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36th Annual International conference of the ieee-Engineering-in-Medicine-and-biology-Society (EMBC)

作者： Guersoy, Gamze Xu, Yun Liang, Jie Univ Illinois Bioinformat Program Dept Bioengn Chicago IL 60607 USA

ISBN: (纸本)9781424479290

Knowledge of the global architecture of the cell nucleus and the spatial organization of genome is critical for understanding gene expression and nuclear function. Single-cell imaging techniques provide a wealth of information on the spatial organization of chromosomes. computational tools for modelling chromosome structure have broad implications in studying the effect of cell nucleus on higher-order genome organization. Here we describe a multichromosome constrained self-avoiding chromatin model for studying ensembles of genome structural models of budding yeast nucleus. We successfully generated a large number of model genomes of yeast with appropriate chromatin fiber diameter, persistence length, and excluded volume under spatial confinement. By incorporating details of the constraints from single-cell imaging studies, our method can model the budding yeast genome realistically. The model developed here provides a general computational framework for studying the overall architecture of budding yeast genome.

关键词： bioinformatics Biological cells computational modeling Computer architecture Genomics Microprocessors Organizations

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Editorial

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ieee-ACM TRANSACTIONS ON computational biology AND bioinformatics 2019年第2期16卷 350-351页

作者： Zhou, Shuigeng Chen, Yi-Ping Phoebe Mamitsuka, Hiroshi Fudan Univ Sch Comp Sci Shanghai Key Lab Intelligent Informat Proc Shanghai 200433 Peoples R China La Trobe Univ Dept Comp Sci & Informat Technol Melbourne Vic 3086 Australia Kyoto Univ Inst Chem Res Bioinformat Ctr Kyoto 6068501 Japan

This special section consists of eight papers selected from the accepted papers of the 27th International conference on Genome Informatics (GIW2016), which was held in Shanghai, China, October 3-5, 2016. These papers cover diverse topics, including gene clustering, protein-protein interaction network inference, essential proteins identification, glycan structure identification, lncRNA function prediction, lncRNA-disease association prediction, signal transduction network construction, and parallel algorithms.

关键词： Special Issues And Sections bioinformatics Computer Science Inference Algorithms Gene Expression Microwave Integrated Circuits Proteins Genomics Parallel Algorithms

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Applied informatics: A paradigm shift in artificial embryonic systems development 16

Applied informatics: A paradigm shift in artificial embryoni...

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16th ieee International Symposium on computational intelligence and Informatics (CINTI)

作者： Csaba, Szasz Tech Univ Cluj Dept Elect Machines & Drives Cluj Napoca Romania

ISBN: (纸本)9781467385206

As it is well known, the synthesis of sophisticated cellular biology processes in artificial silicon structures is quoted as one of today's most highly ranked scientific challenges. However, the failure of most approaches which try to faithfully model cellular biology represents a major impediment which inhibits rapid progress in artificial biological structures development. In other words, the main obstacle seems to be the impossibility to full comprehend biological cell processes evolution and growth in their entirety and especially because of the lack of a precise and authentically models being to reproduce with high fidelity cellular and embryonic phenomena's. In an attempt to devise a model which more closely mimics cellular biology, this paper discusses an original artificial organism model, developed upon a two-layer coarse-fine-grid network approach. The strength of this approach is that it endeavors to capture the complexity of both the cellular networks as well as that of the biological cell itself, by implementing the internal biological phenomena of an organism into a two different network topology hardware layer. In essence, this model not only keeps the full advantages of previously created models that enable the implementation of similar self-replicating or self-repairing, abilities akin to those expressed by its cellular equivalents in nature, but there (according to the nature of cell biology) the inherent need of artificial cell structures to fulfill the entire role of a biological cell in the network is also expressed. At this stage of the research, the main goal it was to demonstrate that the chosen configuration operates correctly and supports the modeling assumptions. Not least of all, such architectures are suitable to deliver useful information about a wide range of imitated cellular processes in a short time and could become a helpful framework for researchers to confirm theoretical principles and experimental work quickly, with the full adv

关键词： bioinformatics embryonic system artificial cell coarse-fine-grid network artificial organism

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Curriculum for a New Five-Year Academic Program in Intelligent Systems Engineering and Software Engineering

Curriculum for a New Five-Year Academic Program in Intellige...

