Browsing by Subject "Data analysis"

Now showing 1 - 7 of 7

Open Access
Architectural requirements for energy efficient execution of graph analytics applications
(IEEE, 2015-11) Özdal, Muhammet Mustafa; Yeşil, Şerif; Kim, T.; Ayupov, A.; Burns, S.; Öztürk, Özcan
Intelligent data analysis has become more important in the last decade especially because of the significant increase in the size and availability of data. In this paper, we focus on the common execution models and characteristics of iterative graph analytics applications. We show that the features that improve work efficiency can lead to significant overheads on existing systems. We identify the opportunities for custom hardware implementation, and outline the desired architectural features for energy efficient computation of graph analytics applications. © 2015 IEEE.
Open Access
Cognitive activity detection and tracing system
(KARE Publishing, Kare Yayıncılık, 2023-08-01) Yıldırım, Onur; Kandemir, Çağla; Kardaşlar, Emre; Sümer, Emre
Cognitive problems like Dementia and Alzheimer’s are usually challenging to diagnose but can be noticed by some signs of their symptoms. The most common symptoms are confusion, trouble finding the right word, memory loss, and difficulty concentrating. This study aims to design a cognitive activity detection and tracing system that contains games and analyzes users’ performances then displays detailed statistics to the users. The proposed Cognitive Activity Detection and Tracing System (CADTS) is software that contains different kinds of games from different categories inside its body that aims to measure cognitive activity by utilizing formulations in the context of the games and give feedback to users concerning the performance analyses done. The purpose of these analyses is to catch the signs of symptoms. An insight into a possible scoring system is provided, and as our results, several descriptive statistics are shared based on the tests conducted.
Open Access
Development of a shiny application for comparative transcriptomics and differential gene expression analysis
(2022-09) Leka, Ronaldo
RNA sequencing has proven to be an effective technique for divulging information about the transcriptome in molecular biology research. Compared to microarrays and early methods of cDNA sequencing, high-throughput RNA sequencing has better resolution, low background noise, a higher range to quantify gene expression, and relatively lower cost. The development of sequencing technique has led to the development of tools for analyzing the high volume of data that is generated. Statistical methods for normalizing, filtering, performing exploratory and differential analysis, and other functional analyses based on RNA sequencing count data have made RNA sequencing one of the most popular techniques in genomics. To help facilitate the use of such statistical tools, web applications developed in R using the shiny package offer an advantageous environment where researchers can use a graphical interface to give inputs and instructions to the underlying server-side libraries that analyze and generate results in tables and plots. This thesis presents a new tool that has been developed for exploratory analysis, data normalization and filtering, differential gene expression analysis (DGEA), correlation analysis, principal component analysis, and functional analysis such as over-representation analysis and gene set enrichment analysis. When compared to other available applications, this new application offers the ability to run multiple methods for DGEA and compare results between them, leading to the output of gene sets that are discovered as DEGs in multiple tests. Here I present the features of this application in detail where I aim to improve upon the applications that are available in the literature. An example dataset from our lab was also investigated by this RNA-seq tool leading to a better understanding of Mineralocorticoid Receptor (MR) signaling in breast cancer.
Open Access
Diverse sequence search and alignment
(2013) Eser, Elif
Sequence similarity tools, such as BLAST, seek sequences from a database most similar to a query. They return results signi cantly similar to the query sequence that are typically also highly similar to each other. Most sequence analysis tasks in bioinformatics require an exploratory approach where the initial results guide the user to new searches. However, diversity has not been considered as an integral component of sequence search tools yet. Repetitions in the result can be avoided by introducing non-redundancy during database construction; however, it is not feasible to dynamically set a level of non-redundancy tailored to a query sequence. We introduce the problem of diverse search and browsing in sequence databases that produces non-redundant results optimized for any given query. We de ne diversity measures for sequences, and propose methods to obtain diverse results extracted from current sequence similarity search tools. We propose a new measure to evaluate the diversity of a set of sequences that is returned as a result of a similarity query. We evaluate the e ectiveness of the proposed methods in post-processing PSI-BLAST results. We also assess the functional diversity of the returned results based on available Gene Ontology annotations. Our experiments show that the proposed methods are able to achieve more diverse yet similar result sets compared to static non-redundancy approaches. In both sequence based and functional diversity evaluation, the proposed diversi cation methods outperform original BLAST results signi cantly. We built an online diverse sequence search tool Div-BLAST that supports queries using BLAST web services. It re-ranks the results diversely according to given parameters.
Open Access
The impact of democracy and media freedom on under-5 mortality, 1961–2011
(Elsevier Ltd, 2017) Wigley, S.; Akkoyunlu-Wigley, A.
Do democracies produce better health outcomes for children than autocracies? We argue that (1) democratic governments have an incentive to reduce child mortality among low-income families and (2) that media freedom enhances their ability to deliver mortality-reducing resources to the poorest. A panel of 167 countries for the years 1961–2011 is used to test those two theoretical claims. We find that level of democracy is negatively associated with under-5 mortality, and that that negative association is greater in the presence of media freedom. These results are robust to the inclusion of country and year fixed effects, time-varying control variables, and the multiple imputation of missing values.
Open Access
PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways
(Oxford University Press, 2002-06) Demir, Emek; Babur, Özgün; Doğrusöz, Uğur; Gürsoy, Atilla; Nişancı, Gürkan; Çetin Atalay, Rengül; Öztürk, Mehmet
Motivation: Availability of the sequences of entire genomes shifts the scientific curiosity towards the identification of function of the genomes in large scale as in genome studies. In the near future, data produced about cellular processes at molecular level will accumulate with an accelerating rate as a result of proteomics studies. In this regard, it is essential to develop tools for storing, integrating, accessing, and analyzing this data effectively. Results: We define an ontology for a comprehensive representation of cellular events. The ontology presented here enables integration of fragmented or incomplete pathway information and supports manipulation and incorporation of the stored data, as well as multiple levels of abstraction. Based on this ontology, we present the architecture of an integrated environment named PATIKA (Pathway Analysis Tool for Integration and Knowledge Acquisition). PATIKA is composed of a server-side, scalable, object-oriented database and client-side editors to provide an integrated, multi-user environment for visualizing and manipulating network of cellular events. This tool features automated pathway layout, functional computation support, advanced querying and a user-friendly graphical interface. We expect that PATIKA will be a valuable tool for rapid knowledge acquisition, microarray generated large-scale data interpretation, disease gene identification, and drug development.
Open Access
PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways
(American Society for Biochemistry and Molecular Biology(ASBMB), 2002-09) Demir, Emek; Babur, Özgün; Doğrusöz, Uğur; Gürsoy, Atilla; Nişancı, Gürkan; Çetin Atalay, Rengül; Öztürk, Mehmet