@article {1538, title = {Multiple instance classification via quadratic programming}, journal = {Journal of Global Optimization}, year = {2022}, pages = {1{\textendash}32}, author = {Emel {\c S}eyma K{\"u}{\c c}{\"u}ka{\c s}c{\i} and Mustafa Gokce Baydogan and Z C Ta{\c s}k{\i}n} } @article {1540, title = {A branch-and-price algorithm for parallel machine campaign planning under sequence dependent family setups and co-production}, journal = {Computers \& Operations Research}, volume = {135}, year = {2021}, pages = {105430}, doi = {https://doi.org/10.1016/j.cor.2021.105430}, author = {Serkan Kalay and Z C Ta{\c s}k{\i}n} } @article {1539, title = {A Branch-Price-and-Cut Algorithm for Optimal Decoding of LDPC Codes}, journal = {Journal of Global Optimization}, volume = {81}, year = {2021}, pages = {805{\textendash}834}, doi = {https://doi.org/10.1007/s10898-021-01073-4}, author = {Banu Kabakulak and Z C Ta{\c s}k{\i}n and Ali Emre Pusane} } @article {1542, title = {An Exact Cutting Plane Algorithm to Solve the Selective Graph Coloring Problem in Perfect Graphs}, journal = {European Journal of Operational Research}, volume = {291(1)}, year = {2021}, pages = {67{\textendash}83}, doi = {https://doi.org/10.1016/j.ejor.2020.09.017}, author = {Oylum {\c S}eker and Ekim, Tinaz and Z C Ta{\c s}k{\i}n} } @article {1424, title = {A linear programming approach to multiple instance learning}, journal = {Turkish Journal of Electrical Engineering \& Computer Sciences}, volume = {29}, year = {2021}, pages = {2186{\textendash}2201}, author = {Emel {\c S}eyma K{\"u}{\c c}{\"u}ka{\c s}c{\i} and Mustafa Gokce Baydogan and Z C Ta{\c s}k{\i}n} } @article {1541, title = {Single Machine Campaign Planning under Sequence Dependent Family Setups and Co-Production}, journal = {Journal of the Operational Research Society}, volume = {72}, year = {2021}, pages = {2091{\textendash}2111}, doi = {https://doi.org/10.1080/01605682.2020.1772016}, author = {Serkan Kalay and Z C Ta{\c s}k{\i}n} } @article {1426, title = {A branch-and-cut algorithm for a bipartite graph construction problem in digital communication systems}, journal = {Networks}, volume = {75}, year = {2020}, pages = {137-157}, abstract = {

Abstract We study a bipartite graph (BG) construction problem that arises in digital communication systems. In a digital communication system, information is sent from one place to another over a noisy communication channel using binary symbols (bits). The original information is encoded by adding redundant bits, which are then used to detect and correct errors that may have been introduced during transmission. Harmful structures, such as small cycles, severely deteriorate the error correction capability of a BG. We introduce an integer programming formulation to generate a BG for a given smallest cycle length. We propose a branch-and-cut algorithm for its solution and investigate the structural properties of the problem to derive valid inequalities and variable fixing rules. We also introduce heuristics to obtain feasible solutions for the problem. The computational experiments show that our algorithm can generate BGs without small cycles in an acceptable amount of time for practically relevant dimensions.

}, keywords = {bipartite graphs, branch-and-cut algorithm, integer programming, symmetry, telecommunications, valid inequalities}, doi = {https://doi.org/10.1002/net.21914}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/net.21914}, author = {Banu Kabakulak and Z C Ta{\c s}k{\i}n and Pusane, Ali E.} } @article {1428, title = {On the Construction of Regular QC-LDPC Codes With Low Error Floor}, journal = {IEEE Communications Letters}, volume = {24}, year = {2020}, pages = {25-28}, doi = {10.1109/LCOMM.2019.2953058}, author = {Sar{\i}duman, Abdullah and Pusane, Ali E. and Z C Ta{\c s}k{\i}n} } @article {1425, title = {Decentralized decomposition algorithms for peer-to-peer linear optimization}, journal = {RAIRO-Oper. Res.}, volume = {54}, year = {2020}, pages = {1835-1861}, doi = {10.1051/ro/2019097}, url = {https://doi.org/10.1051/ro/2019097}, author = {Aydin, M. Asli and Z C Ta{\c s}k{\i}n} } @article {1436, title = {Minimizing the misinformation spread in social networks}, journal = {IISE Transactions}, volume = {52}, year = {2020}, pages = {850-863}, abstract = {

