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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
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Publication Metadata only A kernel-based multilayer perceptron framework to identify pathways related to cancer stages(Springer International Publishing Ag, 2023) Mokhtaridoost, Milad; Department of Industrial Engineering; Soleimanpoor, Marzieh; Gönen, Mehmet; Department of Industrial Engineering; Graduate School of Sciences and Engineering; College of EngineeringStandard machine learning algorithms have limited knowledge extraction capability in discriminating cancer stages based on genomic characterizations, due to the strongly correlated nature of high-dimensional genomic data. Moreover, activation of pathways plays a crucial role in the growth and progression of cancer from early-stage to latestage. That is why we implemented a kernel-based neural network framework that integrates pathways and gene expression data using multiple kernels and discriminates early- and late-stages of cancers. Our goal is to identify the relevant molecular mechanisms of the biological processes which might be driving cancer progression. As the input of developed multilayer perceptron (MLP), we constructed kernel matrices on multiple views of expression profiles of primary tumors extracted from pathways. We used Hallmark and Pathway Interaction Database (PID) datasets to restrict the search area to interpretable solutions. We applied our algorithm to 12 cancer cohorts from the Cancer Genome Atlas (TCGA), including more than 5100 primary tumors. The results showed that our algorithm could extract meaningful and disease-specific mechanisms of cancers. We tested the predictive performance of our MLP algorithm and compared it against three existing classification algorithms, namely, random forests, support vector machines, and multiple kernel learning. Our MLP method obtained better or comparable predictive performance against these algorithms.Publication Metadata only MTTF and availability of semi-Markov missions with non-identical generally distributed component lifetimes(Taylor & Francis) Cekyay, Bora; Department of Industrial Engineering; Özekici, Süleyman; Faculty Member; Department of Industrial Engineering; College of Engineering; 32631We analyze mean time to failure and availability of systems that perform semi-Markov missions. The mission process is the minimal semi-Markov process associated with a Markov renewal process. Therefore, the successive phases of the mission follow a Markov chain, and the phase durations are generally distributed. The lifetimes of the non-identical components in the system are assumed to be generally distributed and are modeled using intrinsic aging concepts. Moreover, the lifetime parameters of the components and the configuration of the system change depending on the phases of the mission. We characterize the mean time to failure through solving a Poisson equation, and we analyze the system availability assuming that repair duration has a general distribution which is dependent on the phase of the mission during which the failure has occurred and on the deterioration level of the system.Publication Metadata only Inferring transferable intermolecular potential models(2008) Üçyigitler, Sinan; Çamurdan, Mehmet C.; Elliott, J. Richard; Department of Industrial Engineering; Türkay, Metin; Faculty Member; Department of Industrial Engineering; College of Engineering; 24956Discontinuous molecular dynamics is combined with thermodynamic perturbation theory to provide an efficient basis for characterising molecular interactions based on vapour pressure and liquid density data. Several prospective potential models are discretised to permit treatment by Barker–Henderson perturbation theory. The potentials are characterised by 11 wells ranging over radial distances from the site diameter to three times that diameter. Considered potential models include the Lennard-Jones (LJ), square-well, Yukawa (Yuk) and multi-line potentials, and their combinations. The optimal model is found to be a combination of square-well and Yuk potentials, with the switch position and Yuk decay set to universal values. This model provides average vapour pressure deviations of less than 10% for a database of 86 aliphatic, aromatic and naphthenic compounds. The LJ potential provides the least competitive accuracy. Considering statistical information criteria facilitates the identification of the optimal model.Publication Metadata only Optimization of supply chain systems with price elasticity of demand(2011) Karasözen, Bülent; Biegler, Lorenz T.; N/A; Department of Industrial Engineering; Kaplan, Uğur; Türkay, Metin; PhD Student; Faculty Member; Department of Industrial Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 24956A centralized multiechelon, multiproduct supply chain network is presented in a multiperiod setting with products that show varying demand against price. An important consideration in such complex supply chains is to maintain system performance at high levels for varying demands that may be sensitive to product price. To examine the price-centric behavior of the customers, the concept of price elasticity of demand is addressed. The proposed approach includes many realistic features of typical supply chain systems such as production planning and scheduling, inventory management, transportation delay, transportation cost, and transportation limits. In addition, the proposed system can be extended to meet unsatisfied demand in future periods by backordering. Effects of the elasticity in price demand in production and inventory decisions are also examined. The supply chain model is formulated as a convex mixed-integer nonlinear programming problem. Reformulations are presented to make the problem tractable. The differential equations are reformulated as difference equations, and unbounded derivatives in the nonlinear objective function are handled with an approximation, with guaranteed bounds on the loss of optimality. The approach is illustrated on a multiechelon, multiproduct supply chain network.Publication Metadata only Turkey's chemicals industry expands into global markets(American Institute of Chemical Engineers, 2015) Department of Industrial Engineering; Türkay, Metin; Faculty Member; Department of Industrial Engineering; College of Engineering; 24956The Turkish chemicals industry has the potential for significant growth, with increasing demand coming from both domestic and global markets. The industry will need to increase production capacity and diversify its product portfolio to capture this potential. Growth in paints and coatings is likely