Journal of Computer Science & Systems Biology, 2015
We consider a synchronous Boolean organism consisting of N cells arranged in a circle, where each... more We consider a synchronous Boolean organism consisting of N cells arranged in a circle, where each cell initially takes on an independently chosen Boolean value. During the lifetime of the organism, each cell updates its own value by responding to the presence (or absence) of diversity amongst its two neighbours' values. We show that if all cells eventually take a value of 0 (irrespective of their initial values) then the organism necessarily has a cell count that is a power of 2. In addition, the converse is also proved: if the number of cells in the organism is a proper power of 2, then no matter what the initial values of the cells are, eventually all cells take on a value of 0 and then cease to change further. We argue that such an absence of structure in the dynamical properties of the organism implies a lack of adaptiveness, and so is evolutionarily disadvantageous. It follows that as the organism doubles in size (say from m to 2m) it will necessarily encounter an intermediate size that is a proper power of 2, and suffers from low adaptiveness. Finally we show, through computational experiments, that one way an organism can grow to more than twice its size and still avoid passing through intermediate sizes that lack structural dynamics, is for the organism to depart from assumptions of homogeneity at the cellular level.
IEEE GLOBECOM 2008 - 2008 IEEE Global Telecommunications Conference, 2008
Abstractó Modern mobile ad-hoc networks (MANETs) fre- quently consist of nodes which exhibit a wi... more Abstractó Modern mobile ad-hoc networks (MANETs) fre- quently consist of nodes which exhibit a wide range of au- tonomy needs. This is particularly true in the settings where MANETs are most compelling, i.e. battleeld, response & rescue, and contexts requiring rapid deployment of mobile users. The time-critical nature of the underlying circumstances frequently requires deployment of both manned and unmanned
A major obstacle in functional near infrared spectroscopy (fNIRS) and imaging is poor optical con... more A major obstacle in functional near infrared spectroscopy (fNIRS) and imaging is poor optical contact of the optodes with the scalp due to obstruction by hair. To overcome this problem a novel brush-fiber extension was made as an attachment to existing commercial flat-face fiber bundle optodes. The goal was that the brush-fiber extension would thread through hair and improve optical
Functional near infrared (fNIR) imaging was used to identify spatiotemporal relations between spa... more Functional near infrared (fNIR) imaging was used to identify spatiotemporal relations between spatially distinct cortical regions activated during various hand and arm motion protocols. Imaging was performed over a field of view (FOV, 12 x 8.4 cm) including the secondary motor, primary sensorimotor, and the posterior parietal cortices over a single brain hemisphere. This is a more extended FOV than typically used in current fNIR studies. Three subjects performed four motor tasks that induced activation over this extended FOV. The tasks included card flipping (pronation and supination) that, to our knowledge, has not been performed in previous functional magnetic resonance imaging (fMRI) or fNIR studies. An earlier rise and a longer duration of the hemodynamic activation response were found in tasks requiring increased physical or mental effort. Additionally, analysis of activation images by cluster component analysis (CCA) demonstrated that cortical regions can be grouped into clust...
Background: Outbreaks of hepatitis C virus (HCV) infection have been reported in HIV-positive men... more Background: Outbreaks of hepatitis C virus (HCV) infection have been reported in HIV-positive men who have sex with men (MSM) in North America, Europe and Asia. Transmission is believed to be the result of exposure to blood during sexual contact. In those infected with HIV, acute HCV infection is more likely to become chronic, treatment for both HIV and HCV is more complicated and HCV disease progression may be accelerated. There is a need for systematic reviews and meta-analyses to synthesize the epidemiology, prevention and methods to control HCV infection in this population. Methods/design: Eligible studies will include quantitative empirical data related to sexual transmission of HCV in HIV-positive MSM, including data describing incidence or prevalence, and associations between risk factors or interventions and the occurrence or progression of HCV disease. Care will be taken to ensure that HCV transmission related to injection drug use is excluded from the incidence estimates. Scientific databases will be searched using a comprehensive search strategy. Proceedings of scientific conferences, reference lists and personal files will also be searched. Quality ratings will be assigned to each eligible report using the Newcastle-Ottawa scale. Pooled estimates of incidence rates and measures of association will be calculated using random effects models. Heterogeneity will be assessed at each stage of data synthesis. Discussion: HIV-positive MSM are a key HCV-affected population in the US and other high-income countries. This review seeks to identify modifiable risk factors and settings that will be the target of interventions, and will consider how to constitute a portfolio of interventions to deliver the greatest health benefit. This question must be considered in relation to the magnitude of HCV infection and its consequences in other key affected populations, namely, young prescription opioid users who have transitioned to illicit opiate injection, and older injection drug users among whom HCV prevalence and incidence are extremely high. This review is part of a series of systematic reviews and meta-analyses that will synthesize the evidence across all these population groups and develop recommendations and decision tools to guide public health resource allocation.
