492 research outputs found
Integrated modelling driven fusion research - Coupling of plasma and neutron transport codes
Funding Information: This work has been carried out within the framework of the EUROfusionConsortium and has received funding from the Euratom research and training programme 2014-2018 and 2019-2020 under grant agreement No 633053. The viewsand opinions expressed herein do not necessarily reflect those of the European Commission. The authors acknowledgethe funding received from the Slovenian Research Agency in the scope of the projects: Trainingof young researchers – 1000-14-0106, Reactor Physics – P2-0073-0106-019, Development of methodology for calibration of neutron detectors with a 14.1 MeV neutron generator - JET fusion reactor case – J2-6752. References [1] O. N. Jarvis, Plasma Phys. Control. Fusion 36, 2 (1994) [2] O. Meneghini et al, Nucl. Fusion, 55, 8 (2015) [3] Ž. Štancar et al, Nucl. Fusion 59, 9 (2019) [4] P. Sirén et al, Nucl. Fusion 58, 1 (2018)Non peer reviewe
A Faster Implementation of Online Run-Length Burrows-Wheeler Transform
Run-length encoding Burrows-Wheeler Transformed strings, resulting in
Run-Length BWT (RLBWT), is a powerful tool for processing highly repetitive
strings. We propose a new algorithm for online RLBWT working in run-compressed
space, which runs in time and bits of space, where
is the length of input string received so far and is the number of runs
in the BWT of the reversed . We improve the state-of-the-art algorithm for
online RLBWT in terms of empirical construction time. Adopting the dynamic list
for maintaining a total order, we can replace rank queries in a dynamic wavelet
tree on a run-length compressed string by the direct comparison of labels in a
dynamic list. The empirical result for various benchmarks show the efficiency
of our algorithm, especially for highly repetitive strings.Comment: In Proc. IWOCA201
Virulenssin evoluutio viruksilla
Tiivistelmä. Virulenssin evoluutioon viruksilla vaikuttaa viruksen genomin rakenne, ympäristö sekä isäntäorganismin immuunipuolustus. Yksi eniten vaikuttavista tekijöistä on populaatiotason valintapaine optimoida virulenssin ja leviämiskyvyn suhde. Etenkin isännänvaihdoksen jälkeinen virulenssin evoluutio on tärkeä tutkimuskohde, jonka avulla voidaan ymmärtää uusia infektioita paremmin. Tässä tutkielmassa perehdytään kahden viruksen, myksoomaviruksen ja HIV-1:n virulenssin evoluutioon
At the crossroads of logics: Automating newswork with artificial intelligence : (Re)defining journalistic logics from the perspective of technologists
As artificial intelligence (AI) technologies become more ubiquitous for streamlining and optimizing work, they are entering fields representing organizational logics at odds with the efficiency logic of automation. One such field is journalism, an industry defined by a logic enacted through professional norms, practices, and values. This paper examines the experience of technologists developing and employing natural language generation (NLG) in news organizations, looking at how they situate themselves and their technology in relation to newswork. Drawing on institutional logics, a theoretical framework from organizational theory, we show how technologists shape their logic for building these emerging technologies based on a theory of rationalizing news organizations, a frame of optimizing newswork, and a narrative of news organizations misinterpreting the technology. Our interviews reveal technologists mitigating tensions with journalistic logic and newswork by labeling stories generated by their systems as nonjournalistic content, seeing their technology as a solution for improving journalism, enabling newswork to move away from routine tasks. We also find that as technologists interact with news organizations, they assimilate elements from journalistic logic beneficial for benchmarking their technology for more lucrative industries.Peer reviewe
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Identification and Density Estimation of American Martens (Martes americana) Using a Novel Camera-Trap Method
