3,093 research outputs found
A New Simulated Annealing Algorithm for the Multiple Sequence Alignment Problem: The approach of Polymers in a Random Media
We proposed a probabilistic algorithm to solve the Multiple Sequence
Alignment problem. The algorithm is a Simulated Annealing (SA) that exploits
the representation of the Multiple Alignment between sequences as a
directed polymer in dimensions. Within this representation we can easily
track the evolution in the configuration space of the alignment through local
moves of low computational cost. At variance with other probabilistic
algorithms proposed to solve this problem, our approach allows for the creation
and deletion of gaps without extra computational cost. The algorithm was tested
aligning proteins from the kinases family. When D=3 the results are consistent
with those obtained using a complete algorithm. For where the complete
algorithm fails, we show that our algorithm still converges to reasonable
alignments. Moreover, we study the space of solutions obtained and show that
depending on the number of sequences aligned the solutions are organized in
different ways, suggesting a possible source of errors for progressive
algorithms.Comment: 7 pages and 11 figure
On the Disambiguation of Weighted Automata
We present a disambiguation algorithm for weighted automata. The algorithm
admits two main stages: a pre-disambiguation stage followed by a transition
removal stage. We give a detailed description of the algorithm and the proof of
its correctness. The algorithm is not applicable to all weighted automata but
we prove sufficient conditions for its applicability in the case of the
tropical semiring by introducing the *weak twins property*. In particular, the
algorithm can be used with all acyclic weighted automata, relevant to
applications. While disambiguation can sometimes be achieved using
determinization, our disambiguation algorithm in some cases can return a result
that is exponentially smaller than any equivalent deterministic automaton. We
also present some empirical evidence of the space benefits of disambiguation
over determinization in speech recognition and machine translation
applications
Goodness-of-Fit Tests for Symmetric Stable Distributions -- Empirical Characteristic Function Approach
We consider goodness-of-fit tests of symmetric stable distributions based on
weighted integrals of the squared distance between the empirical characteristic
function of the standardized data and the characteristic function of the
standard symmetric stable distribution with the characteristic exponent
estimated from the data. We treat as an unknown parameter,
but for theoretical simplicity we also consider the case that is
fixed. For estimation of parameters and the standardization of data we use
maximum likelihood estimator (MLE) and an equivariant integrated squared error
estimator (EISE) which minimizes the weighted integral. We derive the
asymptotic covariance function of the characteristic function process with
parameters estimated by MLE and EISE. For the case of MLE, the eigenvalues of
the covariance function are numerically evaluated and asymptotic distribution
of the test statistic is obtained using complex integration. Simulation studies
show that the asymptotic distribution of the test statistics is very accurate.
We also present a formula of the asymptotic covariance function of the
characteristic function process with parameters estimated by an efficient
estimator for general distributions
Female Faculty: Why So Few and Why Care?
Despite slow ongoing progress in increasing the representation of women in academia, women remain significantly under-represented at senior levels, in particular in the natural sciences and engineering. Not infrequently, this is downplayed by bringing forth arguments such as inherent biological differences between genders, that current policies are adequate to address the issue, or by deflecting this as being “not my problem” among other examples. In this piece we present scientific evidence that counters these claims, as well as a best-practice example, Genie, from Chalmers University of Technology, where one of the authors is currently employed. We also highlight particular challenges caused by the current COVID-19 pandemic. Finally, we conclude by proposing some possible solutions to the situation and emphasize that we need to all do our part, to ensure that the next generation of academics experience a more diverse, inclusive, and equitable working environment
X-Ray Synchrotron White Beam Excitation of Auger Electrons
Auger electron spectra have been measured at the Cornell High Energy Synchrotron Source (CHESS), using the full white beam x-ray spectrum as the excitation source. Ordinary Auger spectra obtained in the laboratory with an electron beam source must employ derivative techniques to distinguish the Auger structures from the large background due to the excitation beam. The synchrotron white beam eliminates this source of background and produces signal rates as high as 107 cps. Superior signal-to-background ratios are found for Auger peaks above a few hundred eV, and count rates are large enough to suggest microprobe applications. X-ray induced Auger satellite peaks were observed with intensities much greater than the electron-induced counterpart; this anomaly is not completely understood
Polarization rotation via a monoclinic phase in the piezoelectric 92%PbZn1/3Nb2/3O3-8%PbTiO3
The origin of ultrahigh piezoelectricity in the relaxor ferroelectric
PbZn1/3Nb2/3O3-PbTiO3 was studied with an electric field applied along the
[001] direction. The zero-field rhombohedral R phase starts to follow the
direct polarization path to tetragonal symmetry via an intermediate monoclinic
M phase, but then jumps irreversibly to an alternate path involving a different
type of monoclinic distortion. Details of the structure and domain
configuration of this novel phase are described. This result suggests that
there is a nearby R-M phase boundary as found in the Pb(Ti,Zr)O3 system.Comment: REVTeX file. 4 pages. New version after referees' comment
Genetic Correlations in Mutation Processes
We study the role of phylogenetic trees on correlations in mutation
processes. Generally, correlations decay exponentially with the generation
number. We find that two distinct regimes of behavior exist. For mutation rates
smaller than a critical rate, the underlying tree morphology is almost
irrelevant, while mutation rates higher than this critical rate lead to strong
tree-dependent correlations. We show analytically that identical critical
behavior underlies all multiple point correlations. This behavior generally
characterizes branching processes undergoing mutation.Comment: revtex, 8 pages, 2 fig
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Physical, chemical, and toxicological characteristics of particulate emissions from current technology gasoline direct injection vehicles
X-ray photoemission spectroscopy determination of the InN/yttria stabilized cubic-zirconia valence band offset
The valence band offset of wurtzite InN(0001)/yttria stabilized cubic-zirconia (YSZ)(111) heterojunctions is determined by x-ray photoemission spectroscopy to be 1.19±0.17 eV giving a conduction band offset of 3.06±0.20 eV. Consequently, a type-I heterojunction forms between InN and YSZ in the straddling arrangement. The low lattice mismatch and high band offsets suggest potential for use of YSZ as a gate dielectric in high-frequency InN-based electronic devices
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