Towards MKM in the Large: Modular Representation and Scalable Software Architecture

MKM has been defined as the quest for technologies to manage mathematical knowledge. MKM "in the small" is well-studied, so the real problem is to scale up to large, highly interconnected corpora: "MKM in the large". We contend that advances in two areas are needed to reach this goal. We need representation languages that support incremental processing of all primitive MKM operations, and we need software architectures and implementations that implement these operations scalably on large knowledge bases. We present instances of both in this paper: the MMT framework for modular theory-graphs that integrates meta-logical foundations, which forms the base of the next OMDoc version; and TNTBase, a versioned storage system for XML-based document formats. TNTBase becomes an MMT database by instantiating it with special MKM operations for MMT.Comment: To appear in The 9th International Conference on Mathematical Knowledge Management: MKM 201

bdbms -- A Database Management System for Biological Data

Biologists are increasingly using databases for storing and managing their data. Biological databases typically consist of a mixture of raw data, metadata, sequences, annotations, and related data obtained from various sources. Current database technology lacks several functionalities that are needed by biological databases. In this paper, we introduce bdbms, an extensible prototype database management system for supporting biological data. bdbms extends the functionalities of current DBMSs to include: (1) Annotation and provenance management including storage, indexing, manipulation, and querying of annotation and provenance as first class objects in bdbms, (2) Local dependency tracking to track the dependencies and derivations among data items, (3) Update authorization to support data curation via content-based authorization, in contrast to identity-based authorization, and (4) New access methods and their supporting operators that support pattern matching on various types of compressed biological data types. This paper presents the design of bdbms along with the techniques proposed to support these functionalities including an extension to SQL. We also outline some open issues in building bdbms.Comment: This article is published under a Creative Commons License Agreement (http://creativecommons.org/licenses/by/2.5/.) You may copy, distribute, display, and perform the work, make derivative works and make commercial use of the work, but, you must attribute the work to the author and CIDR 2007. 3rd Biennial Conference on Innovative Data Systems Research (CIDR) January 710, 2007, Asilomar, California, US

A UML/OCL framework for the analysis of fraph transformation rules

In this paper we present an approach for the analysis of graph transformation rules based on an intermediate OCL representation. We translate different rule semantics into OCL, together with the properties of interest (like rule applicability, conflicts or independence). The intermediate representation serves three purposes: (i) it allows the seamless integration of graph transformation rules with the MOF and OCL standards, and enables taking the meta-model and its OCL constraints (i.e. well-formedness rules) into account when verifying the correctness of the rules; (ii) it permits the interoperability of graph transformation concepts with a number of standards-based model-driven development tools; and (iii) it makes available a plethora of OCL tools to actually perform the rule analysis. This approach is especially useful to analyse the operational semantics of Domain Specific Visual Languages. We have automated these ideas by providing designers with tools for the graphical specification and analysis of graph transformation rules, including a backannotation mechanism that presents the analysis results in terms of the original language notation

Computing Multi-Relational Sufficient Statistics for Large Databases

Databases contain information about which relationships do and do not hold among entities. To make this information accessible for statistical analysis requires computing sufficient statistics that combine information from different database tables. Such statistics may involve any number of {\em positive and negative} relationships. With a naive enumeration approach, computing sufficient statistics for negative relationships is feasible only for small databases. We solve this problem with a new dynamic programming algorithm that performs a virtual join, where the requisite counts are computed without materializing join tables. Contingency table algebra is a new extension of relational algebra, that facilitates the efficient implementation of this M\"obius virtual join operation. The M\"obius Join scales to large datasets (over 1M tuples) with complex schemas. Empirical evaluation with seven benchmark datasets showed that information about the presence and absence of links can be exploited in feature selection, association rule mining, and Bayesian network learning.Comment: 11pages, 8 figures, 8 tables, CIKM'14,November 3--7, 2014, Shanghai, Chin

Web Services: A Process Algebra Approach

It is now well-admitted that formal methods are helpful for many issues raised in the Web service area. In this paper we present a framework for the design and verification of WSs using process algebras and their tools. We define a two-way mapping between abstract specifications written using these calculi and executable Web services written in BPEL4WS. Several choices are available: design and correct errors in BPEL4WS, using process algebra verification tools, or design and correct in process algebra and automatically obtaining the corresponding BPEL4WS code. The approaches can be combined. Process algebra are not useful only for temporal logic verification: we remark the use of simulation/bisimulation both for verification and for the hierarchical refinement design method. It is worth noting that our approach allows the use of any process algebra depending on the needs of the user at different levels (expressiveness, existence of reasoning tools, user expertise)

An Algebra of Hierarchical Graphs

We define an algebraic theory of hierarchical graphs, whose axioms characterise graph isomorphism: two terms are equated exactly when they represent the same graph. Our algebra can be understood as a high-level language for describing graphs with a node-sharing, embedding structure, and it is then well suited for defining graphical representations of software models where nesting and linking are key aspects