Synthesizing Program Input Grammars

We present an algorithm for synthesizing a context-free grammar encoding the language of valid program inputs from a set of input examples and blackbox access to the program. Our algorithm addresses shortcomings of existing grammar inference algorithms, which both severely overgeneralize and are prohibitively slow. Our implementation, GLADE, leverages the grammar synthesized by our algorithm to fuzz test programs with structured inputs. We show that GLADE substantially increases the incremental coverage on valid inputs compared to two baseline fuzzers

Heterogeneous biomedical database integration using a hybrid strategy: a p53 cancer research database.

Complex problems in life science research give rise to multidisciplinary collaboration, and hence, to the need for heterogeneous database integration. The tumor suppressor p53 is mutated in close to 50% of human cancers, and a small drug-like molecule with the ability to restore native function to cancerous p53 mutants is a long-held medical goal of cancer treatment. The Cancer Research DataBase (CRDB) was designed in support of a project to find such small molecules. As a cancer informatics project, the CRDB involved small molecule data, computational docking results, functional assays, and protein structure data. As an example of the hybrid strategy for data integration, it combined the mediation and data warehousing approaches. This paper uses the CRDB to illustrate the hybrid strategy as a viable approach to heterogeneous data integration in biomedicine, and provides a design method for those considering similar systems. More efficient data sharing implies increased productivity, and, hopefully, improved chances of success in cancer research. (Code and database schemas are freely downloadable, http://www.igb.uci.edu/research/research.html.)

MIR task and evaluation techniques

Existing tasks in MIREX have traditionally focused on low-level MIR tasks working with flat (usually DSP-only) ground-truth. These evaluation techniques, however, can not evaluate the increasing number of algorithms that utilize relational data and are not currently utilizing the state of the art in evaluating ranked or ordered output. This paper summarizes the state of the art in evaluating relational ground-truth. These components are then synthesized into novel evaluation techniques that are then applied to 14 concrete music document retrieval tasks, demonstrating how these evaluation techniques can be applied in a practical context

Automated synthesis of data extraction and transformation programs

Due to the abundance of data in today’s data-rich world, end-users increasingly need to perform various data extraction and transformation tasks. While many of these tedious tasks can be performed in a programmatic way, most end-users lack the required programming expertise to automate them and end up spending their valuable time in manually performing various data- related tasks. The field of program synthesis aims to overcome this problem by automatically generating programs from informal specifications, such as input-output examples or natural language. This dissertation focuses on the design and implementation of new systems for automating important classes of data transformation and extraction tasks. It introduces solutions for automating data manipulation tasks on fully- structured data formats like relational tables, or on semi-structured formats such as XML and JSON documents. First, we describe a novel algorithm for synthesizing hierarchical data transformations from input-output examples. A key novelty of our approach is that it reduces the synthesis of tree transformations to the simpler problem of synthesizing transformations over the paths of the tree. We also describe a new and effective algorithm for learning path transformations that combines logical SMT-based reasoning with machine learning techniques based on decision trees. Next, we present a new methodology for learning programs that migrate tree-structured documents to relational table representations from input-output examples. Our approach achieves its goal by decomposing the synthesis task to two subproblems of (A) learning the column extraction logic, and (B) learning the row extraction logic. We propose a technique for learning column extraction programs using deterministic finite automata, and a new algorithm for predicate learning which combines integer linear programing and logic minimization. Finally, we address the problem of automating data extraction tasks from natural language. Specifically, we focus on data retrieval from relational databases and describe a novel approach for learning SQL queries from English descriptions. The method we describe is fully automatic and database-agnostic (i.e., does not require customization for each database). Our method combines semantic parsing techniques from the NLP community with novel programming languages ideas involving probabilistic type inhabitation and automated sketch repair.Computer Science

State-of-the-art on evolution and reactivity

This report starts by, in Chapter 1, outlining aspects of querying and updating resources on the Web and on the Semantic Web, including the development of query and update languages to be carried out within the Rewerse project. From this outline, it becomes clear that several existing research areas and topics are of interest for this work in Rewerse. In the remainder of this report we further present state of the art surveys in a selection of such areas and topics. More precisely: in Chapter 2 we give an overview of logics for reasoning about state change and updates; Chapter 3 is devoted to briefly describing existing update languages for the Web, and also for updating logic programs; in Chapter 4 event-condition-action rules, both in the context of active database systems and in the context of semistructured data, are surveyed; in Chapter 5 we give an overview of some relevant rule-based agents frameworks

XMatch: A language for satisfaction-based selection of Grid services

Grid systems enable the sharing of a large number of geographically-dispersed resources among different communities of users. They require a mapping functionality for the association of users requests expressed in terms of requirements and preferences to actual resources. This functionality should deal with a potentially high number of similar resources and with the diversity of the perceived satisfactions of users. We propose XMatch, a query language enabling the expression of the user request in terms of the expected satisfaction over XML-based representation of available resources. This language offers a compact way for users to express their preferences for Grid resources and enable the maximization of the global preference