation and a corresponding loss-scheduling aimed at the search for new particles of unknown mass in high energy physics ...experiments. We call the loss-scheduling, based on the minimisation of a figure-of-merit related function typical of particle physics, a Punzi-loss function, and the neural network that utilises this loss function a Punzi-net. We show that the Punzi-net outperforms standard multivariate analysis techniques and generalises well to mass hypotheses for which it was not trained. This is achieved by training a single classifier that provides a coherent and optimal classification of all signal hypotheses over the whole search space. Our result constitutes a complementary approach to fully differentiable analyses in particle physics. We implemented this work using PyTorch and provide users full access to a public repository containing all the codes and a training example.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Punzi-loss Abudinén, F; Bertemes, M; Bilokin, S ...
The European physical journal. C, Particles and fields,
02/2022, Volume:
82, Issue:
2
Journal Article
Peer reviewed
Open access
We present the novel implementation of a non-differentiable metric approximation and a corresponding loss-scheduling aimed at the search for new particles of unknown mass in high energy physics ...experiments. We call the loss-scheduling, based on the minimisation of a figure-of-merit related function typical of particle physics, a Punzi-loss function, and the neural network that utilises this loss function a Punzi-net. We show that the Punzi-net outperforms standard multivariate analysis techniques and generalises well to mass hypotheses for which it was not trained. This is achieved by training a single classifier that provides a coherent and optimal classification of all signal hypotheses over the whole search space. Our result constitutes a complementary approach to fully differentiable analyses in particle physics. We implemented this work using PyTorch and provide users full access to a public repository containing all the codes and a training example.
Full text
Available for:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The Belle II Core Software Kuhr, T.; Pulvermacher, C.; Ritter, M. ...
Computing and software for big science,
12/2019, Volume:
3, Issue:
1
Journal Article
Open access
Modern high-energy physics (HEP) enterprises, such as the Belle II experiment (Abe et al, Belle II Technical Design Report. KEK Report 2010-1,
2010
; Kou et al, The Belle II Physics book. KEK ...Preprint 2018-27,
2018
) at the KEK laboratory in Japan, create huge amounts of data. Sophisticated algorithms for simulation, reconstruction, visualization, and analysis are required to fully exploit the potential of these data. We describe the core components of the Belle II software that provide the foundation for the development of complex algorithms and their efficient application on large data sets.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Software Quality Control at Belle II Ritter, M; Kuhr, T; Hauth, T ...
Journal of physics. Conference series,
10/2017, Volume:
898, Issue:
7
Journal Article
Peer reviewed
Open access
Over the last seven years the software stack of the next generation B factory experiment Belle II has grown to over one million lines of C++ and Python code, counting only the part included in ...offline software releases. There are several thousand commits to the central repository by about 100 individual developers per year. To keep a coherent software stack of high quality that it can be sustained and used efficiently for data acquisition, simulation, reconstruction, and analysis over the lifetime of the Belle II experiment is a challenge. A set of tools is employed to monitor the quality of the software and provide fast feedback to the developers. They are integrated in a machinery that is controlled by a buildbot master and automates the quality checks. The tools include different compilers, cppcheck, the clang static analyzer, valgrind memcheck, doxygen, a geometry overlap checker, a check for missing or extra library links, unit tests, steering file level tests, a sophisticated high-level validation suite, and an issue tracker. The technological development infrastructure is complemented by organizational means to coordinate the development.
Belle II Conditions Database Ritter, M; Wood, L; Kuhr, T ...
Journal of physics. Conference series,
09/2018, Volume:
1085, Issue:
3
Journal Article
Peer reviewed
Open access
The Belle II experiment at KEK is preparing for taking first collision data in early 2018. For the success of the experiment it is essential to have information about varying conditions available to ...systems worldwide in a fast and efficient manner that is straightforward for both the user and maintainer. The Belle II Conditions Database was designed to make maintenance as easy as possible. To this end, a HTTP REST service was developed with industry-standard tools such as Swagger for the API interface development, Payara for the Java EE application server, and the Hazelcast in-memory data grid for support of scalable caching as well as transparent distribution of the service across multiple sites. On the client side, the online and offline software has to be able to obtain conditions data from the Belle II Conditions Database in a robust and reliable way under very different situations. As such the client side interface to the Belle II Conditions Database has been designed with a variety of access mechanisms which allow the software to be used with and without an internet connection. Different methods to access the payload information are implemented to allow for a high level of customization per site and to simplify testing of new payloads locally. Changes to the conditions data are usually handled transparently but users can actively check whether an object has changed or register callback functions to be called whenever a conditions data object is updated. In addition a command line user interface has been developed to simplify inspection and modification of the database contents.
The impending Upgrade of the Belle experiment is expected to increase the generated data set by a factor of 50. This means that for the planned pixel detector, which is the closest to the interaction ...point, the data rates are going to increase to up to 28 Gbit s. Combined with data generated by the other detectors, this rate is too big to efficiently send out to offline processing. In order to reduce the data rates online data reduction schemes, in which background is detected and rejected, are going to be employed. In this paper, an approach for efficient online data reduction for the planned pixel detector of Belle-II is presented. Its central part is the NeuroBayes algorithm, which is based on multivariate analysis. It allows the identification of signal and background by analyzing clusters of hits in the pixel detector on FPGAs. The algorithm is leveraging the fact that hits of signal particles can have very different characteristics, compared to background, when passing through the pixel detector. The applicability and advantages in performance are shown through the D* decay. In Belle-II, these decays produce pions with such a small transversal momentum, that they barely escape the pixel detector itself. In a common approach like an extrapolation of tracks from outer detectors to RoIs, these pions are simply lost, since they do not reach all necessary layers of the detector. However, cluster analysis is able to identify and separate these pions from the background, thus keeping their data. For that characteristics of corresponding hits, like the total amount of charge deposited in the pixels, are used for separation. The capability for effective data reduction is underlined by a background reduction of at least 90% and signal efficiency of 95%, for slow pions. An implementation of the algorithm for usage on Virtex-6 FPGAs that are used at the pixel detector was performed. It is shown that the resulting implementation succeeds in replicating the efficiency of the algorithm, implemented in software while throughputs that suffice hard real-time constraints, set by the read-out system of Belle-II, are achieved and efficient use of the resources present on the FPGA is made.
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