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International conference on computational Science and computational intelligence (CSCI)

作者： Solo, Ashu M. G. Maverick Trailblazers Inc Wilmington DE 19805 USA

ISBN: (纸本)9798350361513;9798350372304

This research paper proposes a curriculum for a five-year academic program with a bachelor's degree (honors) in intelligent systems engineering and software engineering and a master's degree in intelligent systems engineering and software engineering. This program includes courses in data structures, compiler design, operating system design, firmware design, database systems, computer graphics and virtual reality design, static and dynamic website design, development of chatbots and voice assistants, software engineering methodology, knowledge-based systems, fuzzy logic, neural networks, evolutionary computation, evolutionary multiojective optimization, machine learning, image processing, computer vision, pattern recognition, voice recognition, natural language processing, data science, control systems, intelligent control systems, robotics, digital signal processing, mathematics, engineering physics, biology, etc. These degrees will allow graduates to have a good understanding of all of the main branches of intelligent systems engineering and software engineering as well as other relevant subjects in electrical and computer engineering.

关键词： education intelligent systems computational intelligence soft computing artificial intelligence machine learning software development firmware development

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Variations on breast density and subtlety of the findings require different computational intelligence pipelines for the diagnosis of clustered microcalcifications

Variations on breast density and subtlety of the findings re...

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ieee 13th International conference on bioinformatics and Bioengineering (BIBE)

作者： Andreadis, Ioannis I. Spyrou, George M. Ligomenides, Panos A. Nikita, Konstantina S. Natl Tech Univ Athens Sch Elect & Comp Engn Athens 15573 Greece Acad Athens Athens Greece Biomed Res Fdn Acad Athens Greece

ISBN: (纸本)9781479931637

In this work, we study the factors that influence the efficacy of a proposed Computer Aided Diagnosis (CADx) framework for the diagnosis of clustered microcalcifications (MCs) using a large dataset of mammograms containing cases of varying breast density and findings' subtlety. The reported results indicate that the proposed framework performs towards the right direction, as it appears high classification performance (A(z)=0.909) for specific subsets of cases, while outperforming at the same time the performance of the radiologists who evaluated the same cases. The effect of the initial enhancement of mammograms in the CADx pipeline is then investigated, by applying three different image enhancement techniques on several subsets of mammograms. We observed that for the considered subsets of dense mammograms, a wavelet-based enhancement algorithm outperformed the rest and provided superior classification performance (A(z)=0.849). We indicate therefore that the density of the breast determines the need of different computational algorithms for the analysis of a mammogram and as a result the a priori knowledge of this factor may be exploited for the optimization of the diagnostic process.

关键词： artificial intelligence image classification image enhancement mammography medical image processing pipeline processing radiology wavelet transforms

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I/O induced scalability limits of bioinformatics applications

I/O induced scalability limits of bioinformatics application...

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7th ieee International conference on bioinformatics and Bioengineering, BIBE

作者： Henschel, Robert Müller, Matthias S. 01062 Dresden Germany

ISBN: (纸本)1424415098

The growing size of sequence, protein and other biological databases results in an increased computational complexity of the analysis process. Often parallelization is the only solution to limit the turnaround time within reasonable limits. Most scalability studies focus on the parallel algorithm and the resulting communication and synchronization patterns of the implementations. In this paper we examine to what extend I/O bottlenecks limit the scalability on current and future architectures. We study the behavior of two different bioinformatics applications (THREADER, HMMER) and show that these applications are representatives of two different classes with distinct I/O profiles and demands. ©2007 ieee.

关键词： Scalability

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Performance evaluation of clustering algorithms on microcalcifications as mammography findings

Performance evaluation of clustering algorithms on microcalc...

