Papers by Mehmet Dalkilic
Computing and Informatics, 2017
Distributed storage systems store some redundant data to keep the degree of availability of the s... more Distributed storage systems store some redundant data to keep the degree of availability of the stored data constant and also to increase the system's resistance against failures. This type of systems usually use pure replication or methods based on RAID systems as redundancy schemes. In this paper, we study the communication cost of a distributed data storage system using Maximum Distance Separable (MDS) erasure codes. Our focus is reduction of the cost of one-tomany communication used in data reconstruction/repair initialization and update operations. We propose the use of two different communication approaches on the area of distributed storage systems for the above operations; Steiner tree approach and multi-shortest path approach. We also analyse these two communication approaches empirically and theoretically. Our theoretical results indicate that Steiner tree approach has lower message usage, whereas, multi-shortest path approach has lower time usage for data reconstruction/repair initialization operations. On the other hand, Steiner tree approach has better message and time metrics for the data update process. Furthermore, our experimental results support these theoretical results. Thus, users can choose between the two approaches depending on their needs and priorities.
This paper mainly proposes a design for a communication infrastructure for Wireless Sensor Networ... more This paper mainly proposes a design for a communication infrastructure for Wireless Sensor Networks. The proposed design prevents message collisions by arranging the time schedules to send, receive, forward and overhear packets of the nodes considering 2-hop graph coloring mechanism. The system aims to exclude the compromised nodes in the network using the overhearing mechanism, and copes with recovering the paths of the legitimate nodes using multipath redundancy. The proposed scheduling-based and overhearing supported infrastructure brings the advantage of providing the Sensor Networks with both reliable communication using backup paths and energy conservation by preventing the collisions.
Advances in information security, privacy, and ethics book series, 2013
Wireless sensor network (WSN) is a promising technology that has attracted the interest of the re... more Wireless sensor network (WSN) is a promising technology that has attracted the interest of the research in the last decade. Security is one of the fundamental issues in sensor networks since sensor nodes are very resource constrained. An attacker may modify, insert and delete new hardware and software components to the system where a single node, a specific part of the sensing area and the whole network may become inoperable. Thus, the design of early attack detection and defense mechanisms must be carefully considered. In this chapter, we survey attacks and their defense mechanisms in WSNs. Attacks are categorized according to the related protocol layer. We also investigate the open research issues and emerging technologies on security in WSNs.
The weak and the strong password preferences
Proceedings of the 3rd international conference on Security of information and networks - SIN '10, 2010
Considering the computer authentication, any password shall not only be private to its owner but ... more Considering the computer authentication, any password shall not only be private to its owner but also be chosen as not to be predicted easily by others. The passwords used in authentication processes of any critical system should be strong as not to be cracked easily. In this context, the strong password choice gets significance for the general system security. This study aims to reveal the proper and improper properties on password preferences via examining the real samples. The method used in this work is first to gather the real passwords in plaintext, then to crack the encrypted forms of them and finally to investigate statistical queries on those passwords in order to distinguish the common weak and strong characteristics. As the case study, the experiments are conducted on real passwords of Turkish users in an actively running system. The results of the experiments are categorized for weak and strong passwords. Moreover, the common tendencies on password choice are evaluated.
Theory and Practice of Cryptography Solutions for Secure Information Systems
Advances in electronics and wireless communication technologies have enabled the development of l... more Advances in electronics and wireless communication technologies have enabled the development of large-scale wireless sensor networks (WSNs). There is numerous applications for wireless sensor networks, and security is vital for many of them. However, WSNs suffer from many constraints, including low computation capability, small memory, limited energy resources, susceptibility to physical capture, the lack of infrastructure, which impose unique security challenges and make innovative approaches desirable. In this paper we present a survey of security issues in WSNs, address the state of the art in research on sensor network security, and discuss some future directions for research.
This paper introduces a measurement ontology for applications to semantic Web applications, speci... more This paper introduces a measurement ontology for applications to semantic Web applications, specifically for emerging domains such as microarray analysis. The semantic Web is the nextgeneration Web of structured data that are automatically shared by software agents, which apply definitions and constraints organized in ontologies to correctly process data from disparate sources. One facet needed to develop semantic Web ontologies of emerging domains is creating ontologies of concepts that are common to these domains. These general, "common-sense" ontologies can be used as building blocks to develop more domain-specific ontologies. However most measurement ontologies concentrate on representing units of measurement and quantities, and not on other measurement concepts such as sampling, mean values, and evaluations of quality based on measurements. In this paper, we elaborate on a measurement ontology that represents all these concepts. We present the generality of the ontology, and describe how it is developed, used for analysis and validated.
