Information Extraction, Data Integration, and Uncertain Data Management: The State of The Art

Information Extraction, data Integration, and uncertain data management are different areas of research that got vast focus in the last two decades. Many researches tackled those areas of research individually. However, information extraction systems should have integrated with data integration methods to make use of the extracted information. Handling uncertainty in extraction and integration process is an important issue to enhance the quality of the data in such integrated systems. This article presents the state of the art of the mentioned areas of research and shows the common grounds and how to integrate information extraction and data integration under uncertainty management cover

Detection of Side Chain Rearrangements Mediating the Motions of Transmembrane Helices in Molecular Dynamics Simulations of G Protein-Coupled Receptors.

Structure and dynamics are essential elements of protein function. Protein structure is constantly fluctuating and undergoing conformational changes, which are captured by molecular dynamics (MD) simulations. We introduce a computational framework that provides a compact representation of the dynamic conformational space of biomolecular simulations. This method presents a systematic approach designed to reduce the large MD simulation spatiotemporal datasets into a manageable set in order to guide our understanding of how protein mechanics emerge from side chain organization and dynamic reorganization. We focus on the detection of side chain interactions that undergo rearrangements mediating global domain motions and vice versa. Side chain rearrangements are extracted from side chain interactions that undergo well-defined abrupt and persistent changes in distance time series using Gaussian mixture models, whereas global domain motions are detected using dynamic cross-correlation. Both side chain rearrangements and global domain motions represent the dynamic components of the protein MD simulation, and are both mapped into a network where they are connected based on their degree of coupling. This method allows for the study of allosteric communication in proteins by mapping out the protein dynamics into an intramolecular network to reduce the large simulation data into a manageable set of communities composed of coupled side chain rearrangements and global domain motions. This computational framework is suitable for the study of tightly packed proteins, such as G protein-coupled receptors, and we present an application on a seven microseconds MD trajectory of CC chemokine receptor 7 (CCR7) bound to its ligand CCL21

TBTK: A quantum mechanics software development kit

TBTK is a software development kit for quantum mechanical calculations and is designed to enable the development of applications that investigate problems formulated on second-quantized form. It also enables method developers to create solvers for tight-binding, DFT, DMFT, quantum transport, etc., that can be easily integrated with each other. Both through the development of completely new solvers, as well as front and back ends to already well established packages. TBTK provides data structures tailored for second-quantization that will encourage reusability and enable scalability for quantum mechanical calculations.Comment: 6 page introduction to the TBTK v1.0.3 (available at https://github.com/dafer45/TBTK

ImageSieve: Exploratory search of museum archives with named entity-based faceted browsing

Over the last few years, faceted search emerged as an attractive alternative to the traditional "text box" search and has become one of the standard ways of interaction on many e-commerce sites. However, these applications of faceted search are limited to domains where the objects of interests have already been classified along several independent dimensions, such as price, year, or brand. While automatic approaches to generate faceted search interfaces were proposed, it is not yet clear to what extent the automatically-produced interfaces will be useful to real users, and whether their quality can match or surpass their manually-produced predecessors. The goal of this paper is to introduce an exploratory search interface called ImageSieve, which shares many features with traditional faceted browsing, but can function without the use of traditional faceted metadata. ImageSieve uses automatically extracted and classified named entities, which play important roles in many domains (such as news collections, image archives, etc.). We describe one specific application of ImageSieve for image search. Here, named entities extracted from the descriptions of the retrieved images are used to organize a faceted browsing interface, which then helps users to make sense of and further explore the retrieved images. The results of a user study of ImageSieve demonstrate that a faceted search system based on named entities can help users explore large collections and find relevant information more effectively

Extracting corpus specific knowledge bases from Wikipedia

Thesauri are useful knowledge structures for assisting information retrieval. Yet their production is labor-intensive, and few domains have comprehensive thesauri that cover domain-specific concepts and contemporary usage. One approach, which has been attempted without much success for decades, is to seek statistical natural language processing algorithms that work on free text. Instead, we propose to replace costly professional indexers with thousands of dedicated amateur volunteers--namely, those that are producing Wikipedia. This vast, open encyclopedia represents a rich tapestry of topics and semantics and a huge investment of human effort and judgment. We show how this can be directly exploited to provide WikiSauri: manually-defined yet inexpensive thesaurus structures that are specifically tailored to expose the topics, terminology and semantics of individual document collections. We also offer concrete evidence of the effectiveness of WikiSauri for assisting information retrieval

A Labeled Graph Kernel for Relationship Extraction

In this paper, we propose an approach for Relationship Extraction (RE) based on labeled graph kernels. The kernel we propose is a particularization of a random walk kernel that exploits two properties previously studied in the RE literature: (i) the words between the candidate entities or connecting them in a syntactic representation are particularly likely to carry information regarding the relationship; and (ii) combining information from distinct sources in a kernel may help the RE system make better decisions. We performed experiments on a dataset of protein-protein interactions and the results show that our approach obtains effectiveness values that are comparable with the state-of-the art kernel methods. Moreover, our approach is able to outperform the state-of-the-art kernels when combined with other kernel methods