ABSTRACT We collaborate in a research program aimed at creating a rigorous framework, experimenta... more ABSTRACT We collaborate in a research program aimed at creating a rigorous framework, experimental infrastructure and computational environment for understanding, experimenting, manipulating and modifying a diverse set of fundamental biological processes at multiple scales and spatio-temporal modes.
On the behavioral inheritance of state-based objects
Abstract We consider the inheritance of state based behavior in object oriented analysis and desi... more Abstract We consider the inheritance of state based behavior in object oriented analysis and design, as it arises, for example, in specifying behavior in the UML using statecharts. We concentrate on behavioral conformity and the resulting substitutability of classes, whereby the inheritance mechanism is to retain original behaviors.
In computer science, one is interested mainly in finite objects. Insofar as infinite objects are ... more In computer science, one is interested mainly in finite objects. Insofar as infinite objects are of interest, they must be computable, ie, recursive, thus admitting an effective finite representation. This leads to the notion of a recursive graph, or, more generally, a recursive structure, model or data base.
Following a suggestion of Pratt, we consider propositional dynamic logic in which programs are no... more Following a suggestion of Pratt, we consider propositional dynamic logic in which programs are nondeterministic finite automata over atomic programs and tests (ie, flowcharts), rather than regular expressions. While the resulting version of PDL, call it APDL, is clearly equivalent in expressive power to PDL, it is also (in the worst case) exponentially more succinct. In particular, deciding its validity problem by reducing it to that of PDL leads to a double exponential time procedure, although PDL itself is decidable in exponential time.
A primary goal for artificial nose (eNose) technology is to report perceptual qualities of novel ... more A primary goal for artificial nose (eNose) technology is to report perceptual qualities of novel odors. Currently, however, eNoses primarily detect and discriminate between odorants they previously “learned”. We tuned an eNose to human odor pleasantness estimates. We then used the eNose to predict the pleasantness of novel odorants, and tested these predictions in naïve subjects who had not participated in the tuning procedure.
Experiments have generated a plethora of data about the genes, molecules, and cells involved in t... more Experiments have generated a plethora of data about the genes, molecules, and cells involved in thymocyte development. Here, we use a computer-driven simulation that uses data about thymocyte development to generate an integrated dynamic representation—a novel technology we have termed reactive animation (RA). RA reveals emergent properties in complex dynamic biological systems. We apply RA to thymocyte development by reproducing and extending the effects of known gene knockouts: CXCR4 and CCR9.
Live sequence charts (LSCs) have been defined recently as an extension of message sequence charts... more Live sequence charts (LSCs) have been defined recently as an extension of message sequence charts (MSCs; or their UML variant, sequence diagrams) for rich inter-object specification. One of the main additions is the notion of universal charts and hot, mandatory behavior, which, among other things, enables one to specify forbidden scenarios. LSCs are thus essentially as expressive as statecharts.
Abstract The paradigm of simulated annealing is applied to the problem of drawing graphs “nicely.... more Abstract The paradigm of simulated annealing is applied to the problem of drawing graphs “nicely.” Our algorithm deals with general undirected graphs with straight-line edges, and employs several simple criteria for the aesthetic quality of the result. The algorithm is flexible, in that the relative weights of the criteria can be changed. For graphs of modest size it produces good results, competitive with those produced by other methods, notably, the “spring method” and its variants.
Biting the silver bullet: Toward a brighter future for system development
Abstract The author responds to two discouraging position papers by FB Brooks, Jr.(see ibid., vol... more Abstract The author responds to two discouraging position papers by FB Brooks, Jr.(see ibid., vol. 20, no. 4, p 10-19, 1987) and DL Parnas (see Commun. ACM, vol. 28, no. 12, p. 1326-35, 1985) regarding the potential of software engineering. While agreeing with most of the specific points made in both papers, he illuminates the brighter side of the coin, emphasizing developments in the field that were too recent or immature to have influenced Brooks and Parnas when they wrote their manuscripts.
We present preliminary results of a new approach to the formal modeling of biological phenomena. ... more We present preliminary results of a new approach to the formal modeling of biological phenomena. The approach stems from the conceptual compatibility of the methods and logic of data collection and analysis in the field of developmental genetics with the languages, methods and tools of scenario-based reactive system design.
