Parametrized Stochastic Grammars for RNA Secondary Structure Prediction

We propose a two-level stochastic context-free grammar (SCFG) architecture for parametrized stochastic modeling of a family of RNA sequences, including their secondary structure. A stochastic model of this type can be used for maximum a posteriori estimation of the secondary structure of any new sequence in the family. The proposed SCFG architecture models RNA subsequences comprising paired bases as stochastically weighted Dyck-language words, i.e., as weighted balanced-parenthesis expressions. The length of each run of unpaired bases, forming a loop or a bulge, is taken to have a phase-type distribution: that of the hitting time in a finite-state Markov chain. Without loss of generality, each such Markov chain can be taken to have a bounded complexity. The scheme yields an overall family SCFG with a manageable number of parameters.Comment: 5 pages, submitted to the 2007 Information Theory and Applications Workshop (ITA 2007

Process algebra for performance evaluation

This paper surveys the theoretical developments in the field of stochastic process algebras, process algebras where action occurrences may be subject to a delay that is determined by a random variable. A huge class of resource-sharing systems – like large-scale computers, client–server architectures, networks – can accurately be described using such stochastic specification formalisms. The main emphasis of this paper is the treatment of operational semantics, notions of equivalence, and (sound and complete) axiomatisations of these equivalences for different types of Markovian process algebras, where delays are governed by exponential distributions. Starting from a simple actionless algebra for describing time-homogeneous continuous-time Markov chains, we consider the integration of actions and random delays both as a single entity (like in known Markovian process algebras like TIPP, PEPA and EMPA) and as separate entities (like in the timed process algebras timed CSP and TCCS). In total we consider four related calculi and investigate their relationship to existing Markovian process algebras. We also briefly indicate how one can profit from the separation of time and actions when incorporating more general, non-Markovian distributions

A uniform framework for modelling nondeterministic, probabilistic, stochastic, or mixed processes and their behavioral equivalences

Labeled transition systems are typically used as behavioral models of concurrent processes, and the labeled transitions define the a one-step state-to-state reachability relation. This model can be made generalized by modifying the transition relation to associate a state reachability distribution, rather than a single target state, with any pair of source state and transition label. The state reachability distribution becomes a function mapping each possible target state to a value that expresses the degree of one-step reachability of that state. Values are taken from a preordered set equipped with a minimum that denotes unreachability. By selecting suitable preordered sets, the resulting model, called ULTraS from Uniform Labeled Transition System, can be specialized to capture well-known models of fully nondeterministic processes (LTS), fully probabilistic processes (ADTMC), fully stochastic processes (ACTMC), and of nondeterministic and probabilistic (MDP) or nondeterministic and stochastic (CTMDP) processes. This uniform treatment of different behavioral models extends to behavioral equivalences. These can be defined on ULTraS by relying on appropriate measure functions that expresses the degree of reachability of a set of states when performing single-step or multi-step computations. It is shown that the specializations of bisimulation, trace, and testing equivalences for the different classes of ULTraS coincide with the behavioral equivalences defined in the literature over traditional models

Towards Autopoietic Computing

A key challenge in modern computing is to develop systems that address complex, dynamic problems in a scalable and efficient way, because the increasing complexity of software makes designing and maintaining efficient and flexible systems increasingly difficult. Biological systems are thought to possess robust, scalable processing paradigms that can automatically manage complex, dynamic problem spaces, possessing several properties that may be useful in computer systems. The biological properties of self-organisation, self-replication, self-management, and scalability are addressed in an interesting way by autopoiesis, a descriptive theory of the cell founded on the concept of a system's circular organisation to define its boundary with its environment. In this paper, therefore, we review the main concepts of autopoiesis and then discuss how they could be related to fundamental concepts and theories of computation. The paper is conceptual in nature and the emphasis is on the review of other people's work in this area as part of a longer-term strategy to develop a formal theory of autopoietic computing.Comment: 10 Pages, 3 figure

A Max-Plus Model of Asynchronous Cellular Automata

This paper presents a new framework for asynchrony. This has its origins in our attempts to better harness the internal decision making process of cellular automata (CA). Thus, we show that a max-plus algebraic model of asynchrony arises naturally from the CA requirement that a cell receives the state of each neighbour before updating. The significant result is the existence of a bijective mapping between the asynchronous system and the synchronous system classically used to update cellular automata. Consequently, although the CA outputs look qualitatively different, when surveyed on "contours" of real time, the asynchronous CA replicates the synchronous CA. Moreover, this type of asynchrony is simple - it is characterised by the underlying network structure of the cells, and long-term behaviour is deterministic and periodic due to the linearity of max-plus algebra. The findings lead us to proffer max-plus algebra as: (i) a more accurate and efficient underlying timing mechanism for models of patterns seen in nature, and (ii) a foundation for promising extensions and applications.Comment: in Complex Systems (Complex Systems Publications Inc), Volume 23, Issue 4, 201