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Motivation: The topic of this paper is the estimation of alignments and mutation rates based on stochastic sequence-evolution models that allow insertions and deletions of subsequences ("fragments") and not just single bases. The model we propose is a variant of a model introduced by Thorne, Kishino, and Felsenstein (1992). The computational tractability of the model depends on certain restrictions in the insertion/deletion process; possible effects we discuss.
Results: The process of fragment insertion and deletion in the sequence-evolution model induces a hidden Markov structure at the level of alignments and thus makes possible efficient statistical alignment algorithms. As an example we apply a sampling procedure to assess the variability in alignment and mutation parameter estimates for HVR1 sequences of human and orangutan, improving results of previous work. Simulation studies give evidence that estimation methods based on the proposed model also give satisfactory results when applied to data for which the restrictions in the insertion/deletion process do not hold.
Availability: The source code of the software for sampling alignments and mutation rates for a pair of DNA sequences according to the fragment insertion and deletion model is freely available from www.math.uni-frankfurt.de/~stoch/software/mcmcsalut under the terms of the GNU public license (GPL, 2000).
The synchronization of neuronal firing activity is considered an important mechanism in cortical information processing. The tendency of multiple neurons to synchronize their joint firing activity can be investigated with the 'unitary event' analysis (Grün, 1996). This method is based on the nullhypothesis of independent Bernoulli processes and can therefore not tell whether coincidences observed between more than two processes can be considered "genuine" higher- order coincidences or whether they might be caused by coincidences of lower order that coincide by chance ("chance coincidences"). In order to distinguish between genuine and chance coincidences, a parametric model of independent interaction processes (MIIP) is presented. In the framework of this model, Maximum-Likelihood estimates are derived for the firing rates of n single processes and for the rates with which genuine higher order correlations occur. The asymptotic normality of these estimates is used to derive their asymptotic variance and in order to investigate whether higher order coincidences can be considered genuine or whether they can be explained by chance coincidences. The empirical test power of this procedure for n=2 and n=3 processes and for finite analysis windows is derived with simulations and compared to the asymptotic values. Finally, the model is extended in order to allow for the analysis of correlations that are caused by jittered coincidences.
We review the representation problem based on factoring and show that this problem gives rise to alternative solutions to a lot of cryptographic protocols in the literature. And, while the solutions so far usually either rely on the RSA problem or the intractability of factoring integers of a special form (e.g., Blum integers), the solutions here work with the most general factoring assumption. Protocols we discuss include identification schemes secure against parallel attacks, secure signatures, blind signatures and (non-malleable) commitments.
We show that non-interactive statistically-secret bit commitment cannot be constructed from arbitrary black-box one-to-one trapdoor functions and thus from general public-key cryptosystems. Reducing the problems of non-interactive crypto-computing, rerandomizable encryption, and non-interactive statistically-sender-private oblivious transfer and low-communication private information retrieval to such commitment schemes, it follows that these primitives are neither constructible from one-to-one trapdoor functions and public-key encryption in general. Furthermore, our separation sheds some light on statistical zeroknowledge proofs. There is an oracle relative to which one-to-one trapdoor functions and one-way permutations exist, while the class of promise problems with statistical zero-knowledge proofs collapses in P. This indicates that nontrivial problems with statistical zero-knowledge proofs require more than (trapdoor) one-wayness.
We present an efficient variant of LLL-reduction of lattice bases in the sense of Lenstra, Lenstra, Lov´asz [LLL82]. We organize LLL-reduction in segments of size k. Local LLL-reduction of segments is done using local coordinates of dimension 2k. Strong segment LLL-reduction yields bases of the same quality as LLL-reduction but the reduction is n-times faster for lattices of dimension n. We extend segment LLL-reduction to iterated subsegments. The resulting reduction algorithm runs in O(n3 log n) arithmetic steps for integer lattices of dimension n with basis vectors of length 2O(n), compared to O(n5) steps for LLL-reduction.
We show that P(n)*(P(n)) for p = 2 with its geometrically induced structure maps is not an Hopf algebroid because neither the augmentation Epsilon nor the coproduct Delta are multiplicative. As a consequence the algebra structure of P(n)*(P(n)) is slightly different from what was supposed to be the case. We give formulas for Epsilon(xy) and Delta(xy) and show that the inversion of the formal group of P(n) is induced by an antimultiplicative involution Xi : P(n) -> P(n). Some consequences for multiplicative and antimultiplicative automorphisms of K(n) for p = 2 are also discussed.
We reconsider estimates for the heat kernel on weighted graphs recently found by Metzger and Stollmann. In the case that the weights satisfy a positive lower bound as well as a finite upper bound, we obtain a specialized lower estimate and a proper generalization of a previous upper estimate. Reviews: Math. Rev. 1979406, Zbl. Math. 0934.46042
The dynamical quantum Zeno effect is studied in the context of von Neumann algebras. It is shown that the Zeno dynamics coincides with the modular dynamics of a localized subalgebra. This relates the modular operator of that subalgebra to the modular operator of the original algebra by a variant of the Kato-Lie-Trotter product formula.
This extended write-up of a talk gives an introductory survey of mathematical problems of the quantization of gauge systems. Using the Schwinger model as an exactly tractable but nontrivial example which exhibits general features of gauge quantum field theory, I cover the following subjects: The axiomatics of quantum field theory, formulation of quantum field theory in terms of Wightman functions, reconstruction of the state space, the local formulation of gauge theories, indefiniteness of the Wightman functions in general and in the special case of the Schwinger model, the state space of the Schwinger model, special features of the model. New results are contained in the Mathematical Appendix, where I consider in an abstract setting the Pontrjagin space structure of a special class of indefinite inner product spaces - the so called quasi-positive ones. This is motivated by the indefinite inner product space structure appearing in the above context and generalizes results of Morchio and Strocchi [J. Math. Phys. 31 (1990) 1467], and Dubin and Tarski [J. Math. Phys. 7 (1966) 574]. See the corresponding paper: Schmidt, Andreas U.: "Infinite Infrared Regularization and a State Space for the Heisenberg Algebra" and the presentation "Infinite Infrared Regularization in Krein Spaces".