Reliable Information Retrieval Research Articles

Study of the error correction capability of multiple sequence alignment algorithm (MAFFT) in DNA storage

Synchronization (insertions–deletions) errors are still a major challenge for reliable information retrieval in DNA storage. Unlike traditional error correction codes (ECC) that add redundancy in the stored information, multiple sequence alignment (MSA) solves this problem by searching the conserved subsequences. In this paper, we conduct a comprehensive simulation study on the error correction capability of a typical MSA algorithm, MAFFT. Our results reveal that its capability exhibits a phase transition when there are around 20% errors. Below this critical value, increasing sequencing depth can eventually allow it to approach complete recovery. Otherwise, its performance plateaus at some poor levels. Given a reasonable sequencing depth (≤ 70), MSA could achieve complete recovery in the low error regime, and effectively correct 90% of the errors in the medium error regime. In addition, MSA is robust to imperfect clustering. It could also be combined with other means such as ECC, repeated markers, or any other code constraints. Furthermore, by selecting an appropriate sequencing depth, this strategy could achieve an optimal trade-off between cost and reading speed. MSA could be a competitive alternative for future DNA storage.

CredibleExpertRank: Leveraging Social Network Analysis and Opinion Mining to Facilitate Reliable Information Retrieval on Knowledge-Sharing Sites

CredibleExpertRank: Leveraging Social Network Analysis and Opinion Mining to Facilitate Reliable Information Retrieval on Knowledge-Sharing Sites

CellMeSH: probabilistic cell-type identification using indexed literature.

MotivationSingle-cell RNA sequencing (scRNA-seq) is widely used for analyzing gene expression in multi-cellular systems and provides unprecedented access to cellular heterogeneity. scRNA-seq experiments aim to identify and quantify all cell types present in a sample. Measured single-cell transcriptomes are grouped by similarity and the resulting clusters are mapped to cell types based on cluster-specific gene expression patterns. While the process of generating clusters has become largely automated, annotation remains a laborious ad hoc effort that requires expert biological knowledge.ResultsHere, we introduce CellMeSH—a new automated approach to identifying cell types for clusters based on prior literature. CellMeSH combines a database of gene–cell-type associations with a probabilistic method for database querying. The database is constructed by automatically linking gene and cell-type information from millions of publications using existing indexed literature resources. Compared to manually constructed databases, CellMeSH is more comprehensive and is easily updated with new data. The probabilistic query method enables reliable information retrieval even though the gene–cell-type associations extracted from the literature are noisy. CellMeSH is also able to optionally utilize prior knowledge about tissues or cells for further annotation improvement. CellMeSH achieves top-one and top-three accuracies on a number of mouse and human datasets that are consistently better than existing approaches.Availability and implementationWeb server at https://uncurl.cs.washington.edu/db_query and API at https://github.com/shunfumao/cellmesh.Supplementary information Supplementary data are available at Bioinformatics online.

Lexical Ambiguity in Arabic Information Retrieval: The Case of Six Web-Based Search Engines

In recent years, both research and industry have shown an increasing interest in developing reliable information retrieval (IR) systems that can effectively address the growing demands of users worldwide. In spite of the relative success of IR systems in addressing the needs of users and even adapting to their environments, many problems remain unresolved. One main problem is lexical ambiguity which has negative impacts on the performance and reliability of IR systems. To date, lexical ambiguity has been one of the most frequently reported problems in the Arabic IR systems despite the development of different word sense disambiguation (WSD) techniques. This is largely attributed to the limitations of such techniques in addressing the issue of linguistic peculiarities. Hence, this study addresses these limitations by exploring the reasons for lexical ambiguity in IR applications in Arabic as one step towards reliable and practical solutions. For this purpose, the performances of six search engines Google, Bing, Baidu, Yahoo, Yandex, and Ask are evaluated. Results indicate that lexical ambiguities in Arabic IR applications are mainly due to the unique morphological and orthographic system of the Arabic language, in addition to its diglossia and the multiple colloquial dialects where sometimes mutual intelligibility is not achieved. For better disambiguation and IR performances in Arabic, this study proposes that clustering models based on supervised machine learning theory should be trained to address the morphological diversity of Arabic and its unique orthographic system. Search engines should also be adapted to the geographic location of the users in order to address the issue of vernacular dialects of Arabic. They should also be trained to automatically identify the different dialects. Finally, search engines should consider all varieties of Arabic and be able to interpret the queries regardless of the particular language adopted by the user.

СИСТЕМА ПОИСКА И АНАЛИЗА ДОСТОВЕРНОЙ ИНФОРМАЦИИ В СЕТИ ИНТЕРНЕТ

Now in the world a problem of reliable information retrieval in the Internet network is especially critical. It is defined by increased data capacity and by the absence of control over data placement. It is offered to determine information reliability by methods of fuzzy logic at the correct formation of retrieval request. For the estimate of completeness, truth and integrity of data obtained it is offered to rely upon the analysis of information from other pages of a site found. In accordance with this the notions of topical closeness of site pages and reliability of information presented in the remaining sections. To organize an output are compiled the rules for the integral reliability output of a site page. For example, if information on a page does not coincide with analyzed one and is reliable then one can suppose that related information is reliable. Further, with the use of Mam-dani controller is carried out a defuzzification. A technology for a retrieval request organization is offered to increase an information content retrieval. The technologies offered for retrieval and analysis of information allow increasing effectiveness and a retrieval rate of reliable, integrated and true information in the Internet network.