AbstractThe Influence Maximization Problem has been widely studied in recent years, due to rich application areas including marketing. It involves finding k nodes to trigger a spread such that the expected number of influenced nodes is maximized. The problem we address in this study is an extension of the reverse influence maximization problem, i.e., misinformation minimization problem where two players make decisions sequentially in the form of a Stackelberg game. The first player aims to minimize the spread of misinformation whereas the second player aims its maximization. Two algorithms, one greedy heuristic and one matheuristic, are proposed for the first player{\textquoteright}s problem. In both of them, the second player{\textquoteright}s problem is approximated by Sample Average Approximation, a well-known method for solving two-stage stochastic programming problems, that is augmented with a state-of-the-art algorithm developed for the influence maximization problem.

}, doi = {10.1080/24725854.2019.1680909}, url = {https://doi.org/10.1080/24725854.2019.1680909}, author = {K{\"u}bra Tan{\i}nm{\i}{\c s} and Necati Aras and I. Kuban Altinel and Evren G{\"u}ney} } @article {1427, title = {A strong integer programming formulation for hybrid flowshop scheduling}, journal = {Journal of the Operational Research Society}, volume = {71}, year = {2020}, pages = {2042-2052}, doi = {10.1080/01605682.2019.1654414}, url = {https://doi.org/10.1080/01605682.2019.1654414}, author = {Ali Tamer {\"U}nal and Semra A{\u g}ral{\i} and Z C Ta{\c s}k{\i}n} } @article {1433, title = {A column generation heuristic for {VMAT} planning with adaptive {CVaR} constraints}, journal = {Physics in Medicine {\&} Biology}, volume = {64}, year = {2019}, month = {oct}, pages = {205024}, abstract = {

In this study we develop an efficient computational procedure that generates medically acceptable treatment plans for volumetric modulated arc therapy with constant gantry speed. Our proposed method is a column generation heuristic based on a mixed integer linear programming model, where the objective function contains minimization of total monitor unit of the treatment plan and dose-volume requirements are included as conditional value-at-risk constraints. Our heuristic generates a full treatment arc for the restricted master problem and calibrates the right hand side parameters of the conditional value-at-risk constraints in the first phase. In the second phase, this initial solution is improved by performing column generation. This is a fully automated procedure and produces treatment plans in a single call without any human intervention. We evaluate its performance on real prostate cancer data by comparing the quality of the generated plans with those obtained by a widely used commercial treatment planning system. Our analysis shows that the results are promising, and the generated plans satisfy the prescription restrictions and require fewer monitor units on average compared to the ones obtained using Eclipse.

}, doi = {10.1088/1361-6560/ab416e}, url = {https://doi.org/10.1088/1361-6560/ab416e}, author = {P{\i}nar Dursun and Z C Ta{\c s}k{\i}n and I. Kuban Altinel and Hatice Bilge and Nazmiye D{\"o}nmez Kesen and Murat Okutan and Ethem Nezih Oral} } @article {1431, title = {A decomposition approach to solve the selective graph coloring problem in some perfect graph families}, journal = {Networks}, volume = {73}, year = {2019}, pages = {145-169}, abstract = {

Graph coloring is the problem of assigning a minimum number of colors to all vertices of a graph such that no two adjacent vertices receive the same color. The selective graph coloring problem is a generalization of the standard graph coloring problem; given a graph with a partition of its vertex set into clusters, the objective is to choose exactly one vertex per cluster so that, among all possible selections, the number of colors necessary to color the vertices in the selection is minimum. This study focuses on a decomposition based exact solution framework for selective coloring in some perfect graph families: in particular, permutation, generalized split, and chordal graphs where the selective coloring problem is known to be NP-hard. Our method combines integer programming techniques and combinatorial algorithms for the graph classes of interest. We test our method on graphs with different sizes and densities, present computational results and compare them with solving an integer programming formulation of the problem by CPLEX, and a state-of-the art algorithm from the literature. Our computational experiments indicate that our decomposition approach significantly improves solution performance in low-density graphs, and regardless of edge-density in the class of chordal graphs.

