In the Maze of Data Languages

In data languages the positions of strings and trees carry a label from a finite alphabet and a data value from an infinite alphabet. Extensions of automata and logics over finite alphabets have been defined to recognize data languages, both in the string and tree cases. In this paper we describe and compare the complexity and expressiveness of such models to understand which ones are better candidates as regular models

The use of ideas of Information Theory for studying "language" and intelligence in ants

In this review we integrate results of long term experimental study on ant "language" and intelligence which were fully based on fundamental ideas of Information Theory, such as the Shannon entropy, the Kolmogorov complexity, and the Shannon's equation connecting the length of a message ($l$) and its frequency $(p)$, i.e. $l = - \log p$ for rational communication systems. This approach, new for studying biological communication systems, enabled us to obtain the following important results on ants' communication and intelligence: i) to reveal "distant homing" in ants, that is, their ability to transfer information about remote events; ii) to estimate the rate of information transmission; iii) to reveal that ants are able to grasp regularities and to use them for "compression" of information; iv) to reveal that ants are able to transfer to each other the information about the number of objects; v) to discover that ants can add and subtract small numbers. The obtained results show that Information Theory is not only wonderful mathematical theory, but many its results may be considered as Nature laws

C-Sheep: Controlling Entities in a 3D Virtual World as a Tool for Computer Science Education

One of the challenges in teaching computer science in general and computer programming in particular is to maintain the interest of students, who often perceive the subject as difficult and tedious. To this end, we introduce C-Sheep, a mini-language-like system for computer science education, using a state of the art rendering engine, usually found in entertainment systems. The intention is to motivate students to spend more time programming, which can be achieved by providing an enjoyable experience. Computer programming is an essential skill for software developers and as such is always an integral part of every computer science curriculum. However, even if students are pursuing a computer science related degree, it can be very difficult to interest them in the act of computer programming, the writing of software, itself. In the C-Sheep system this is addressed by using the visual gimmickry of modern computer games, which allows programs to provide instant visualisation of algorithms. This visual feedback is invaluable to the understanding of how the algorithm works, and - if there are unintended results - how errors in the program can be debugged. The C-Sheep programming language is a (100% compatible) subset of the ANSI C programming language. Apart from just being a tool for learning the basics of the C programming language, C-Sheep implements the C control structures that are required for teaching the basic computer science principles encountered in structured programming. Unlike other teaching languages which have minimal syntax and which are variable free to provide an environment with minimal complexity, C-Sheep allows the declaration and use of variables. C-Sheep also supports the definition of sub-routines (functions) which can be called recursively. "The Meadow" virtual environment is the virtual world in which entities (in our case sheep) controlled by C-Sheep programs exist. This micro world provides a graphical representation of the algorithms used in the programs controlling the virtual entities. Their position and orientation within the virtual world visualise the current state of the program. "The Meadow" is based on our proprietary "Crossbow" game engine which incorporates a virtual machine for executing CSheep programs. The Crossbow Engine is a compact game engine which is flexible in design and offers a number of features common to more complex engines. The Crossbow Virtual Machine used with C-Sheep in "The Meadow" - an improvement on the ZBL/0 virtual machine - is a module of the Crossbow Engine. The C-Sheep system also provides a counterpart library for C, mirroring the CSheep library functions of the virtual machine. This allows C-Sheep programs to be compiled into an executable using a normal off-the-shelf C/C++ compiler. This executable can then be run from within the native working environment of the operating system. The purpose of this library is to simplify the migration from the educational mini-language to real-world systems by allowing novice programmers to make an easy transition from using the C-Sheep system to using the C programming language

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Optimizing Abstract Abstract Machines

The technique of abstracting abstract machines (AAM) provides a systematic approach for deriving computable approximations of evaluators that are easily proved sound. This article contributes a complementary step-by-step process for subsequently going from a naive analyzer derived under the AAM approach, to an efficient and correct implementation. The end result of the process is a two to three order-of-magnitude improvement over the systematically derived analyzer, making it competitive with hand-optimized implementations that compute fundamentally less precise results.Comment: Proceedings of the International Conference on Functional Programming 2013 (ICFP 2013). Boston, Massachusetts. September, 201

BRAHMS: Novel middleware for integrated systems computation

Biological computational modellers are becoming increasingly interested in building large, eclectic models, including components on many different computational substrates, both biological and non-biological. At the same time, the rise of the philosophy of embodied modelling is generating a need to deploy biological models as controllers for robots in real-world environments. Finally, robotics engineers are beginning to find value in seconding biomimetic control strategies for use on practical robots. Together with the ubiquitous desire to make good on past software development effort, these trends are throwing up new challenges of intellectual and technological integration (for example across scales, across disciplines, and even across time) - challenges that are unmet by existing software frameworks. Here, we outline these challenges in detail, and go on to describe a newly developed software framework, BRAHMS. that meets them. BRAHMS is a tool for integrating computational process modules into a viable, computable system: its generality and flexibility facilitate integration across barriers, such as those described above, in a coherent and effective way. We go on to describe several cases where BRAHMS has been successfully deployed in practical situations. We also show excellent performance in comparison with a monolithic development approach. Additional benefits of developing in the framework include source code self-documentation, automatic coarse-grained parallelisation, cross-language integration, data logging, performance monitoring, and will include dynamic load-balancing and 'pause and continue' execution. BRAHMS is built on the nascent, and similarly general purpose, model markup language, SystemML. This will, in future, also facilitate repeatability and accountability (same answers ten years from now), transparent automatic software distribution, and interfacing with other SystemML tools. (C) 2009 Elsevier Ltd. All rights reserved

Writing biology with mutant mice: the monstrous potential of post genomic life

Social scientific accounts identified in the biological grammars of early genomics a monstrous reductionism, ‘an example of brute life, the minimalist essence of things’ (Rabinow, 1996, p. 89). Concern about this reductionism focused particularly on its links to modernist notions of control; the possibility of calculating, predicting and intervening in the biological futures of individuals and populations. Yet, the trajectories of the post genomic sciences have not unfolded in this way, challenging scientists involved in the production and integration of complex biological data and the interpretative strategies of social scientists honed in critiquing this reductionism. The post genomic sciences are now proliferating points from which to understand relations in biology, between genes and environments, as well as between species and spaces, opening up future possibilities and different ways of thinking about life. This paper explores the emerging topologies and temporalities of one form of post genomic research, drawing upon ethnographic research on international efforts in functional genomics, which are using mutant mice to understand mammalian gene function. Using vocabularies on the monstrous from Derrida and Haraway, I suggest an alternative conceptualisation of monstrosity within biology, in which the ascendancy of mice in functional genomics acts as a constant supplement to the reductionist grammars of genomics. Rather than searching for the minimalist essence of things, this form of functional genomics has become an exercise in the production and organization of biological surplus and excess, which is experimental, corporeal and affective. The uncertain functioning of monsters in this contexts acts as a generative catalyst for scientists and social scientists, proliferating perspectives from which to listen to and engage with the mutating landscapes, forms of life, and languages of a post genomic biology