ABSTRACT Functional neurological imaging has been shown to be valuable in evaluating brain plasti... more ABSTRACT Functional neurological imaging has been shown to be valuable in evaluating brain plasticity in children with cerebral palsy (CP). In recent studies it has been demonstrated that functional near-infrared spectroscopy (fNIRS) is a viable and sensitive method for imaging motor cortex activities in children with CP. However, during unilateral finger tapping tasks children with CP often exhibit mirror motions (unintended motions in the non-tapping hand), and current fNIRS image formation techniques do not account for this. Therefore, the resulting fNIRS images contain activation from intended and unintended motions. In this study, cortical activity was mapped with fNIRS on four children with CP and five controls during a finger tapping task. Finger motion and arm muscle activation were concurrently measured using motion tracking cameras and electromyography (EMG). Subject-specific regressors were created from motion capture and EMG data and used in a general linear model (GLM) analysis in an attempt to create fNIRS images representative of different motions. The analysis provided an fNIRS image representing activation due to motion and muscle activity for each hand. This method could prove to be valuable in monitoring brain plasticity in children with CP by providing more consistent images between measurements. Additionally, muscle effort versus cortical effort was compared between control and CP subjects. More cortical effort was required to produce similar muscle effort in children with CP. It is possible this metric could be a valuable diagnostic tool in determining response to treatment.
2008 3rd International Conference on Malicious and Unwanted Software (MALWARE), 2008
In this paper, we present a new implicit encoding technique that makes use of lower-layer packet ... more In this paper, we present a new implicit encoding technique that makes use of lower-layer packet reordering to superimpose covert messages onto a reliable data stream. In particular, since the TCP layer provides a reliable inorder data stream over the unreliable network layer's IP datagram service, we can encode covert messages by artificially permuting IP packets before they leave the source and reading the permutation at the destination prior to delivering the payload to TCP. Applying such permutations will not adversely affect TCP's ability to reconstitute the transport layer data stream, since TCP is designed to be robust against out of order network layer packet delivery. We describe the design and operation of PERMEATE, an open-source covert channel toolkit which implements such a permutational covert channel over TCP, and we provide a quantitative assessment of it's efficacy and efficiency as a covert channel.
2008 International Wireless Communications and Mobile Computing Conference, 2008
We present a new dynamic scheme which continuously redistributes a fixed power budget among mobil... more We present a new dynamic scheme which continuously redistributes a fixed power budget among mobile wireless nodes participating in a multi-hop wireless connection, with the objective of maximizing the expected lifetime of the connection. Our experimental simulations indicate that the proposed power budget distribution scheme yields a significant increase in connection lifetime. We quantify the sensitivity of the performance gains to various system parameters, including connection size, node density, power budget size, and mean node velocities. We then compare the efficacy of our scheme with two schemes: one that simply distributes the power budget uniformly, and one that distributes the power budget dynamically with the objective of minimizing end-to-end bit error rate (BER). In comparing the relative performance of the three schemes we obtain a qualitative assessment of the inherent oppositions and tradeoffs between the objectives of BER minimization and lifetime maximization.
In this paper, we propose a non-commutative keyexchange scheme which generalizes the classical El... more In this paper, we propose a non-commutative keyexchange scheme which generalizes the classical ElGamal Cipher to polycyclic groups. We describe the criteria for groups which would provide good candidates for such cryptosystems, we also examine the complexity of the decision problems related to these key exchange.