We describe a methodology for executing scenario-based requirements of reactive systems, focusing... more We describe a methodology for executing scenario-based requirements of reactive systems, focusing on “playing-out” the behavior using formal verification techniques for driving the execution. The methodology is implemented in full in our play-engine too. The approach appears to be useful in many stages in the development of reactive systems, and might also pave the way to systems that are constructed directly from their requirements, without the need for intra-object or intra-component modeling or coding.
Abstract A logic program consists of a set of Horn clauses, and can be used to express a query on... more Abstract A logic program consists of a set of Horn clauses, and can be used to express a query on relational data bases. It is shown that logic programs express precisely the queries in YE+(the set of queries representable by a fixpoint applied to a positive existential query). Queries expressible by logic programs are thus not first-order queries in general, nor are all the first-order queries expressible as logic programs. Several ways of adding negation to logic programs are examined.
Abstract Statecharts, popular for modeling system behavior in the structural analysis paradigm, a... more Abstract Statecharts, popular for modeling system behavior in the structural analysis paradigm, are part of a fully executable language set for modeling object-oriented systems. The languages form the core of the emerging Unified Modeling Language. The authors embarked on an effort to develop an integrated set of diagrammatic languages for object modeling, built around statecharts, and to construct a supporting tool that produces a fully executable model and allows automatic code synthesis.
The motivation for this paper, the rst in a planned series of three parts, is the multitude of co... more The motivation for this paper, the rst in a planned series of three parts, is the multitude of concepts surrounding the proper de nition of complex modeling languages for systems and software, and the confusion that this often causes. Particularly relevant is the case of the recently standardized UML, which we refer to quite extensively as we proceed. Our intention is to discuss and clarify the notions involved in de ning modeling languages. The main theme is the distinction between syntax and semantics, the nature and purpose of each, their usage and style, and the various means for de ning and dealing with them. Underlying the exposition are the dichotomies of textual vs. visual languages, structural vs. behavioral speci cation, and requirements vs. system models. We hope that the paper will beuseful to language designers, methodologists, tool vendors and educators.
Abstract The simple set WL of deterministic while programs is defined and a number of known metho... more Abstract The simple set WL of deterministic while programs is defined and a number of known methods for proving the correctness of these programs are surveyed. Emphasis is placed on the tradeoff existing between data-directed and syntax-directed methods, and on providing, especially for the latter, a uniform description enabling comparison and assessment.
Abstract We extend live sequence charts (LSCs), a highly expressive variant of sequence diagrams,... more Abstract We extend live sequence charts (LSCs), a highly expressive variant of sequence diagrams, and provide the extension with an executable semantics. The extension involves support for instances that can bind to multiple objects and symbolic variables that can bind to arbitrary values. The result is a powerful executable language for expressing behavioral requirements on the level of inter-object interaction.
Biological systems can be modeled beneficially as reactive systems, using languages and tools dev... more Biological systems can be modeled beneficially as reactive systems, using languages and tools developed for the construction of man-made systems. Our long-term aim is to model a full multi-cellular animal as a reactive system; specifically, the C. elegans nematode worm, which is complex, but very well-defined in terms of anatomy and genetics.
Abstract We extend live sequence charts (LSCs), a highly expressive variant of sequence diagrams,... more Abstract We extend live sequence charts (LSCs), a highly expressive variant of sequence diagrams, with timing constructs, thus making the language suitable for specifying the behavioral requirements of time-intensive systems. We follow R. Alur and TA Henzinger (see Software Tools for Technology Transfer, vol. 1, p. 86-109, 1997) in basing the extension on a single clock object.
Abstract We investigate the descriptive succinctness of three fundamental notions for modeling co... more Abstract We investigate the descriptive succinctness of three fundamental notions for modeling concurrency: nondeterminism and pure parallelism, the two facets of alternation, and bounded cooperative concurrency, whereby a system configuration consists of a bounded number of cooperating states.
We propose a new feature extraction method for use with chemical sensors. It is based on fitting ... more We propose a new feature extraction method for use with chemical sensors. It is based on fitting a parametric analytic model of the sensor's response over time to the measured signal, and taking the set of best-fitting parameters as the features. The process of finding the features is fast and robust, and the resulting set of features is shown to significantly enhance the performance of subsequent classification algorithms.
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Papers by David Harel