to continue, driven by the construction of new buildings to support the Urban Transformation Law, under which 6.5 million buildings will be demolished and replaced. The majority of the chemicals produced in Turkey are sold as raw materials and intermediates to several other industries.Publication Metadata only The quality of ECG data acquisition, and diagnostic performance of a novel adhesive patch for ambulatory cardiac rhythm monitoring in arrhythmia detection(Churchill Livingstone Inc Medical Publishers, 2019) Deliormanli, Bilgen Gulsen; Adiguzel, Omer; Li, Ko-Mai; Yılmaz, Elif Nur; N/A; N/A; N/A; Department of Industrial Engineering; Karaoğuz, Mustafa Remzi; Yurtseven, Ece; Aslan, Gamze; Gönen, Mehmet; Doctor; Teaching Faculty; Doctor; Faculty Member; Department of Industrial Engineering; N/A; School of Medicine; N/A; College of Engineering; Koç University Hospital; N/A; Koç University Hospital; N/A; N/A; 176021; N/A; 237468Background: Short and long ambulatory electrocardiographic monitoring with different systems is a widely used method to detect cardiac arrhythmias. In this study, we aimed to evaluate the effectiveness of a novel monitoring device on cardiac arrhythmia detection. Methods: We used two different protocols to evaluate device performance. For the first one, 36 healthy subjects were enrolled. The standard 12-lead, 24-h Holter monitoring and the novel single lead electrocardiogram (ECG) Patch Monitor (EPM) device (BeyondCare (R), Rooti Labs Ltd., Taipei, Taiwan) were simultaneously applied to all subjects for 24 h. The quality of ECG data acquisition of novel system was compared to that of standard Holter. The second phase included 73 patients that were referred from our outpatient arrhythmia clinic for evaluation of their symptoms relevant to the cardiac arrhythmias. Advanced algorithms, statistical methods (cross-correlation method, Pearson's correlation coefficient, Bland-Altman plots) were used to process and verify the acquired data. Results: The overall average beat per minute correlation between BeyondCare (R) and standard 12-lead Holter was found 98% in 33 healthy subjects. The mean percentage of invalid measurements in BeyondCare (R) was 1.6% while the Holter's was 1.7%. In the second protocol of the study, prospective data from 67 patients who were referred for evaluation of their symptoms relevant to cardiac arrhythmias, showed that the mean BeyondCare (R) wear time was 4.7 +/- 0.5 days out of five total days per protocol. The mean analyzable wear time was 93.6%. The water-resistant design enabled 73.5% of the participants to take a shower. 7.3% of participants had minor skin irritations related to the electrodes. Among the patients with detected arrhythmia (40.2% of all patients), 29.6% had their first arrhythmia after the initial two days period. A clinically significant pause was detected in one patient, ventricular tachycardia was detected in four patients, and supraventricular tachycardia was detected in 15 patients. Paroxysmal atrial fibrillation was identified in seven patients. Three of them had their first episodes after the second day of monitoring. Conclusion: BeyondCare (R) Patch was well-tolerated and allowed prolonged time periods for continuous ECG monitoring, may result in an improvement in clinical accuracy and detection of arrhythmias by cloud-based artificial intelligence operating system. (C) 2019 Elsevier Inc. .Publication Metadata only Admission and termination control of a two class loss system(Taylor & Francis Inc, 2011) Ulukuş, Mehmet Yasin; Güllü, Refik; Department of Industrial Engineering; Örmeci, Lerzan; Faculty Member; Department of Industrial Engineering; College of Engineering; 32863We consider dynamic admission and termination control policies in a Markovian loss system with two classes, each with a fixed reward, a termination cost, an arrival and service rate. The system may admit or reject an arriving job or admit it by terminating a job in the system to maximize its total expected discounted reward. We prove that (1) when there is an idle server, it is never optimal to terminate a job, (2) there exists an optimal threshold policy for both admission and termination decisions. Furthermore, we identify the conditions which ensure that a class is "preferred" or "strongly preferred."Publication Metadata only Characterizing the performance of process flexibility structures(Elsevier, 2007) N/A; Department of Business Administration; Department of Industrial Engineering; Karaesmen, Zeynep Akşin; Karaesmen, Fikri; Faculty Member; Faculty Member; Department of Business Administration; Department of Industrial Engineering; College of Administrative Sciences and Economics; College of Engineering; 4534; 3579The objective is to identify preferred flexibility structures in service or manufacturing systems, when demand is random and capacity is finite. Considering a network flow type model as the basis of the analysis, general structural properties of flexibility design pertaining to the marginal values of flexibility and capacity are identified.Publication Metadata only The parallel genetic algorithm for designing dna randomizations in a combinatorial protein experiment(Springer-Verlag Berlin, 2006) Blazewicz, Jacek; Dziurdza, Beniamin; Markiewicz, Wojciech T; Department of Industrial Engineering; Oğuz, Ceyda; Faculty Member; Department of Industrial Engineering; College of Engineering; 6033Evolutionary methods of protein engineering such as phage display have revolutionized drug design and the means of studying molecular binding. In order to obtain the highest experimental efficiency, the distributions of constructed combinatorial libraries should be carefully adjusted. The presented approach takes into account diversity- completeness trade-off and tries to maximize the number of new amino acid sequences generated in each cycle of the experiment. In the paper, the mathematical model is introduced and the parallel genetic algorithm for the defined optimization problem is described. Its implementation on the SunFire 6800 computer proves a high efficiency of the proposed approach.Publication Metadata only A tandem queueing model with coupled processors(Elsevier, 2003) Resing, Jacques; Department of Industrial Engineering; Örmeci, Lerzan; Faculty Member; Department of Industrial Engineering; College of Engineering; 32863We consider a tandem queue with coupled processors and analyze the two-dimensional Markov process representing the numbers of jobs in the two stations. A functional equation for the generating function of the stationary distribution of this two-dimensional process is derived and solved through the theory of Riemann-Hilbert boundary value problems.