From coinductive proofs to exact real arithmetic: theory and applications

Based on a new coinductive characterization of continuous functions we extract certified programs for exact real number computation from constructive proofs. The extracted programs construct and combine exact real number algorithms with respect to the binary signed digit representation of real numbers. The data type corresponding to the coinductive definition of continuous functions consists of finitely branching non-wellfounded trees describing when the algorithm writes and reads digits. We discuss several examples including the extraction of programs for polynomials up to degree two and the definite integral of continuous maps

Maximizing Protein Translation Rate in the Ribosome Flow Model: the Homogeneous Case

Gene translation is the process in which intracellular macro-molecules, called ribosomes, decode genetic information in the mRNA chain into the corresponding proteins. Gene translation includes several steps. During the elongation step, ribosomes move along the mRNA in a sequential manner and link amino-acids together in the corresponding order to produce the proteins. The homogeneous ribosome flow model(HRFM) is a deterministic computational model for translation-elongation under the assumption of constant elongation rates along the mRNA chain. The HRFM is described by a set of n first-order nonlinear ordinary differential equations, where n represents the number of sites along the mRNA chain. The HRFM also includes two positive parameters: ribosomal initiation rate and the (constant) elongation rate. In this paper, we show that the steady-state translation rate in the HRFM is a concave function of its parameters. This means that the problem of determining the parameter values that maximize the translation rate is relatively simple. Our results may contribute to a better understanding of the mechanisms and evolution of translation-elongation. We demonstrate this by using the theoretical results to estimate the initiation rate in M. musculus embryonic stem cell. The underlying assumption is that evolution optimized the translation mechanism. For the infinite-dimensional HRFM, we derive a closed-form solution to the problem of determining the initiation and transition rates that maximize the protein translation rate. We show that these expressions provide good approximations for the optimal values in the n-dimensional HRFM already for relatively small values of n. These results may have applications for synthetic biology where an important problem is to re-engineer genomic systems in order to maximize the protein production rate

Faster Query Answering in Probabilistic Databases using Read-Once Functions

A boolean expression is in read-once form if each of its variables appears exactly once. When the variables denote independent events in a probability space, the probability of the event denoted by the whole expression in read-once form can be computed in polynomial time (whereas the general problem for arbitrary expressions is #P-complete). Known approaches to checking read-once property seem to require putting these expressions in disjunctive normal form. In this paper, we tell a better story for a large subclass of boolean event expressions: those that are generated by conjunctive queries without self-joins and on tuple-independent probabilistic databases. We first show that given a tuple-independent representation and the provenance graph of an SPJ query plan without self-joins, we can, without using the DNF of a result event expression, efficiently compute its co-occurrence graph. From this, the read-once form can already, if it exists, be computed efficiently using existing techniques. Our second and key contribution is a complete, efficient, and simple to implement algorithm for computing the read-once forms (whenever they exist) directly, using a new concept, that of co-table graph, which can be significantly smaller than the co-occurrence graph.Comment: Accepted in ICDT 201

Certainty Closure: Reliable Constraint Reasoning with Incomplete or Erroneous Data

Constraint Programming (CP) has proved an effective paradigm to model and solve difficult combinatorial satisfaction and optimisation problems from disparate domains. Many such problems arising from the commercial world are permeated by data uncertainty. Existing CP approaches that accommodate uncertainty are less suited to uncertainty arising due to incomplete and erroneous data, because they do not build reliable models and solutions guaranteed to address the user's genuine problem as she perceives it. Other fields such as reliable computation offer combinations of models and associated methods to handle these types of uncertain data, but lack an expressive framework characterising the resolution methodology independently of the model. We present a unifying framework that extends the CP formalism in both model and solutions, to tackle ill-defined combinatorial problems with incomplete or erroneous data. The certainty closure framework brings together modelling and solving methodologies from different fields into the CP paradigm to provide reliable and efficient approches for uncertain constraint problems. We demonstrate the applicability of the framework on a case study in network diagnosis. We define resolution forms that give generic templates, and their associated operational semantics, to derive practical solution methods for reliable solutions.Comment: Revised versio