A Process Calculus for Expressing Finite Place/Transition Petri Nets

We introduce the process calculus Multi-CCS, which extends conservatively CCS with an operator of strong prefixing able to model atomic sequences of actions as well as multiparty synchronization. Multi-CCS is equipped with a labeled transition system semantics, which makes use of a minimal structural congruence. Multi-CCS is also equipped with an unsafe P/T Petri net semantics by means of a novel technique. This is the first rich process calculus, including CCS as a subcalculus, which receives a semantics in terms of unsafe, labeled P/T nets. The main result of the paper is that a class of Multi-CCS processes, called finite-net processes, is able to represent all finite (reduced) P/T nets.Comment: In Proceedings EXPRESS'10, arXiv:1011.601

Kripke Semantics for Martin-L\"of's Extensional Type Theory

It is well-known that simple type theory is complete with respect to non-standard set-valued models. Completeness for standard models only holds with respect to certain extended classes of models, e.g., the class of cartesian closed categories. Similarly, dependent type theory is complete for locally cartesian closed categories. However, it is usually difficult to establish the coherence of interpretations of dependent type theory, i.e., to show that the interpretations of equal expressions are indeed equal. Several classes of models have been used to remedy this problem. We contribute to this investigation by giving a semantics that is standard, coherent, and sufficiently general for completeness while remaining relatively easy to compute with. Our models interpret types of Martin-L\"of's extensional dependent type theory as sets indexed over posets or, equivalently, as fibrations over posets. This semantics can be seen as a generalization to dependent type theory of the interpretation of intuitionistic first-order logic in Kripke models. This yields a simple coherent model theory, with respect to which simple and dependent type theory are sound and complete

Ontology design patterns to disambiguate relations between genes and gene products in GENIA

MOTIVATION: Annotated reference corpora play an important role in biomedical information extraction. A semantic annotation of the natural language texts in these reference corpora using formal ontologies is challenging due to the inherent ambiguity of natural language. The provision of formal definitions and axioms for semantic annotations offers the means for ensuring consistency as well as enables the development of verifiable annotation guidelines. Consistent semantic annotations facilitate the automatic discovery of new information through deductive inferences. RESULTS: We provide a formal characterization of the relations used in the recent GENIA corpus annotations. For this purpose, we both select existing axiom systems based on the desired properties of the relations within the domain and develop new axioms for several relations. To apply this ontology of relations to the semantic annotation of text corpora, we implement two ontology design patterns. In addition, we provide a software application to convert annotated GENIA abstracts into OWL ontologies by combining both the ontology of relations and the design patterns. As a result, the GENIA abstracts become available as OWL ontologies and are amenable for automated verification, deductive inferences and other knowledge-based applications. AVAILABILITY: Documentation, implementation and examples are available from http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/

Ecological diversity : measuring the unmeasurable

Diversity is a concept central to ecology, and its measurement is essential for any study of ecosystem health. But summarizing this complex and multidimensional concept in a single measure is problematic. Dozens of mathematical indices have been proposed for this purpose, but these can provide contradictory results leading to misleading or incorrect conclusions about a community's diversity. In this review, we summarize the key conceptual issues underlying the measurement of ecological diversity, survey the indices most commonly used in ecology, and discuss their relative suitability. We advocate for indices that: (i) satisfy key mathematical axioms; (ii) can be expressed as so-called effective numbers; (iii) can be extended to account for disparity between types; (iv) can be parameterized to obtain diversity profiles; and (v) for which an estimator (preferably unbiased) can be found so that the index is useful for practical applications

Appalachian Coalfield Delegation Position Paper on Sustainable Energy

Appalachian grassroots groups(with support provided by the DataCenter) release a scathing report on the impact of coal mining to the United Nations Commission on Sustainable Development. The Delegation created an historic moment with its powerful stories and diverse outreach. Alliances were forged and the civil society discourse on energy, particularly what is sustainable energy and who gets to define it, has been challenged. Their answer---"it comes from the people!" As most government officials continue to ignore the atrocities of mountain top removal, coal sludge impoundments, and underground injections of sludge, it is up to the people of the Appalachian coal fields to let the world know the harsh realities of an economy built on seemingly cheap electricity