Proceedings of the 2007 international conference on Wireless communications and mobile computing, 2007
Ghassen Brahim, Ala Al-Fuquaha, Dionisyios Kountanis Dept. of Computer Science, Western Michigan ... more Ghassen Brahim, Ala Al-Fuquaha, Dionisyios Kountanis Dept. of Computer Science, Western Michigan University Kalamazoo, MI., 49009 [email protected] ... Bilal Khan Dept. of Mathematics and Computer Science, John Jay College of Criminal Justice 899 Tenth ...
2008 Advanced Software Engineering and Its Applications, 2008
In the software development life cycle, maintenance is a key phase that determines long term and ... more In the software development life cycle, maintenance is a key phase that determines long term and effective use of any software. Maintenance can become very lengthy and costly for large software systems when structure of the system is complicated. One of the factors complicating the structure of the software system is subsystem boundaries becoming ambiguous due to system evolution, lack of up to date documentation and high turn over rate of software professionals (leading to non availability of original designers of the software systems). Software module clustering helps software professionals to recover high-level structure of the system by decomposing the system into smaller manageable subsystems, containing interdependent modules. Automated approaches simplify the software clustering process, which otherwise is quite a tedious task for medium and large software systems. We treat software clustering as an optimization problem and propose an automated technique to get near optimal decompositions of relatively independent subsystems, containing interdependent modules. We propose the use of self adaptive Evolution Strategies to search a large solution space consisting of modules and their relationships. We compare our proposed approach with a widely used genetic algorithm based approach on a number of test systems. Our proposed approach shows considerable improvement in terms of quality and effectiveness of the solutions for all tests cases.
... Bilal Khan and Shaleeza Sohail National University of Sciences and Technology (NUST) College ... more ... Bilal Khan and Shaleeza Sohail National University of Sciences and Technology (NUST) College of E & ME Department of Computer Engineering ... We were able to find very few research works in Soft-ware Clustering literature that has formally compared the consistency of the ...
The understanding of how the formation of metal nanoparticles in aqueous solutions is influenced ... more The understanding of how the formation of metal nanoparticles in aqueous solutions is influenced by the presence of presynthesized nanoparticles is important for precise control over size, shape, and composition of nanoparticles. New insights into the catalytic mechanism of Pt nanoparticles are gained by studying the formation of gold nanoparticles from the reduction of AuCl 4in aqueous solution in the presence of presynthesized Pt nanoparticles as a model system. The measurement of changes of the surface plasmon resonance band of gold nanoparticles, along with TEM analysis of particle size and morphology, provided an important means for assessing the reaction kinetics. The reductive mediation of Pt-H species on the Pt nanocrystal surface is believed to play an important role in the Pt-catalyzed formation of gold nanoparticles. This important physical insight is evidenced by comparison of the rates of the Pt-catalyzed formation of gold nanoparticles in the presence and in the absence of hydrogen (H 2), which adsorb dissociatively on a Pt nanocrystal surface forming Pt-H species. Pt-H effectively mediates the reduction of AuCl 4toward the formation of gold nanoparticles. Implications of the findings to the controllability over size, composition, and morphology of metal nanoparticles in the aqueous synthesis environment are also discussed.
There is considerable research relating the structure of Boolean networks to their state space dy... more There is considerable research relating the structure of Boolean networks to their state space dynamics. In this paper, we extend the standard model to include the effects of thermal noise, which has the potential to deflect the trajectory of a dynamical system within its state space, sending it from one stable attractor to another. We introduce a new "thermal robustness" measure, which quantifies a Boolean network's resilience to such deflections. In particular, we investigate the impact of structural homogeneity on two dynamical properties: thermal robustness and attractor density. Through computational experiments on cyclic Boolean networks, we ascertain that as a homogeneous Boolean network grows in size, it tends to underperform most of its heterogeneous counterparts with respect to at least one of these two dynamical properties. These results strongly suggest that during an organism's growth and morphogenesis, cellular differentiation is required if the organism seeks to exhibit both an increasing number of attractors and resilience to thermal noise.