Information retrieval system using the keyword concept net of the P2P service-based in the mobile cloud environment

In the mobile cloud environment, the information retrieval system based on the P2P is very important. In case of an information search that is not consistent with the meta profile in the data distribution technique, the reliability of the searched data cannot be assured. This study suggests the reliable information retrieval system of the P2P service based in the mobile cloud environment. The proposed system is applied to the keyword based concept net applying the ontology method. Additionally, for effective information retrieval of peers, the connectivity between the keyword concepts is applied. Here, the applied concept net consists of keyword focused net, field recommended by the professional group net, and business process concept net. This system is available to search and analysis in a mobile peer aspect by constructing the interface as a category-based concept net keyword with the information search about the business process cooperation; through this type of the classification system, the cooperation information is structured. The information search methodology using the keyword concept network of the ontology-based that is the topic of this study can suggest to sharing, expert, mobile, governance as the business process cooperative service. In addition, it is possible to change into the business process method through the social cooperation of the mobile environment. Therefore, the process improvement, control, and policy can be supported through the business process visualization.

Inverse problems of gravimetry as retrieval of reliable information under uncertainty

The guaranteed approach to the solution of inverse problems of gravimetry, which is fundamentally different from the common solution, is presented. Instead of providing single (optimum) estimates of the model parameters, whose quality is, generally, random, the interpretation in the suggested approach yields that volume of reliable information on disturbing objects, which is contained in the field measurements, together with the a priori constraints. The method of solving the inverse problem of gravimetry is developed within this approach, where, in contrast to the conventional approach, both the geometrical parameters of the geological bodies and the densities of their composing rocks are treated as unknowns. The generalized assembly algorithm suggested by V.N. Strakhov is proposed as a basic working tool to implement this approach. The results of testing this algorithm and the guaranteed approach itself on the model and practical examples are discussed.

A knowledge-based search engine to navigate the information thicket of nanotoxicology

The risk assessment of nano-sized materials (NM) currently suffers from great uncertainties regarding their putative toxicity for humans and the environment. An extensive amount of the respective original research literature has to be evaluated before a targeted and hypothesis-driven Environmental and Health Safety research can be stipulated. Furthermore, to comply with the European animal protection legislation in vitro testing has to be preferred whenever possible. Against this background, there is the need for tools that enable producers of NM and risk assessors for a fast and comprehensive data retrieval, thereby linking the 3Rs principle to the hazard identification of NM.Here we report on the development of a knowledge-based search engine that is tailored to the particular needs of risk assessors in the area of NM. Comprehensive retrieval of data from studies utilising in vitro as well as in vivo methods relying on the PubMed database is presented exemplarily with a titanium dioxide case study. A fast, relevant and reliable information retrieval is of paramount importance for the scientific community dedicated to develop safe NM in various product areas, and for risk assessors obliged to identify data gaps, to define additional data requirements for approval of NM and to create strategies for integrated testing using alternative methods.

An improved Huffman coding method for archiving text, images, and music characters in DNA

An improved Huffman coding method for information storage in DNA is described. The method entails the utilization of modified unambiguous base assignment that enables efficient coding of characters. A plasmid-based library with efficient and reliable information retrieval and assembly with uniquely designed primers is described. We illustrate our approach by synthesis of DNA that encodes text, images, and music, which could easily be retrieved by DNA sequencing using the specific primers. The method is simple and lends itself to automated information retrieval.

Service-learning on a private, liberal arts campus in rural Kentucky: enhancing student understanding of multiple factors influencing local, regional, and global food security

To identify components of a service-learning experience and recognize its potential to foster collaborative learning and skill enhancement in time and organizational management, effective communication, and the retrieval of reliable information regarding world hunger. Service-learning can foster the integration of theory, application, and service in undergraduate education. It includes an academic component and assessment criteria, a service project, and a formal reflection phase. Incorporating service-learning into course objectives provides a balance among specific learning goals, expected outcomes, and responses to actual community needs. This poster presentation describes a Hunger Awareness Project in a nutrition course for approximately forty students from more than five different academic disciplines, including Dietetics. The academic component counts as a percentage of the final grade and includes specific learning objectives and expected outcomes accomplished through a review of literature, writing assignments, and oral presentations. Using research questions, small groups probe the multiple causes of world hunger. This phase emphasizes effective library research strategies and evaluative criteria for selecting credible references. In addition, accurate interpretation of statistical data is emphasized. Students work collaboratively with our campus outreach program to plan, organize, implement, and evaluate two service events—a citywide food drive supporting our local food pantry and a hunger banquet. The group reflection component examines results from these events and allows students to voice personal insights about the project and its value to our local community. The service-learning component enhances student understanding of world hunger through effective library research, allows students to participate in a project whose need is identified by the community, enables them to reflect upon personal growth, and supports assessment of the learning outcomes identified in course objectives.

SIGIR 2003 workshop on distributed information retrieval

During the last decade companies, governments, and research groups worldwide have directed significant effort towards the creation of sophisticated digital libraries across a variety of disciplines. As digital libraries proliferate, in a variety of media, and from a variety of sources, problems of resource selection and data fusion become major obstacles. Traditional search engines, even very large systems such as Google, are unable to provide access to the “Hidden Web” of information that is only available via digital library search interfaces. Effective, reliable information retrieval also requires the ability to pose multimedia queries across many digital libraries. The answer to a query about the lyrics to a folk song might be text or an audio recording, but few systems today could deliver both data types in response to a single, simple query. Distributed Information Retrieval addresses issues that arise when people have routine access to thousands of multimedia digital libraries.