}, keywords = {chordal graphs, decomposition algorithm, generalized split graphs, integer programming, partition coloring, permutation graphs, selective graph coloring}, doi = {https://doi.org/10.1002/net.21850}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/net.21850}, author = {{\c S}eker, Oylum and Ekim, Tinaz and Z C Ta{\c s}k{\i}n} } @article {1432, title = {The determination of optimal treatment plans for Volumetric Modulated Arc Therapy (VMAT)}, journal = {European Journal of Operational Research}, volume = {272}, year = {2019}, pages = {372-388}, abstract = {

The success of radiation therapy depends on the ability to deliver the proper amount of radiation to cancerous cells while protecting healthy tissues. As a natural consequence, any new treatment technology improves quality standards concerning primarily this issue. Similar to the widely used Intensity Modulated Radiation Therapy (IMRT), the radiation resource is outside of the patient{\textquoteright}s body and the beam is shaped by a multi-leaf collimator mounted on the linear accelerator{\textquoteright}s head during the state-of-the-art Volumetric Modulated Arc Therapy (VMAT) as well. However, unlike IMRT, the gantry of the accelerator may rotate along one or more arcs and deliver radiation continuously. This property makes VMAT powerful in obtaining high conformal plans in terms of dose distribution; but the apertures are interdependent and optimal treatment planning problem cannot be decomposed into simpler independent subproblems as a consequence. In this work, we consider optimal treatment planning problem for VMAT. First, we formulate a mixed-integer linear program minimizing total radiation dose intensity subject to clinical requirements embedded within the constraints. Then, we develop efficient solution procedures combining Benders decomposition with certain acceleration strategies. We investigate their performance on a large set of test instances obtained from an anonymous real prostate cancer data.

}, keywords = {algorithms, Benders decomposition, integer programming, Radiation therapy, VMAT}, issn = {0377-2217}, doi = {https://doi.org/10.1016/j.ejor.2018.06.023}, url = {https://www.sciencedirect.com/science/article/pii/S0377221718305514}, author = {P{\i}nar Dursun and Z C Ta{\c s}k{\i}n and I. Kuban Altinel} } @article {1437, title = {Influence maximization with deactivation in social networks}, journal = {European Journal of Operational Research}, volume = {278}, year = {2019}, pages = {105-119}, abstract = {

In this paper, we consider an extension of the well-known Influence Maximization Problem in a social network which deals with finding a set of k nodes to initiate a diffusion process so that the total number of influenced nodes at the end of the process is maximized. The extension focuses on a competitive variant where two decision makers are involved. The first one, the leader, tries to maximize the total influence spread by selecting the most influential nodes and the second one, the follower, tries to minimize it by deactivating some of these nodes. The formulated bilevel model is solved by complete enumeration for small-sized instances and by a matheuristic for large-sized instances. In both cases, the lower level problem, which is a stochastic optimization problem, is approximated via the Sample Average Approximation method.

}, keywords = {Bilevel modeling, Influence maximization, Matheuristics, Metaheuristics, Stochastic optimization}, issn = {0377-2217}, doi = {https://doi.org/10.1016/j.ejor.2019.04.010}, url = {https://www.sciencedirect.com/science/article/pii/S0377221719303303}, author = {K{\"u}bra Tan{\i}nm{\i}{\c s} and Necati Aras and I. Kuban Altinel} } @article {1434, title = {Minimum cost noncrossing flow problem on layered networks}, journal = {Discrete Applied Mathematics}, volume = {261}, year = {2019}, pages = {2-21}, abstract = {

In this work we focus on an extension of the minimum cost flow problem in layered networks. Feasible arc flows must satisfy a specific compatibility restriction in addition to flow balance and capacity restrictions. Namely, at most one of the crossing arcs is allowed to have positive flow on it. This variant of the minimum cost flow problem, which we call the minimum cost noncrossing flow problem, can frequently be encountered in real life. The determination of optimal temporal quay crane allocations to berthed vessels in container terminals, and optimal train schedules through the stations on the same railroad line are two examples. We first analyze the complexity of the problem and show that the noncrossing flow problem is in fact NP-complete in a layered network. Then, we introduce mixed-integer linear programming formulations and discuss a polynomially solvable special case. Next we show a sufficient condition for the existence of a crossing in an optimal solution, which can be used for preprocessing the arcs in order to reduce the problem size. Our computational experiments on a large test set show that our preprocessing algorithm can significantly reduce the number of arcs.