In this paper, we describe how to construct physical computer network topologies which can suppor... more In this paper, we describe how to construct physical computer network topologies which can support the establishment of overlays that reduce or increase the distances between nodes. Reducing pairwise distances (i.e., compression) implies that the overlay enjoys significantly lower inter-node latencies compared to the ambient physical network; such an overlay can be used to implement a "high-performance mode" for disaster situations in which network responsiveness is of critical importance. On the other hand, increasing pairwise distances (i.e., expansion) implies that the overlay exhibits significantly higher inter-node latencies compared to the ambient physical network; such an overlay can be used to implement a brief "dilated state" in networks that have been infected by a malicious worm, where slowing down the infection spread allows greater time for antidote generation. We show that it is possible to design physical networks which support overlays whose logical link bandwidth is equal to the physical link bandwidth while providing arbitrarily high compression or expansion. We also show that it is possible to "grow" such networks over time in a scalable way, that is to say, it is possible to retain the compression/expansion properties while augmenting the network with new nodes, by making relatively small adjustments to the physical and overlay network structure.
We demonstrate the utility of functional near-infrared spectroscopy ͑fNIRS͒ as a tool for physici... more We demonstrate the utility of functional near-infrared spectroscopy ͑fNIRS͒ as a tool for physicians to study cortical plasticity in children with cerebral palsy ͑CP͒. Motor cortex activation patterns were studied in five healthy children and five children with CP ͑8.4± 2.3 years old in both groups͒ performing a finger-tapping protocol. Spatial ͑distance from center and area difference͒ and temporal ͑duration and time-to-peak͒ image metrics are proposed as potential biomarkers for differentiating abnormal cortical activation in children with CP from healthy pediatric controls. In addition, a similarity image-analysis concept is presented that unveils areas that have similar activation patterns as that of the maximum activation area, but are not discernible by visual inspection of standard activation images. Metrics derived from the images presenting areas of similarity are shown to be sensitive identifiers of abnormal activation patterns in children with CP. Importantly, the proposed similarity concept and related metrics may be applicable to other studies for the identification of cortical activation patterns by fNIRS.
International Journal of Algebra and Computation, 2007
In this paper we discuss a general approach to positive theories of groups. As an application we ... more In this paper we discuss a general approach to positive theories of groups. As an application we get a robust description of positive theories of groups with regular free Lyndon length function. Our approach combines techniques of infinite words (see [17, 3]), cancellation diagrams introduced in [14], and Merzlyakov's method [15].
ABSTRACT We propose two methods for aggregation of peer group topology in hierarchical ATM networ... more ABSTRACT We propose two methods for aggregation of peer group topology in hierarchical ATM networks. Both proposed aggregation methods transform a given peer group into a star graph representation. Our first approach optimally preserves, in a least square sense, the original costs of routing through the peer group. Our second approach assigns a weighted vector to the nucleus of the Logical Group Node, which quantifies the error in the compact representation. The two schemes are dual, in the sense that the first is best suited for peergroups where traffic patterns are unpredictable, and the second is suited for peergroups where traffic patterns can be characterized. Both the proposed schemes are practical: For peer groups with nodes V, links E, and n border nodes B ⊂ V, the approaches run in O(n|V|log|V| + n|E|+ poly(n)) time. The size of the final representation is small (linear in the number of border nodes) and can be computed efficiently. The scalability of the proposed algorithms makes them well-suited for use in practice. We also present a general method for measuring the degree of confidence in an aggregation scheme.
ABSTRACT This paper describes results from a network survey of Nain – a predominantly Inuit commu... more ABSTRACT This paper describes results from a network survey of Nain – a predominantly Inuit community of ~1200 people located on the northern coast of Labrador. As part of a larger social network research project, we used peer-referral sampling to recruit 330 residents for interviews about food sharing, housing, public health and community traditions. The peer-referral chains were analysed statistically to determine the presence and absence of social divisions in the community. The results of these analyses show that ethnic identification, relocation status and household income were the most significant social divisions in the community, while gender, education level and employment status show little or no effect on patterns of between-group interconnection. We argue that statistical patterns in the presence (and absence) of intergroup links offer novel ways to examine the interrelationship between recent economic development and the historical disruptions caused by Inuit community relocations in the 1950s.
String capsule endoscopy: a novel application for the preoperative identification of a small-bowe... more String capsule endoscopy: a novel application for the preoperative identification of a small-bowel obscure GI bleeding source (with video). ... Khan B, Ramirez FC, Shaukat M, Gilani N, Shah DK. ... Department of Gastroenterology, Phoenix VA Medical Center/Banner Good ...
