2,998 research outputs found
Asymptotic Level Density of the Elastic Net Self-Organizing Feature Map
Whileas the Kohonen Self Organizing Map shows an asymptotic level density
following a power law with a magnification exponent 2/3, it would be desired to
have an exponent 1 in order to provide optimal mapping in the sense of
information theory. In this paper, we study analytically and numerically the
magnification behaviour of the Elastic Net algorithm as a model for
self-organizing feature maps. In contrast to the Kohonen map the Elastic Net
shows no power law, but for onedimensional maps nevertheless the density
follows an universal magnification law, i.e. depends on the local stimulus
density only and is independent on position and decouples from the stimulus
density at other positions.Comment: 8 pages, 10 figures. Link to publisher under
http://link.springer.de/link/service/series/0558/bibs/2415/24150939.ht
Parameter estimation in pair hidden Markov models
This paper deals with parameter estimation in pair hidden Markov models
(pair-HMMs). We first provide a rigorous formalism for these models and discuss
possible definitions of likelihoods. The model being biologically motivated,
some restrictions with respect to the full parameter space naturally occur.
Existence of two different Information divergence rates is established and
divergence property (namely positivity at values different from the true one)
is shown under additional assumptions. This yields consistency for the
parameter in parametrization schemes for which the divergence property holds.
Simulations illustrate different cases which are not covered by our results.Comment: corrected typo
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
Assessing symmetry of financial returns series
Testing symmetry of a probability distribution is a common question arising
from applications in several fields. Particularly, in the study of observables
used in the analysis of stock market index variations, the question of symmetry
has not been fully investigated by means of statistical procedures. In this
work a distribution-free test statistic Tn for testing symmetry, derived by
Einmahl and McKeague, based on the empirical likelihood approach, is used to
address the study of symmetry of financial returns. The asymptotic points of
the test statistic Tn are also calculated and a procedure for assessing
symmetry for the analysis of the returns of stock market indices is presented.Comment: Econophysics paper. 6 pages 2 figure
Addition-Deletion Networks
We study structural properties of growing networks where both addition and
deletion of nodes are possible. Our model network evolves via two independent
processes. With rate r, a node is added to the system and this node links to a
randomly selected existing node. With rate 1, a randomly selected node is
deleted, and its parent node inherits the links of its immediate descendants.
We show that the in-component size distribution decays algebraically, c_k ~
k^{-beta}, as k-->infty. The exponent beta=2+1/(r-1) varies continuously with
the addition rate r. Structural properties of the network including the height
distribution, the diameter of the network, the average distance between two
nodes, and the fraction of dangling nodes are also obtained analytically.
Interestingly, the deletion process leads to a giant hub, a single node with a
macroscopic degree whereas all other nodes have a microscopic degree.Comment: 8 pages, 5 figure
Recommended from our members
Physical, chemical, and toxicological characteristics of particulate emissions from current technology gasoline direct injection vehicles
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
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
- …