A Swiss Pocket Knife for Computability

This research is about operational- and complexity-oriented aspects of classical foundations of computability theory. The approach is to re-examine some classical theorems and constructions, but with new criteria for success that are natural from a programming language perspective. Three cornerstones of computability theory are the S-m-ntheorem; Turing's "universal machine"; and Kleene's second recursion theorem. In today's programming language parlance these are respectively partial evaluation, self-interpretation, and reflection. In retrospect it is fascinating that Kleene's 1938 proof is constructive; and in essence builds a self-reproducing program. Computability theory originated in the 1930s, long before the invention of computers and programs. Its emphasis was on delimiting the boundaries of computability. Some milestones include 1936 (Turing), 1938 (Kleene), 1967 (isomorphism of programming languages), 1985 (partial evaluation), 1989 (theory implementation), 1993 (efficient self-interpretation) and 2006 (term register machines). The "Swiss pocket knife" of the title is a programming language that allows efficient computer implementation of all three computability cornerstones, emphasising the third: Kleene's second recursion theorem. We describe experiments with a tree-based computational model aiming for both fast program generation and fast execution of the generated programs.Comment: In Proceedings Festschrift for Dave Schmidt, arXiv:1309.455

Extended Recursion-Based Formalization of Virus Mutation

International audienceComputer viruses are programs that can replicate themselves by infecting other programs in a system. Bonfante, Kaczmarek and Marion have recently proposed a classification of viruses which relies on the recursion theory and its recursion theorems. We propose an extension of their formalism to consider in a more practical way the mutation of viruses. In particular, we are interested in modelling any depth of mutation, not just the first two levels. We show that this formalism still relies on recursion theorems, whatever the depth of mutation, even in the case of infinite depth. We also extend furthermore this formalism to model the viability of viral replication, which ensures that an infected program still can propagate the virus. An application of the proposed formalism to the class of combined viruses (multi-part viruses) is studied. Finally, given that metamorphic viruses can be modelled by grammars operating on grammars, we study a recursion-based approach of formal grammars and show that the recursion theorems of the recursion theory can be ported to the formal grammars theory

On the Semantics of Intensionality and Intensional Recursion

Intensionality is a phenomenon that occurs in logic and computation. In the most general sense, a function is intensional if it operates at a level finer than (extensional) equality. This is a familiar setting for computer scientists, who often study different programs or processes that are interchangeable, i.e. extensionally equal, even though they are not implemented in the same way, so intensionally distinct. Concomitant with intensionality is the phenomenon of intensional recursion, which refers to the ability of a program to have access to its own code. In computability theory, intensional recursion is enabled by Kleene's Second Recursion Theorem. This thesis is concerned with the crafting of a logical toolkit through which these phenomena can be studied. Our main contribution is a framework in which mathematical and computational constructions can be considered either extensionally, i.e. as abstract values, or intensionally, i.e. as fine-grained descriptions of their construction. Once this is achieved, it may be used to analyse intensional recursion.Comment: DPhil thesis, Department of Computer Science & St John's College, University of Oxfor

On Abstract Computer Virology from a Recursion-theoretic Perspective

We are concerned with theoretical aspects of computer viruses. For this, we suggest a new definition of viruses which is clearly based on the iteration theorem and above all on Kleene's recursion theorem. We show that we capture in a natural way previous definitions, and in particular the one of Adleman. We establish generic virus constructions and we illustrate them by various examples. Lastly, we show results on virus detection

Causality, Information and Biological Computation: An algorithmic software approach to life, disease and the immune system

Biology has taken strong steps towards becoming a computer science aiming at reprogramming nature after the realisation that nature herself has reprogrammed organisms by harnessing the power of natural selection and the digital prescriptive nature of replicating DNA. Here we further unpack ideas related to computability, algorithmic information theory and software engineering, in the context of the extent to which biology can be (re)programmed, and with how we may go about doing so in a more systematic way with all the tools and concepts offered by theoretical computer science in a translation exercise from computing to molecular biology and back. These concepts provide a means to a hierarchical organization thereby blurring previously clear-cut lines between concepts like matter and life, or between tumour types that are otherwise taken as different and may not have however a different cause. This does not diminish the properties of life or make its components and functions less interesting. On the contrary, this approach makes for a more encompassing and integrated view of nature, one that subsumes observer and observed within the same system, and can generate new perspectives and tools with which to view complex diseases like cancer, approaching them afresh from a software-engineering viewpoint that casts evolution in the role of programmer, cells as computing machines, DNA and genes as instructions and computer programs, viruses as hacking devices, the immune system as a software debugging tool, and diseases as an information-theoretic battlefield where all these forces deploy. We show how information theory and algorithmic programming may explain fundamental mechanisms of life and death.Comment: 30 pages, 8 figures. Invited chapter contribution to Information and Causality: From Matter to Life. Sara I. Walker, Paul C.W. Davies and George Ellis (eds.), Cambridge University Pres

Fixed speed competition on the configuration model with infinite variance degrees: unequal speeds

We study competition of two spreading colors starting from single sources on the configuration model with i.i.d. degrees following a power-law distribution with exponent tau in (2,3). In this model two colors spread with a fixed but not necessarily equal speed on the unweighted random graph. We show that if the speeds are not equal, then the faster color paints almost all vertices, while the slower color can paint only a random subpolynomial fraction of the vertices. We investigate the case when the speeds are equal and typical distances in a follow-up paper.Comment: 44 pages, 9 picture