Journal of Computer Science & Systems Biology, 2015
We consider a synchronous Boolean organism consisting of N cells arranged in a circle, where each... more We consider a synchronous Boolean organism consisting of N cells arranged in a circle, where each cell initially takes on an independently chosen Boolean value. During the lifetime of the organism, each cell updates its own value by responding to the presence (or absence) of diversity amongst its two neighbours' values. We show that if all cells eventually take a value of 0 (irrespective of their initial values) then the organism necessarily has a cell count that is a power of 2. In addition, the converse is also proved: if the number of cells in the organism is a proper power of 2, then no matter what the initial values of the cells are, eventually all cells take on a value of 0 and then cease to change further. We argue that such an absence of structure in the dynamical properties of the organism implies a lack of adaptiveness, and so is evolutionarily disadvantageous. It follows that as the organism doubles in size (say from m to 2m) it will necessarily encounter an intermediate size that is a proper power of 2, and suffers from low adaptiveness. Finally we show, through computational experiments, that one way an organism can grow to more than twice its size and still avoid passing through intermediate sizes that lack structural dynamics, is for the organism to depart from assumptions of homogeneity at the cellular level.
IEEE GLOBECOM 2008 - 2008 IEEE Global Telecommunications Conference, 2008
Abstractó Modern mobile ad-hoc networks (MANETs) fre- quently consist of nodes which exhibit a wi... more Abstractó Modern mobile ad-hoc networks (MANETs) fre- quently consist of nodes which exhibit a wide range of au- tonomy needs. This is particularly true in the settings where MANETs are most compelling, i.e. battleeld, response & rescue, and contexts requiring rapid deployment of mobile users. The time-critical nature of the underlying circumstances frequently requires deployment of both manned and unmanned
A major obstacle in functional near infrared spectroscopy (fNIRS) and imaging is poor optical con... more A major obstacle in functional near infrared spectroscopy (fNIRS) and imaging is poor optical contact of the optodes with the scalp due to obstruction by hair. To overcome this problem a novel brush-fiber extension was made as an attachment to existing commercial flat-face fiber bundle optodes. The goal was that the brush-fiber extension would thread through hair and improve optical
Functional near infrared (fNIR) imaging was used to identify spatiotemporal relations between spa... more Functional near infrared (fNIR) imaging was used to identify spatiotemporal relations between spatially distinct cortical regions activated during various hand and arm motion protocols. Imaging was performed over a field of view (FOV, 12 x 8.4 cm) including the secondary motor, primary sensorimotor, and the posterior parietal cortices over a single brain hemisphere. This is a more extended FOV than typically used in current fNIR studies. Three subjects performed four motor tasks that induced activation over this extended FOV. The tasks included card flipping (pronation and supination) that, to our knowledge, has not been performed in previous functional magnetic resonance imaging (fMRI) or fNIR studies. An earlier rise and a longer duration of the hemodynamic activation response were found in tasks requiring increased physical or mental effort. Additionally, analysis of activation images by cluster component analysis (CCA) demonstrated that cortical regions can be grouped into clust...
Background: Outbreaks of hepatitis C virus (HCV) infection have been reported in HIV-positive men... more Background: Outbreaks of hepatitis C virus (HCV) infection have been reported in HIV-positive men who have sex with men (MSM) in North America, Europe and Asia. Transmission is believed to be the result of exposure to blood during sexual contact. In those infected with HIV, acute HCV infection is more likely to become chronic, treatment for both HIV and HCV is more complicated and HCV disease progression may be accelerated. There is a need for systematic reviews and meta-analyses to synthesize the epidemiology, prevention and methods to control HCV infection in this population. Methods/design: Eligible studies will include quantitative empirical data related to sexual transmission of HCV in HIV-positive MSM, including data describing incidence or prevalence, and associations between risk factors or interventions and the occurrence or progression of HCV disease. Care will be taken to ensure that HCV transmission related to injection drug use is excluded from the incidence estimates. Scientific databases will be searched using a comprehensive search strategy. Proceedings of scientific conferences, reference lists and personal files will also be searched. Quality ratings will be assigned to each eligible report using the Newcastle-Ottawa scale. Pooled estimates of incidence rates and measures of association will be calculated using random effects models. Heterogeneity will be assessed at each stage of data synthesis. Discussion: HIV-positive MSM are a key HCV-affected population in the US and other high-income countries. This review seeks to identify modifiable risk factors and settings that will be the target of interventions, and will consider how to constitute a portfolio of interventions to deliver the greatest health benefit. This question must be considered in relation to the magnitude of HCV infection and its consequences in other key affected populations, namely, young prescription opioid users who have transitioned to illicit opiate injection, and older injection drug users among whom HCV prevalence and incidence are extremely high. This review is part of a series of systematic reviews and meta-analyses that will synthesize the evidence across all these population groups and develop recommendations and decision tools to guide public health resource allocation.
