Deductive Optimization of Relational Data Storage

Optimizing the physical data storage and retrieval of data are two key database management problems. In this paper, we propose a language that can express a wide range of physical database layouts, going well beyond the row- and column-based methods that are widely used in database management systems. We use deductive synthesis to turn a high-level relational representation of a database query into a highly optimized low-level implementation which operates on a specialized layout of the dataset. We build a compiler for this language and conduct experiments using a popular database benchmark, which shows that the performance of these specialized queries is competitive with a state-of-the-art in memory compiled database system

Twelve Theses on Reactive Rules for the Web

Reactivity, the ability to detect and react to events, is an essential functionality in many information systems. In particular, Web systems such as online marketplaces, adaptive (e.g., recommender) systems, and Web services, react to events such as Web page updates or data posted to a server. This article investigates issues of relevance in designing high-level programming languages dedicated to reactivity on the Web. It presents twelve theses on features desirable for a language of reactive rules tuned to programming Web and Semantic Web applications

Deductive Biocomputing

BACKGROUND: As biologists increasingly rely upon computational tools, it is imperative that they be able to appropriately apply these tools and clearly understand the methods the tools employ. Such tools must have access to all the relevant data and knowledge and, in some sense, “understand” biology so that they can serve biologists' goals appropriately and “explain” in biological terms how results are computed. METHODOLOGY/PRINCIPAL FINDINGS: We describe a deduction-based approach to biocomputation that semiautomatically combines knowledge, software, and data to satisfy goals expressed in a high-level biological language. The approach is implemented in an open source web-based biocomputing platform called BioDeducta, which combines SRI's SNARK theorem prover with the BioBike interactive integrated knowledge base. The biologist/user expresses a high-level conjecture, representing a biocomputational goal query, without indicating how this goal is to be achieved. A subject domain theory, represented in SNARK's logical language, transforms the terms in the conjecture into capabilities of the available resources and the background knowledge necessary to link them together. If the subject domain theory enables SNARK to prove the conjecture—that is, to find paths between the goal and BioBike resources—then the resulting proofs represent solutions to the conjecture/query. Such proofs provide provenance for each result, indicating in detail how they were computed. We demonstrate BioDeducta by showing how it can approximately replicate a previously published analysis of genes involved in the adaptation of cyanobacteria to different light niches. CONCLUSIONS/SIGNIFICANCE: Through the use of automated deduction guided by a biological subject domain theory, this work is a step towards enabling biologists to conveniently and efficiently marshal integrated knowledge, data, and computational tools toward resolving complex biological queries