The increasing amount of genomic and molecular information is the basis for understanding higherorder biological systems, such as the cell and the 15 organism, and their interactions with the environment, as well as for medical, industrial and other practical applications. The KEGG resource

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for the modeling and simulation of genetic regulatory networks will be indispensable. This paper reviews formalisms that have been employed in mathematical biology and bioinformatics to describe genetic regulatory systems, in particular directed graphs, Bayesian networks, Boolean networks and their generalizations

conditions and leads to a uniform treatment of rules and proofs whereby rules are viewed as proofs of higher-order judgements and proof checking is reduced to type checking. The practical benefit of our treatment of formal systems is that logic-independent tools such as proof editors and proof checkers

the converse claim; that the state of computer architecture has been a strong influence on our models of thought. The Von Neumann model of computation has lead Artificial Intelligence in particular directions. Intelligence in biological systems is completely different. Recent work in behavior-based Artificial

coreference, quantification, and many other higher-order phenomena, but also broad, in that it covers every instance of every verb in the corpus and allows representative statistics to be calculated. We discuss the criteria used to define the sets of semantic roles used in the annotation process

Inspired by empirical studies of networked systems such as the Internet, social networks, and biological networks, researchers have in recent years developed a variety of techniques and models to help us understand or predict the behavior of these systems. Here we review developments in this field

For both biological systems and machines, vision begins with a large and unwieldy array of measurements of the amount of light reflected from surfaces in the environment. The goal of vision is to recover physical properties of objects in the scene, such as the location of object boundaries

If we are eventually to understand the capability of higher organisms for perceptual recognition, generalization, recall, and thinking, we must first have answers to three fundamental questions: 1. How is information about the physical world sensed, or detected, by the biological system? 2. In what