ABSTRACT Functional neurological imaging has been shown to be valuable in evaluating brain plasti... more ABSTRACT Functional neurological imaging has been shown to be valuable in evaluating brain plasticity in children with cerebral palsy (CP). In recent studies it has been demonstrated that functional near-infrared spectroscopy (fNIRS) is a viable and sensitive method for imaging motor cortex activities in children with CP. However, during unilateral finger tapping tasks children with CP often exhibit mirror motions (unintended motions in the non-tapping hand), and current fNIRS image formation techniques do not account for this. Therefore, the resulting fNIRS images contain activation from intended and unintended motions. In this study, cortical activity was mapped with fNIRS on four children with CP and five controls during a finger tapping task. Finger motion and arm muscle activation were concurrently measured using motion tracking cameras and electromyography (EMG). Subject-specific regressors were created from motion capture and EMG data and used in a general linear model (GLM) analysis in an attempt to create fNIRS images representative of different motions. The analysis provided an fNIRS image representing activation due to motion and muscle activity for each hand. This method could prove to be valuable in monitoring brain plasticity in children with CP by providing more consistent images between measurements. Additionally, muscle effort versus cortical effort was compared between control and CP subjects. More cortical effort was required to produce similar muscle effort in children with CP. It is possible this metric could be a valuable diagnostic tool in determining response to treatment.
2008 3rd International Conference on Malicious and Unwanted Software (MALWARE), 2008
In this paper, we present a new implicit encoding technique that makes use of lower-layer packet ... more In this paper, we present a new implicit encoding technique that makes use of lower-layer packet reordering to superimpose covert messages onto a reliable data stream. In particular, since the TCP layer provides a reliable inorder data stream over the unreliable network layer's IP datagram service, we can encode covert messages by artificially permuting IP packets before they leave the source and reading the permutation at the destination prior to delivering the payload to TCP. Applying such permutations will not adversely affect TCP's ability to reconstitute the transport layer data stream, since TCP is designed to be robust against out of order network layer packet delivery. We describe the design and operation of PERMEATE, an open-source covert channel toolkit which implements such a permutational covert channel over TCP, and we provide a quantitative assessment of it's efficacy and efficiency as a covert channel.
2008 International Wireless Communications and Mobile Computing Conference, 2008
We present a new dynamic scheme which continuously redistributes a fixed power budget among mobil... more We present a new dynamic scheme which continuously redistributes a fixed power budget among mobile wireless nodes participating in a multi-hop wireless connection, with the objective of maximizing the expected lifetime of the connection. Our experimental simulations indicate that the proposed power budget distribution scheme yields a significant increase in connection lifetime. We quantify the sensitivity of the performance gains to various system parameters, including connection size, node density, power budget size, and mean node velocities. We then compare the efficacy of our scheme with two schemes: one that simply distributes the power budget uniformly, and one that distributes the power budget dynamically with the objective of minimizing end-to-end bit error rate (BER). In comparing the relative performance of the three schemes we obtain a qualitative assessment of the inherent oppositions and tradeoffs between the objectives of BER minimization and lifetime maximization.
In this paper, we propose a non-commutative keyexchange scheme which generalizes the classical El... more In this paper, we propose a non-commutative keyexchange scheme which generalizes the classical ElGamal Cipher to polycyclic groups. We describe the criteria for groups which would provide good candidates for such cryptosystems, we also examine the complexity of the decision problems related to these key exchange.
