Distributed hierarchical automata with applications to genetics in procaryotes.

Thesis. 1978. Ph.D.--Massachusetts Institute of Technology. Dept. of Electrical Engineering and Computer Science.MICROFICHE COPY AVAILABLE IN ARCHIVES AND ENGINEERING.Includes bibliographical references.Ph.D

A Bayesian Approach to Learning Hidden Markov Model Topology with Applications to Biological Sequence Analysis

Hidden-Markov-Models (HMMs) are a widely and successfully used tool in statistical modeling and statistical pattern recognition. One fundamental problem in the application of HMMs is finding the underlying architecture or topology, particularly when there is no strong evidence from the application domain — e.g., when doing black box modeling. Topology is important with regard to good parameter estimates and with regard to performance: A model with “too many” states — and hence too many parameters — requires too much training data while an model with “not enough” states impedes the HMM from capturing subtle statistical patterns. We have developed a novel algorithm that, given sequence data originating from an ergodic process, infers an HMM, its topology and its parameters. We introduce a Bayesian approach

Biological Evolution and Statistical Physics

This review is an introduction to theoretical models and mathematical calculations for biological evolution, aimed at physicists. The methods in the field are naturally very similar to those used in statistical physics, although the majority of publications appeared in biology journals. The review has three parts, which can be read independently. The first part deals with evolution in fitness landscapes and includes Fisher's theorem, adaptive walks, quasispecies models, effects of finite population sizes, and neutral evolution. The second part studies models of coevolution, including evolutionary game theory, kin selection, group selection, sexual selection, speciation, and coevolution of hosts and parasites. The third part discusses models for networks of interacting species and their extinction avalanches. Throughout the review, attention is paid to giving the necessary biological information, and to pointing out the assumptions underlying the models, and their limits of validity.Comment: Review article accepted for publication in Advances in Physics. 106 page

Aerospace medicine and biology: A continuing bibliography with indexes (supplement 406)

This bibliography lists 346 reports, articles and other documents introduced into the NASA Scientific and Technical Information System during Oct. 1995. Subject coverage includes: aerospace medicine and physiology, life support systems and man/system technology, protective clothing, exobiology and extraterrestrial life, planetary biology, and flight crew behavior and performance

Complexity, Language, and Life: Mathematical Approaches

In May 1984 the Swedish Council for Scientific Research convened a small group of investigators at the scientific research station at Abisko, Sweden, for the purpose of examining various conceptual and mathematical views of the evolution of complex systems. The stated theme of the meeting was deliberately kept vague, with only the purpose of discussing alternative mathematically based approaches to the modeling of evolving processes being given as a guideline to the participants. In order to limit the scope to some degree, it was decided to emphasize living rather than nonliving processes and to invite participants from a range of disciplinary specialities spanning the spectrum from pure and applied mathematics to geography and analytic philosophy. The results of the meeting were quite extraordinary; while there was no intent to focus the papers and discussion into predefined channels, an immediate self-organizing effect took place and the deliberations quickly oriented themselves into three main streams: conceptual and formal structures for characterizing system complexity; evolutionary processes in biology and ecology; the emergence of complexity through evolution in natural languages. The chapters presented in this volume are not the proceedings of the meeting. Following the meeting, the organizers felt that the ideas and spirit of the gathering should be preserved in some written form, so the participants were each requested to produce a chapter, explicating the views they presented at Abisko, written specifically for this volume. The results of this exercise are contained in this book

Aerospace medicine and biology: A continuing bibliography with indexes (supplement 400)

This bibliography lists 397 reports, articles and other documents introduced into the NASA Scientific and Technical Information System during April 1995. Subject coverage includes: aerospace medicine and physiology, life support systems and man/system technology, protective clothing, exobiology and extraterrestrial life, planetary biology, and flight crew behavior and performance