Biochemical Reaction Rules with Constraints

International audienceWe propose React(C), an expressive programming language for stochastic modeling and simulation in systems biology, that is based on biochemical reactions with constraints. We prove that React(C) can express the stochastic pi-calculus, in contrast to previous rule-based programming languages, and further illustrate the high expressiveness of React(C). We present a stochastic simulator for React(C) independently of the choice of the constraint language C. Our simulator must decide for a given reaction rule whether it can be applied to the current biochemical solution. We show that this decision problem is NP-complete for arbitrary constraint systems C, and that it can be solved in polynomial time for rules of bounded arity. In practice, we propose to solve this problem by constraint programming

The VEX-93 environment as a hybrid tool for developing knowledge systems with different problem solving techniques

The paper describes VEX-93 as a hybrid environment for developing knowledge-based and problem solver systems. It integrates methods and techniques from artificial intelligence, image and signal processing and data analysis, which can be mixed. Two hierarchical levels of reasoning contains an intelligent toolbox with one upper strategic inference engine and four lower ones containing specific reasoning models: truth-functional (rule-based), probabilistic (causal networks), fuzzy (rule-based) and case-based (frames). There are image/signal processing-analysis capabilities in the form of programming languages with more than one hundred primitive functions. User-made programs are embeddable within knowledge basis, allowing the combination of perception and reasoning. The data analyzer toolbox contains a collection of numerical classification, pattern recognition and ordination methods, with neural network tools and a data base query language at inference engines's disposal. VEX-93 is an open system able to communicate with external computer programs relevant to a particular application. Metaknowledge can be used for elaborate conclusions, and man-machine interaction includes, besides windows and graphical interfaces, acceptance of voice commands and production of speech output. The system was conceived for real-world applications in general domains, but an example of a concrete medical diagnostic support system at present under completion as a cuban-spanish project is mentioned. Present version of VEX-93 is a huge system composed by about one and half millions of lines of C code and runs in microcomputers under Windows 3.1.Postprint (published version

Assess Applicability of the Functional Programming Paradigms in Embedded Hardware

Programming in embedded lighting domain is commonly done using the C language with the Object Oriented programming paradigm at Philips Lighting. However applying that paradigm in combination with the low-level language like C creates a conceptual gap between the requirements and design and actual implementation. This results in reduced source code readability and maintainability. Functional programming paradigm was expected to alleviate this problem by reducing the gap and enhancing readability. A proof of concept was built on an advanced, IP-connected, digital LED driver (Power over Ethernet) device. The actual code was inspired by the rule-based decision engine concept developed by EnLight.Based on the hardware specifications of the device, the existing code to communicate with, and adherence to the functional paradigm, Lua was chosen to build the proof with. The implementation of the decision engine was altered to exploit characteristics of functional programming, such as representing actions as functions rather than as an enumeration value, using the common filter function to replace loops, and many more.The proof of concept was able to run in the device. It was also relatively more readable and maintainable. However, it was slightly slower, less memory efficient, and less capable in dealing with low-level problems such as garbage compared to the engine in C language

Deriving Abstractions from a Software Object Network

High level abstractions from programs can be obtained by extracting relational information from programs to form a software object network, and deriving high level abstractions from that network. The authors show how to obtain several interesting abstractions such as subsystems, ripple effects, logical layers and modules from a software object network represented by a C program database. These abstractions assist programmers in understanding the program structure and point out potential areas for improvement. This document then demonstrates how rule-based software restructing can be performed by accessing the relational information stored in the program database. Keywords: Computer programming; CIA(C Information Abstraction)

Dyadic Existential Rules

Existential rules form an expressive Datalog-based language to specify ontological knowledge. The presence of existential quantification in rule-heads, however, makes the main reasoning tasks undecidable. To overcome this limitation, in the last two decades, a number of classes of existential rules guaranteeing the decidability of query answering have been proposed. Unfortunately, only some of these classes fully encompass Datalog and, often, this comes at the price of higher computational complexity. Moreover, expressive classes are typically unable to exploit tools developed for classes exhibiting lower expressiveness. To mitigate these shortcomings, this paper introduces a novel general syntactic condition that allows us to define, systematically and in a uniform way, from any decidable class $\mathcal{C}$ of existential rules, a new class called Dyadic-$\mathcal{C}$ enjoying the following properties: $(i)$ it is decidable; $(ii)$ it generalises Datalog; $(iii)$ it generalises $\mathcal{C}$; $(iv)$ it can effectively exploit any reasoner for query answering over $\mathcal{C}$; and $(v)$ its computational complexity does not exceed the highest between the one of $\mathcal{C}$ and the one of Datalog. Under consideration in Theory and Practice of Logic Programming (TPLP).Comment: Under consideration in Theory and Practice of Logic Programming (TPLP

Theoretical study of intramolecular vibrational relaxation of acetylenic CH vibration for v=1 and 2 in large polyatomic molecules (CX3)3YCCH, where X=H or D and Y=C or Si

Quantum calculations are reported for the intramolecular vibrational energy redistribution and absorption spectra of the first two excited states of the acetylenic CH stretch vibration in the polyatomic molecules (CX3)3YCCH, where X=H or D and Y=C or Si. Using approximate potential energy surfaces, comparison is made with the corresponding recent experimental spectra. It is found that a model of intramolecular vibrational relaxation based on the assumption of sequential off-resonance transitions via third and fourth order vibrational couplings (as opposed to direct high order couplings) is in agreement with experimental results on spectral linewidths. In a semiclassical limit this type of relaxation corresponds to a dynamic tunneling in phase space. It is shown that the local density of resonances of third and fourth order, rather than the total density of states, plays a central role for the relaxation. It is found that in the Si molecule an accidental absence of appropriate resonances results in a bottleneck in the initial stages of relaxation. As a result, an almost complete localization of the initially prepared excitation occurs. It is shown that an increase of the mass alone of the central atom from C to Si cannot explain the observed difference in the C and Si molecules. The spectral linewidths were calculated with the Golden Rule formula after prediagonalization of the relevant vibrational states which are coupled in the molecule to the CH vibration, directly or indirectly. For the spectral calculations, in addition to the direct diagonalization, a modified recursive residue generation method was used, allowing one to avoid diagonalization of the transformed Lanczos Hamiltonian. With this method up to 30 000 coupled states could be analyzed on a computer with relatively small memory. The efficiency of C programming language for the problem is discussed