Proceedings of the 2007 international conference on Wireless communications and mobile computing, 2007
Ghassen Brahim, Ala Al-Fuquaha, Dionisyios Kountanis Dept. of Computer Science, Western Michigan ... more Ghassen Brahim, Ala Al-Fuquaha, Dionisyios Kountanis Dept. of Computer Science, Western Michigan University Kalamazoo, MI., 49009 [email protected] ... Bilal Khan Dept. of Mathematics and Computer Science, John Jay College of Criminal Justice 899 Tenth ...
2008 Advanced Software Engineering and Its Applications, 2008
In the software development life cycle, maintenance is a key phase that determines long term and ... more In the software development life cycle, maintenance is a key phase that determines long term and effective use of any software. Maintenance can become very lengthy and costly for large software systems when structure of the system is complicated. One of the factors complicating the structure of the software system is subsystem boundaries becoming ambiguous due to system evolution, lack of up to date documentation and high turn over rate of software professionals (leading to non availability of original designers of the software systems). Software module clustering helps software professionals to recover high-level structure of the system by decomposing the system into smaller manageable subsystems, containing interdependent modules. Automated approaches simplify the software clustering process, which otherwise is quite a tedious task for medium and large software systems. We treat software clustering as an optimization problem and propose an automated technique to get near optimal decompositions of relatively independent subsystems, containing interdependent modules. We propose the use of self adaptive Evolution Strategies to search a large solution space consisting of modules and their relationships. We compare our proposed approach with a widely used genetic algorithm based approach on a number of test systems. Our proposed approach shows considerable improvement in terms of quality and effectiveness of the solutions for all tests cases.
... Bilal Khan and Shaleeza Sohail National University of Sciences and Technology (NUST) College ... more ... Bilal Khan and Shaleeza Sohail National University of Sciences and Technology (NUST) College of E & ME Department of Computer Engineering ... We were able to find very few research works in Soft-ware Clustering literature that has formally compared the consistency of the ...
The understanding of how the formation of metal nanoparticles in aqueous solutions is influenced ... more The understanding of how the formation of metal nanoparticles in aqueous solutions is influenced by the presence of presynthesized nanoparticles is important for precise control over size, shape, and composition of nanoparticles. New insights into the catalytic mechanism of Pt nanoparticles are gained by studying the formation of gold nanoparticles from the reduction of AuCl 4in aqueous solution in the presence of presynthesized Pt nanoparticles as a model system. The measurement of changes of the surface plasmon resonance band of gold nanoparticles, along with TEM analysis of particle size and morphology, provided an important means for assessing the reaction kinetics. The reductive mediation of Pt-H species on the Pt nanocrystal surface is believed to play an important role in the Pt-catalyzed formation of gold nanoparticles. This important physical insight is evidenced by comparison of the rates of the Pt-catalyzed formation of gold nanoparticles in the presence and in the absence of hydrogen (H 2), which adsorb dissociatively on a Pt nanocrystal surface forming Pt-H species. Pt-H effectively mediates the reduction of AuCl 4toward the formation of gold nanoparticles. Implications of the findings to the controllability over size, composition, and morphology of metal nanoparticles in the aqueous synthesis environment are also discussed.
There is considerable research relating the structure of Boolean networks to their state space dy... more There is considerable research relating the structure of Boolean networks to their state space dynamics. In this paper, we extend the standard model to include the effects of thermal noise, which has the potential to deflect the trajectory of a dynamical system within its state space, sending it from one stable attractor to another. We introduce a new "thermal robustness" measure, which quantifies a Boolean network's resilience to such deflections. In particular, we investigate the impact of structural homogeneity on two dynamical properties: thermal robustness and attractor density. Through computational experiments on cyclic Boolean networks, we ascertain that as a homogeneous Boolean network grows in size, it tends to underperform most of its heterogeneous counterparts with respect to at least one of these two dynamical properties. These results strongly suggest that during an organism's growth and morphogenesis, cellular differentiation is required if the organism seeks to exhibit both an increasing number of attractors and resilience to thermal noise.
