Probabilistic parsing

Postprin

Probability around the Quantum Gravity. Part 1: Pure Planar Gravity

In this paper we study stochastic dynamics which leaves quantum gravity equilibrium distribution invariant. We start theoretical study of this dynamics (earlier it was only used for Monte-Carlo simulation). Main new results concern the existence and properties of local correlation functions in the thermodynamic limit. The study of dynamics constitutes a third part of the series of papers where more general class of processes were studied (but it is self-contained), those processes have some universal significance in probability and they cover most concrete processes, also they have many examples in computer science and biology. At the same time the paper can serve an introduction to quantum gravity for a probabilist: we give a rigorous exposition of quantum gravity in the planar pure gravity case. Mostly we use combinatorial techniques, instead of more popular in physics random matrix models, the central point is the famous $\alpha =-7/2$ exponent.Comment: 40 pages, 11 figure

Prospects for Declarative Mathematical Modeling of Complex Biological Systems

Declarative modeling uses symbolic expressions to represent models. With such expressions one can formalize high-level mathematical computations on models that would be difficult or impossible to perform directly on a lower-level simulation program, in a general-purpose programming language. Examples of such computations on models include model analysis, relatively general-purpose model-reduction maps, and the initial phases of model implementation, all of which should preserve or approximate the mathematical semantics of a complex biological model. The potential advantages are particularly relevant in the case of developmental modeling, wherein complex spatial structures exhibit dynamics at molecular, cellular, and organogenic levels to relate genotype to multicellular phenotype. Multiscale modeling can benefit from both the expressive power of declarative modeling languages and the application of model reduction methods to link models across scale. Based on previous work, here we define declarative modeling of complex biological systems by defining the operator algebra semantics of an increasingly powerful series of declarative modeling languages including reaction-like dynamics of parameterized and extended objects; we define semantics-preserving implementation and semantics-approximating model reduction transformations; and we outline a "meta-hierarchy" for organizing declarative models and the mathematical methods that can fruitfully manipulate them

Probabilistic Parsing Strategies

We present new results on the relation between purely symbolic context-free parsing strategies and their probabilistic counter-parts. Such parsing strategies are seen as constructions of push-down devices from grammars. We show that preservation of probability distribution is possible under two conditions, viz. the correct-prefix property and the property of strong predictiveness. These results generalize existing results in the literature that were obtained by considering parsing strategies in isolation. From our general results we also derive negative results on so-called generalized LR parsing.Comment: 36 pages, 1 figur

Polynomial Time Algorithms for Multi-Type Branching Processes and Stochastic Context-Free Grammars

We show that one can approximate the least fixed point solution for a multivariate system of monotone probabilistic polynomial equations in time polynomial in both the encoding size of the system of equations and in log(1/\epsilon), where \epsilon > 0 is the desired additive error bound of the solution. (The model of computation is the standard Turing machine model.) We use this result to resolve several open problems regarding the computational complexity of computing key quantities associated with some classic and heavily studied stochastic processes, including multi-type branching processes and stochastic context-free grammars

Genomics and proteomics: a signal processor's tour

The theory and methods of signal processing are becoming increasingly important in molecular biology. Digital filtering techniques, transform domain methods, and Markov models have played important roles in gene identification, biological sequence analysis, and alignment. This paper contains a brief review of molecular biology, followed by a review of the applications of signal processing theory. This includes the problem of gene finding using digital filtering, and the use of transform domain methods in the study of protein binding spots. The relatively new topic of noncoding genes, and the associated problem of identifying ncRNA buried in DNA sequences are also described. This includes a discussion of hidden Markov models and context free grammars. Several new directions in genomic signal processing are briefly outlined in the end

Non-Standard Sound Synthesis with Dynamic Models

Full version unavailable due to 3rd party copyright restrictions.This Thesis proposes three main objectives: (i) to provide the concept of a new generalized non-standard synthesis model that would provide the framework for incorporating other non-standard synthesis approaches; (ii) to explore dynamic sound modeling through the application of new non-standard synthesis techniques and procedures; and (iii) to experiment with dynamic sound synthesis for the creation of novel sound objects. In order to achieve these objectives, this Thesis introduces a new paradigm for non-standard synthesis that is based in the algorithmic assemblage of minute wave segments to form sound waveforms. This paradigm is called Extended Waveform Segment Synthesis (EWSS) and incorporates a hierarchy of algorithmic models for the generation of microsound structures. The concepts of EWSS are illustrated with the development and presentation of a novel non-standard synthesis system, the Dynamic Waveform Segment Synthesis (DWSS). DWSS features and combines a variety of algorithmic models for direct synthesis generation: list generation and permutation, tendency masks, trigonometric functions, stochastic functions, chaotic functions and grammars. The core mechanism of DWSS is based in an extended application of Cellular Automata. The potential of the synthetic capabilities of DWSS is explored in a series of Case Studies where a number of sound object were generated revealing (i) the capabilities of the system to generate sound morphologies belonging to other non-standard synthesis approaches and, (ii) the capabilities of the system of generating novel sound objects with dynamic morphologies. The introduction of EWSS and DWSS is preceded by an extensive and critical overview on the concepts of microsound synthesis, algorithmic composition, the two cultures of computer music, the heretical approach in composition, non- standard synthesis and sonic emergence along with the thorough examination of algorithmic models and their application in sound synthesis and electroacoustic composition. This Thesis also proposes (i) a new definition for “algorithmic composition”, (ii) the term “totalistic algorithmic composition”, and (iii) four discrete aspects of non-standard synthesis