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ieee 13th International conference on bioinformatics and Bioengineering (BIBE)

作者： Ikonomakis, Emmanouil K. Spyrou, George M. Ligomenides, Panos A. Vrahatis, Michael N. Univ Patras Dept Math Computat Intelligence Lab CILab GR-26110 Patras Greece Acad Athens Biomed Res Fdn Biomed Informat Unit Athens 11527 Greece

ISBN: (纸本)9781479931637

Breast cancer can be prevented with regular mammography screening. Yet, the incorporation of computational intelligence relies on training classifiers on a set of predefined Regions of Interest (ROIs). Data Clustering has been applied to address the problem of ROI detection, yet no extensive research has been carried out on which algorithm to utilize. This contribution focuses on microcalcification clustering as a Data Clustering application, giving insights concerning the performance of three main clustering algorithms.

关键词： cancer image classification mammography medical image processing object detection pattern clustering performance evaluation

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IAS: Interaction Specific GO Term Associations for Predicting Protein-Protein Interaction Networks

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ieee-ACM TRANSACTIONS ON computational biology AND bioinformatics 2018年第4期15卷 1247-1258页

作者： Yerneni, Satwica Khan, Ishita K. Wei, Qing Kihara, Daisuke Mayo Clin Div Biomed Stat & Informat Rochester MN 55905 USA Purdue Univ Dept Comp Sci W Lafayette IN 47906 USA Purdue Univ Dept Biol Sci W Lafayette IN 47906 USA

Proteins carry out their function in a cell through interactions with other proteins. A large scale protein-protein interaction (PPI)network of an organism provides static yet an essential structure of interactions, which is valuable clue for understanding the functions of proteins and pathways. PPIs are determined primarily by experimental methods;however, computational PPI prediction methods can supplement or verify PPIs identified by experiment. Here, we developed a novel scoring method for predicting PPIs from Gene Ontology (GO) annotations of proteins. Unlike existing methods that consider functional similarity as an indication of interaction between proteins, the new score, named the protein-protein Interaction Association Score (IAS), was computed from GO term associations of known interacting protein pairs in 49 organisms. IAS was evaluated on PPI data of six organisms and found to outperform existing GO term-based scoring methods. Moreover, consensus scoring methods that combine different scores further improved performance of PPI prediction.

关键词： bioinformatics proteins computational systems biology biological interactions

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IPRIns: A tool with the improved precision and recall for insertion detection in the human genome 9

IPRIns: A tool with the improved precision and recall for in...

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9th ieee International conference on bioinformatics and computational biology, ICBCB 2021

作者： Piwluang, Sakkayaphab Wichadakul, Duangdao Software Engineering Program Faculty of Engineering Chulalongkorn University Department of Computer Engineering Bangkok Thailand Faculty of Engineering Chulalongkorn University Department of Computer Engineering Bangkok Thailand

ISBN: (纸本)9780738132020

An insertion is a specific type of the structural variations. The identification of insertions in a human genome is essential for the study of diseases or their functional effects. There are many tools available for identifying the insertion type with different methods and strategies. However, most of them could not deliver both good recall and precision, especially for the real datasets sequenced with the paired-end short reads. In this paper, we propose iPRIns, a new computational method for detecting insertions aiming to improve both precision and recall. The proposed method with discovering and filtering processes outperformed all other three tools for 5 out of 10 real datasets, the variations of NA12878, for both precision and recall. iPRIns is released under the open-source GPLv3 license. The source code and documentation are available at https://***/cucpbioinfo/iPRIns. © 2021 ieee.

关键词： bioinformatics

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Service-oriented science: Scaling eScience impact - (Abstract) 06

Service-oriented science: Scaling eScience impact - (Abstrac...

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ieee/WIC/ACM International conference on Intelligent Agent Technology

作者： Foster, Ian Univ Chicago Computat Inst Argonne Natl Lab Chicago IL 60637 USA

ISBN: (纸本)9780769527482

computational approaches to problem solving have proven their worth in many fields of science, allowing the collection and analysis of unprecedented quantities of data, and the exploration via simulation of previously obscure phenomena. New "systems" approaches in fields as diverse as biology [12], earthquake science [11], and environmental science [3] are enabled by, and are spurring the further development of, such computational approaches. But as computational and system-level science methods become increasingly sophisticated, we must ask: how do we scale their impact, from the specialist to entire communities [7]?

关键词： biology computing Biological system modeling Earthquakes Information technology Service oriented architecture Earth Laboratories Problem-solving computational modeling Analytical models

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