In this paper, we describe how to construct physical computer network topologies which can suppor... more In this paper, we describe how to construct physical computer network topologies which can support the establishment of overlays that reduce or increase the distances between nodes. Reducing pairwise distances (i.e., compression) implies that the overlay enjoys significantly lower inter-node latencies compared to the ambient physical network; such an overlay can be used to implement a "high-performance mode" for disaster situations in which network responsiveness is of critical importance. On the other hand, increasing pairwise distances (i.e., expansion) implies that the overlay exhibits significantly higher inter-node latencies compared to the ambient physical network; such an overlay can be used to implement a brief "dilated state" in networks that have been infected by a malicious worm, where slowing down the infection spread allows greater time for antidote generation. We show that it is possible to design physical networks which support overlays whose logical link bandwidth is equal to the physical link bandwidth while providing arbitrarily high compression or expansion. We also show that it is possible to "grow" such networks over time in a scalable way, that is to say, it is possible to retain the compression/expansion properties while augmenting the network with new nodes, by making relatively small adjustments to the physical and overlay network structure.
We demonstrate the utility of functional near-infrared spectroscopy ͑fNIRS͒ as a tool for physici... more We demonstrate the utility of functional near-infrared spectroscopy ͑fNIRS͒ as a tool for physicians to study cortical plasticity in children with cerebral palsy ͑CP͒. Motor cortex activation patterns were studied in five healthy children and five children with CP ͑8.4± 2.3 years old in both groups͒ performing a finger-tapping protocol. Spatial ͑distance from center and area difference͒ and temporal ͑duration and time-to-peak͒ image metrics are proposed as potential biomarkers for differentiating abnormal cortical activation in children with CP from healthy pediatric controls. In addition, a similarity image-analysis concept is presented that unveils areas that have similar activation patterns as that of the maximum activation area, but are not discernible by visual inspection of standard activation images. Metrics derived from the images presenting areas of similarity are shown to be sensitive identifiers of abnormal activation patterns in children with CP. Importantly, the proposed similarity concept and related metrics may be applicable to other studies for the identification of cortical activation patterns by fNIRS.
International Journal of Algebra and Computation, 2007
In this paper we discuss a general approach to positive theories of groups. As an application we ... more In this paper we discuss a general approach to positive theories of groups. As an application we get a robust description of positive theories of groups with regular free Lyndon length function. Our approach combines techniques of infinite words (see [17, 3]), cancellation diagrams introduced in [14], and Merzlyakov's method [15].
ABSTRACT We propose two methods for aggregation of peer group topology in hierarchical ATM networ... more ABSTRACT We propose two methods for aggregation of peer group topology in hierarchical ATM networks. Both proposed aggregation methods transform a given peer group into a star graph representation. Our first approach optimally preserves, in a least square sense, the original costs of routing through the peer group. Our second approach assigns a weighted vector to the nucleus of the Logical Group Node, which quantifies the error in the compact representation. The two schemes are dual, in the sense that the first is best suited for peergroups where traffic patterns are unpredictable, and the second is suited for peergroups where traffic patterns can be characterized. Both the proposed schemes are practical: For peer groups with nodes V, links E, and n border nodes B ⊂ V, the approaches run in O(n|V|log|V| + n|E|+ poly(n)) time. The size of the final representation is small (linear in the number of border nodes) and can be computed efficiently. The scalability of the proposed algorithms makes them well-suited for use in practice. We also present a general method for measuring the degree of confidence in an aggregation scheme.
ABSTRACT This paper describes results from a network survey of Nain – a predominantly Inuit commu... more ABSTRACT This paper describes results from a network survey of Nain – a predominantly Inuit community of ~1200 people located on the northern coast of Labrador. As part of a larger social network research project, we used peer-referral sampling to recruit 330 residents for interviews about food sharing, housing, public health and community traditions. The peer-referral chains were analysed statistically to determine the presence and absence of social divisions in the community. The results of these analyses show that ethnic identification, relocation status and household income were the most significant social divisions in the community, while gender, education level and employment status show little or no effect on patterns of between-group interconnection. We argue that statistical patterns in the presence (and absence) of intergroup links offer novel ways to examine the interrelationship between recent economic development and the historical disruptions caused by Inuit community relocations in the 1950s.
String capsule endoscopy: a novel application for the preoperative identification of a small-bowe... more String capsule endoscopy: a novel application for the preoperative identification of a small-bowel obscure GI bleeding source (with video). ... Khan B, Ramirez FC, Shaukat M, Gilani N, Shah DK. ... Department of Gastroenterology, Phoenix VA Medical Center/Banner Good ...
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