From local laboratory data to public domain database in search of indirect association of diseases: AJAX based gene data search engine.

This paper presents an extensible schema for capturing laboratory gene variance data with its meta-data properties in a semi-structured environment. This paper also focuses on the issues of creating a local and task specific component database which is a subset of global data resources. An XML based genetic disorder component database schema is developed with adequate flexibilities to facilitate searching of gene mutation data. A web based search engine is developed that allows researchers to query a set of gene parameters obtained from local XML schema and subsequently allow them to automatically establish a link with the public domain gene databases. The application applies AJAX (Asynchronous Javascript and XML), a cutting-edge web technology, to carry out the gene data searching function

Non-Strict Independence-Based Program Parallelization Using Sharing and Freeness Information.

The current ubiquity of multi-core processors has brought renewed interest in program parallelization. Logic programs allow studying the parallelization of programs with complex, dynamic data structures with (declarative) pointers in a comparatively simple semantic setting. In this context, automatic parallelizers which exploit and-parallelism rely on notions of independence in order to ensure certain efficiency properties. “Non-strict” independence is a more relaxed notion than the traditional notion of “strict” independence which still ensures the relevant efficiency properties and can allow considerable more parallelism. Non-strict independence cannot be determined solely at run-time (“a priori”) and thus global analysis is a requirement. However, extracting non-strict independence information from available analyses and domains is non-trivial. This paper provides on one hand an extended presentation of our classic techniques for compile-time detection of non-strict independence based on extracting information from (abstract interpretation-based) analyses using the now well understood and popular Sharing + Freeness domain. This includes algorithms for combined compile-time/run-time detection which involve special run-time checks for this type of parallelism. In addition, we propose herein novel annotation (parallelization) algorithms, URLP and CRLP, which are specially suited to non-strict independence. We also propose new ways of using the Sharing + Freeness information to optimize how the run-time environments of goals are kept apart during parallel execution. Finally, we also describe the implementation of these techniques in our parallelizing compiler and recall some early performance results. We provide as well an extended description of our pictorial representation of sharing and freeness information

Solving Functional Constraints by Variable Substitution

Functional constraints and bi-functional constraints are an important constraint class in Constraint Programming (CP) systems, in particular for Constraint Logic Programming (CLP) systems. CP systems with finite domain constraints usually employ CSP-based solvers which use local consistency, for example, arc consistency. We introduce a new approach which is based instead on variable substitution. We obtain efficient algorithms for reducing systems involving functional and bi-functional constraints together with other non-functional constraints. It also solves globally any CSP where there exists a variable such that any other variable is reachable from it through a sequence of functional constraints. Our experiments on random problems show that variable elimination can significantly improve the efficiency of solving problems with functional constraints

Simple, compact and robust approximate string dictionary

This paper is concerned with practical implementations of approximate string dictionaries that allow edit errors. In this problem, we have as input a dictionary $D$ of $d$ strings of total length $n$ over an alphabet of size $\sigma$. Given a bound $k$ and a pattern $x$ of length $m$, a query has to return all the strings of the dictionary which are at edit distance at most $k$ from $x$, where the edit distance between two strings $x$ and $y$ is defined as the minimum-cost sequence of edit operations that transform $x$ into $y$. The cost of a sequence of operations is defined as the sum of the costs of the operations involved in the sequence. In this paper, we assume that each of these operations has unit cost and consider only three operations: deletion of one character, insertion of one character and substitution of a character by another. We present a practical implementation of the data structure we recently proposed and which works only for one error. We extend the scheme to $2\leq k<m$. Our implementation has many desirable properties: it has a very fast and space-efficient building algorithm. The dictionary data structure is compact and has fast and robust query time. Finally our data structure is simple to implement as it only uses basic techniques from the literature, mainly hashing (linear probing and hash signatures) and succinct data structures (bitvectors supporting rank queries).Comment: Accepted to a journal (19 pages, 2 figures

Algorithmic Aspects of Cyclic Combinational Circuit Synthesis

Digital circuits are called combinational if they are memoryless: if they have outputs that depend only on the current values of the inputs. Combinational circuits are generally thought of as acyclic (i.e., feed-forward) structures. And yet, cyclic circuits can be combinational. Cycles sometimes occur in designs synthesized from high-level descriptions, as well as in bus-based designs [16]. Feedback in such cases is carefully contrived, typically occurring when functional units are connected in a cyclic topology. Although the premise of cycles in combinational circuits has been accepted, and analysis techniques have been proposed [7], no one has attempted the synthesis of circuits with feedback at the logic level. We have argued the case for a paradigm shift in combinational circuit design [10]. We should no longer think of combinational logic as acyclic in theory or in practice, since most combinational circuits are best designed with cycles. We have proposed a general methodology for the synthesis of multilevel networks with cyclic topologies and incorporated it in a general logic synthesis environment. In trials, benchmark circuits were optimized significantly, with improvements of up to 30%I n the area. In this paper, we discuss algorithmic aspects of cyclic circuit design. We formulate a symbolic framework for analysis based on a divide-and-conquer strategy. Unlike previous approaches, our method does not require ternary-valued simulation. Our analysis for combinationality is tightly coupled with the synthesis phase, in which we assemble a combinational network from smaller combinational components. We discuss the underpinnings of the heuristic search methods and present examples as well as synthesis results for benchmark circuits. In this paper, we discuss algorithmic aspects of cyclic circuit design. We formulate a symbolic framework for analysis based on a divide-and-conquer strategy. Unlike previous approaches, our method does not require ternary-valued simulation. Our analysis for combinationality is tightly coupled with the synthesis phase, in which we assemble a combinational network from smaller combinational components. We discuss the underpinnings of the heuristic search methods and present examples as well as synthesis results for benchmark circuits