COMPUTER SIMULATION AND COMPUTABILITY OF BIOLOGICAL SYSTEMS

The ability to simulate a biological organism by employing a computer is related to the ability of the computer to calculate the behavior of such a dynamical system, or the "computability" of the system.* However, the two questions of computability and simulation are not equivalent. Since the question of computability can be given a precise answer in terms of recursive functions, automata theory and dynamical systems, it will be appropriate to consider it first. The more elusive question of adequate simulation of biological systems by a computer will be then addressed and a possible connection between the two answers given will be considered. A conjecture is formulated that suggests the possibility of employing an algebraic-topological, "quantum" computer (Baianu, 1971b) for analogous and symbolic simulations of biological systems that may include chaotic processes that are not, in genral, either recursively or digitally computable. Depending on the biological network being modelled, such as the Human Genome/Cell Interactome or a trillion-cell Cognitive Neural Network system, the appropriate logical structure for such simulations might be either the Quantum MV-Logic (QMV) discussed in recent publications (Chiara, 2004, and references cited therein)or Lukasiewicz Logic Algebras that were shown to be isomorphic to MV-logic algebras (Georgescu et al, 2001)

Active classification with comparison queries

We study an extension of active learning in which the learning algorithm may ask the annotator to compare the distances of two examples from the boundary of their label-class. For example, in a recommendation system application (say for restaurants), the annotator may be asked whether she liked or disliked a specific restaurant (a label query); or which one of two restaurants did she like more (a comparison query). We focus on the class of half spaces, and show that under natural assumptions, such as large margin or bounded bit-description of the input examples, it is possible to reveal all the labels of a sample of size $n$ using approximately $O(\log n)$ queries. This implies an exponential improvement over classical active learning, where only label queries are allowed. We complement these results by showing that if any of these assumptions is removed then, in the worst case, $\Omega(n)$ queries are required. Our results follow from a new general framework of active learning with additional queries. We identify a combinatorial dimension, called the \emph{inference dimension}, that captures the query complexity when each additional query is determined by $O(1)$ examples (such as comparison queries, each of which is determined by the two compared examples). Our results for half spaces follow by bounding the inference dimension in the cases discussed above.Comment: 23 pages (not including references), 1 figure. The new version contains a minor fix in the proof of Lemma 4.

On the Complexity of the Class of Regions Computable by a Two-Layered Perceptron

This work is concerned with the computational complexity of the recognition of \mbox{LP}_2, the class of regions of the Euclidian space that can be classified exactly by a two-layered perceptron. Several subclasses of \mbox{LP}_2 of particular interest are also considered. We show that the recognition problems of \mbox{LP}_2 and of other classes considered here are intractable, even in some favorable circumstances. We then identify special cases having polynomial time algorithms

Theoretical Interpretations and Applications of Radial Basis Function Networks

Medical applications usually used Radial Basis Function Networks just as Artificial Neural Networks. However, RBFNs are Knowledge-Based Networks that can be interpreted in several way: Artificial Neural Networks, Regularization Networks, Support Vector Machines, Wavelet Networks, Fuzzy Controllers, Kernel Estimators, Instanced-Based Learners. A survey of their interpretations and of their corresponding learning algorithms is provided as well as a brief survey on dynamic learning algorithms. RBFNs' interpretations can suggest applications that are particularly interesting in medical domains

A guided tour of asynchronous cellular automata

Research on asynchronous cellular automata has received a great amount of attention these last years and has turned to a thriving field. We survey the recent research that has been carried out on this topic and present a wide state of the art where computing and modelling issues are both represented.Comment: To appear in the Journal of Cellular Automat

Boolean Delay Equations: A simple way of looking at complex systems

Boolean Delay Equations (BDEs) are semi-discrete dynamical models with Boolean-valued variables that evolve in continuous time. Systems of BDEs can be classified into conservative or dissipative, in a manner that parallels the classification of ordinary or partial differential equations. Solutions to certain conservative BDEs exhibit growth of complexity in time. They represent therewith metaphors for biological evolution or human history. Dissipative BDEs are structurally stable and exhibit multiple equilibria and limit cycles, as well as more complex, fractal solution sets, such as Devil's staircases and ``fractal sunbursts``. All known solutions of dissipative BDEs have stationary variance. BDE systems of this type, both free and forced, have been used as highly idealized models of climate change on interannual, interdecadal and paleoclimatic time scales. BDEs are also being used as flexible, highly efficient models of colliding cascades in earthquake modeling and prediction, as well as in genetics. In this paper we review the theory of systems of BDEs and illustrate their applications to climatic and solid earth problems. The former have used small systems of BDEs, while the latter have used large networks of BDEs. We moreover introduce BDEs with an infinite number of variables distributed in space (``partial BDEs``) and discuss connections with other types of dynamical systems, including cellular automata and Boolean networks. This research-and-review paper concludes with a set of open questions.Comment: Latex, 67 pages with 15 eps figures. Revised version, in particular the discussion on partial BDEs is updated and enlarge

Center for Aeronautics and Space Information Sciences

This report summarizes the research done during 1991/92 under the Center for Aeronautics and Space Information Science (CASIS) program. The topics covered are computer architecture, networking, and neural nets