Camera-traps are increasingly used to estimate wildlife abundance, yet few studies exist for small-sized carnivores or comparing efficacy against traditional methods. We developed a camera-trap to identify the unique ventral patches of American martens (Martes americana). Our method was designed to: (1) determine the optimal trap configuration to photograph ventral patches; (2) evaluate the use of temporally clustered photographs to determine independence and improve identification; and (3) determine factors that influence identification probability. We tested our method by comparing camera- and live-trap density estimates using spatial capture–recapture (SCR) models. The ventral patches of radio-collared martens were most visible when traps were placed 15–20 cm above a feeding platform. Radio-collared martens (n = 14) visited camera-traps for long periods (median = 7 min) with long intervals between visits (median = 419 min), and visits by different martens at the same trap \u3c15 min apart was infrequent (n = 3) during both years. Similarly, there was complete agreement among observers that clustered photos of un-collared martens were always of the same individual. Pairwise agreement was high between observers; eight un-collared martens were identifiable by consensus on 90% (54 of 60) of recorded visits. Factors influencing identification probability were directly related to the time martens spent feeding at traps (β = 0.143, P = 0.01) and inversely proportional to the time that elapsed since traps were baited (β = −0.344, P = 0.006). Density estimates were higher and more precise for camera-trapping (0.60, 0.35–1.01 martens/km2) than live-trapping (0.45, 0.16–1.22 martens/km2), providing evidence that SCR density estimates may be biased when capture heterogeneity is present, yet cannot be accounted for due to small sample size. Our camera-trap method provides a minimally invasive and accurate tool for monitoring marten populations
Relative Suffix Trees
Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into reducing the space usage, leading ultimately to compressed suffix trees. These compressed data structures can efficiently simulate the suffix tree, while using space proportional to a compressed representation of the sequence. In this work, we take a new approach to compressed suffix trees for repetitive sequence collections, such as collections of individual genomes. We compress the suffix trees of individual sequences relative to the suffix tree of a reference sequence. These relative data structures provide competitive time/space trade-offs, being almost as small as the smallest compressed suffix trees for repetitive collections, and competitive in time with the largest and fastest compressed suffix trees.Peer reviewe
Low Space External Memory Construction of the Succinct Permuted Longest Common Prefix Array
The longest common prefix (LCP) array is a versatile auxiliary data structure
in indexed string matching. It can be used to speed up searching using the
suffix array (SA) and provides an implicit representation of the topology of an
underlying suffix tree. The LCP array of a string of length can be
represented as an array of length words, or, in the presence of the SA, as
a bit vector of bits plus asymptotically negligible support data
structures. External memory construction algorithms for the LCP array have been
proposed, but those proposed so far have a space requirement of words
(i.e. bits) in external memory. This space requirement is in some
practical cases prohibitively expensive. We present an external memory
algorithm for constructing the bit version of the LCP array which uses
bits of additional space in external memory when given a
(compressed) BWT with alphabet size and a sampled inverse suffix array
at sampling rate . This is often a significant space gain in
practice where is usually much smaller than or even constant. We
also consider the case of computing succinct LCP arrays for circular strings
Composite repetition-aware data structures
In highly repetitive strings, like collections of genomes from the same
species, distinct measures of repetition all grow sublinearly in the length of
the text, and indexes targeted to such strings typically depend only on one of
these measures. We describe two data structures whose size depends on multiple
measures of repetition at once, and that provide competitive tradeoffs between
the time for counting and reporting all the exact occurrences of a pattern, and
the space taken by the structure. The key component of our constructions is the
run-length encoded BWT (RLBWT), which takes space proportional to the number of
BWT runs: rather than augmenting RLBWT with suffix array samples, we combine it
with data structures from LZ77 indexes, which take space proportional to the
number of LZ77 factors, and with the compact directed acyclic word graph
(CDAWG), which takes space proportional to the number of extensions of maximal
repeats. The combination of CDAWG and RLBWT enables also a new representation
of the suffix tree, whose size depends again on the number of extensions of
maximal repeats, and that is powerful enough to support matching statistics and
constant-space traversal.Comment: (the name of the third co-author was inadvertently omitted from
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