Proceedings of the 2005 ACM symposium on Applied computing - SAC '05, 2005
We present a new application for experimental biologists, the Curation Alignment Tool for Protein... more We present a new application for experimental biologists, the Curation Alignment Tool for Protein Analysis (CATPA), that allows for the efficient and effective creation, storage, management, and querying of experimentally curated protein families. As the number of discovered genomic and proteomic sequences outpaces our ability to understand them, the experimental biologist, who is our primary link in fundamentally and essentially understanding genomic and proteomic information, is left further behind in our race to automate and semi-automate information discovery.
Estimation of Variation within Transcriptome de novo Assemblies, co-assemblies of Paralogs, Heterozygosity or Polyploidy Possibly Accumulated Within the Isotigs of a Newbler Assembly
Transcriptome references built from sequencing reads provide foundations for gene discovery and f... more Transcriptome references built from sequencing reads provide foundations for gene discovery and functional genomics studies, sequence-based marker development and quantitative expression analysis, especially in species and accessions lacking the benefit of a whole genome reference. Use of a common set of assembly parameters cannot adequately account for the breadth of natural diversity among transcriptome profiles, and yet most commonly, consensus transcript sequences are not further scrutinized. Most notably with sequence data from heterozygotes, polyploids, and taxa with large gene families, transcript assemblers sometimes compress sets of paralogs, homoeologs and/or alleles into a single isotig, or transcript, leading to an incorrect picture of the gene expression profile. Here we describe an algorithm that estimates variation lost in an isotig consensus sequence, defined as error within the isotigs during assembly. Single nucleotide polymorphisms are called after mapping back to...
A new set of Random Forests with varying dynamic data reduction and voting techniques
2014 International Conference on Data Science and Advanced Analytics (DSAA), 2014
Studying the Milky Way Galaxy Using ParaHeap-k
Computer, 2014
ABSTRACT
DSQL — An SQL for Structured Documents Extended Abstract
Lecture Notes in Computer Science, 2002
ABSTRACT
Proceedings of the 2005 ACM symposium on Applied computing - SAC '05, 2005
We present Circle, a classification algorithm based on the priciples of boolean function minimmiz... more We present Circle, a classification algorithm based on the priciples of boolean function minimmization. This classification process uses a recursive method to generate a set of impli-
ICARCV 2004 8th Control, Automation, Robotics and Vision Conference, 2004., 2004
We present a novel classifier based upon principles of logic-theoretic Boolean function minimizat... more We present a novel classifier based upon principles of logic-theoretic Boolean function minimization. The classifier, called Circle, recursively produces a set of implicants (or rules). The implicant set contains information not only about the presence of features, but also about their absence in determining class values. Thus, Circle's implicant set is initially non-monotonic with respect to inserting new tuples that have feature values that were not in the training set. One important benefit of this non-monotonicity, however, is that Circle is capable of being robust in the presence of novel feature values. We have created a full implementation of Circle using Java as a host language and Oracle database backend. Because we are interested in data mining in bioinformatics, particularly genomic data, the database was borne out of necessity to both manage and effectively query the information.
Journal of Database Management, 2000
This paper introduces a measurement ontology for applications to semantic Web applications, speci... more This paper introduces a measurement ontology for applications to semantic Web applications, specifically for emerging domains such as microarray analysis. The semantic Web is the nextgeneration Web of structured data that are automatically shared by software agents, which apply definitions and constraints organized in ontologies to correctly process data from disparate sources. One facet needed to develop semantic Web ontologies of emerging domains is creating ontologies of concepts that are common to these domains. These general, "common-sense" ontologies can be used as building blocks to develop more domain-specific ontologies. However most measurement ontologies concentrate on representing units of measurement and quantities, and not on other measurement concepts such as sampling, mean values, and evaluations of quality based on measurements. In this paper, we elaborate on a measurement ontology that represents all these concepts. We present the generality of the ontology, and describe how it is developed, used for analysis and validated.
The weak and the strong password preferences
Proceedings of the 3rd international conference on Security of information and networks - SIN '10, 2010
Considering the computer authentication, any password shall not only be private to its owner but ... more Considering the computer authentication, any password shall not only be private to its owner but also be chosen as not to be predicted easily by others. The passwords used in authentication processes of any critical system should be strong as not to be cracked easily. In this context, the strong password choice gets significance for the general system security. This study aims to reveal the proper and improper properties on password preferences via examining the real samples. The method used in this work is first to gather the real passwords in plaintext, then to crack the encrypted forms of them and finally to investigate statistical queries on those passwords in order to distinguish the common weak and strong characteristics. As the case study, the experiments are conducted on real passwords of Turkish users in an actively running system. The results of the experiments are categorized for weak and strong passwords. Moreover, the common tendencies on password choice are evaluated.
A Survey on Security in Wireless Sensor Networks
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Papers by Mehmet Dalkilic