}, keywords = {integer programming, Layered networks, Network flows, Noncrossing flow}, issn = {0166-218X}, doi = {https://doi.org/10.1016/j.dam.2018.09.016}, url = {https://www.sciencedirect.com/science/article/pii/S0166218X18304815}, author = {I. Kuban Altinel and Necati Aras and Zeynep {\c S}uvak and Z C Ta{\c s}k{\i}n} } @article {1430, title = {Optimization{\textendash}based decoding algorithms for LDPC convolutional codes in communication systems}, journal = {IISE Transactions}, volume = {51}, year = {2019}, pages = {1061-1074}, abstract = {

AbstractIn a digital communication system, information is sent from one place to another over a noisy communication channel. It may be possible to detect and correct errors that occur during the transmission if one encodes the original information by adding redundant bits. Low{\textendash}Density Parity{\textendash}Check (LDPC) convolutional codes, a member of the LDPC code family, encode the original information to improve error correction capability. In practice these codes are used to decode very long information sequences, where the information arrives in subsequent packets over time, such as video streams. We consider the problem of decoding the received information with minimum error from an optimization point of view and investigate integer programming{\textendash}based exact and heuristic decoding algorithms for its solution. In particular, we consider relax{\textendash}and{\textendash}fix heuristics that decode information in small windows. Computational results indicate that our approaches identify near{\textendash}optimal solutions significantly faster than a commercial solver in high channel error rates. Our proposed algorithms can find higher quality solutions compared with the state of the art iterative decoding heuristic.

}, doi = {10.1080/24725854.2018.1550692}, url = {https://doi.org/10.1080/24725854.2018.1550692}, author = {Banu Kabakulak and Z C Ta{\c s}k{\i}n and Ali Emre Pusane} } @article {1429, title = {Using branch-and-price to determine optimal treatment plans for volumetric modulated arc therapy (VMAT)}, journal = {Computers \& Operations Research}, volume = {110}, year = {2019}, pages = {1-17}, abstract = {

Volumetric Modulated Arc Therapy (VMAT) is the state-of-the-art technique for external radiation therapy treatment. In this method, radiation can be delivered continuously on one or more arcs during the rotation of the gantry of the linear accelerator. This property makes VMAT powerful in obtaining high conformal plans in terms of dose distribution within short treatment times. However, the apertures composed by the leaves of the multileaf collimator (MLC) system that shapes continuously the radiation are interdependent, which makes treatment planning hard. We propose a mixed integer linear programming model for VMAT planning problem and exact branch-and-price algorithms to solve it. The objective of the model is to minimize total radiation that is delivered to the patient, and pricing subproblem is decomposable by rows of the MLC and can be solved as a shortest path problem. We generate a large set of test instances from a real data set and evaluate the performance of the proposed branch-and-price algorithm. Computational results reveal that new algorithms are efficient and capable of finding optimal solutions for large problem instances.

}, keywords = {Branch-and-price, Column generation, integer programming, Radiation therapy, Shortest path problem, VMAT}, issn = {0305-0548}, doi = {https://doi.org/10.1016/j.cor.2019.05.018}, url = {https://www.sciencedirect.com/science/article/pii/S0305054819301315}, author = {P{\i}nar Dursun and Z C Ta{\c s}k{\i}n and I. Kuban Altinel} } @article {1157, title = {Autoregressive forests for multivariate time series modeling}, journal = {Pattern Recognition}, volume = {73}, year = {2018}, pages = {202 - 215}, keywords = {Classification, Ensemble learning, Multivariate time series, Time series representation, Vector autoregression}, issn = {0031-3203}, doi = {https://doi.org/10.1016/j.patcog.2017.08.016}, url = {http://www.sciencedirect.com/science/article/pii/S0031320317303291}, author = {Kerem Sinan Tuncel and Mustafa Gokce Baydogan} } @article {1435, title = {Integer Programming Formulations and Benders Decomposition for the Maximum Induced Matching Problem}, journal = {INFORMS Journal on Computing}, volume = {30}, year = {2018}, pages = {43-56}, abstract = {

We investigate the maximum induced matching problem (MIM), which is the problem of finding an induced matching having the largest cardinality on an undirected graph. The problem is known to be NP-hard for general graphs. We first propose a vertex-based integer programming formulation for MIM, which is more compact compared to an edge-based formulation found in the literature. We also introduce the maximum weight induced matching problem (MWIM), which generalizes MIM so that vertices and edges have weights. We adapt the edge-based formulation to MWIM, and propose a quadratic programming formulation of MWIM based on our vertex-based formulation. We then linearize our quadratic programming formulation, and devise a Benders decomposition algorithm that exploits a special structure of the linearized formulation. We also propose valid inequalities and formulation tightening procedures to improve the efficiency of our approach. Our computational tests on a large suite of randomly generated graphs show that our vertex-based formulation and decomposition approach significantly improve the solvability of MIM and MWIM, especially on dense graphs. The online appendix and data are available at https://doi.org/10.1287/ijoc.2017.0764.

}, doi = {10.1287/ijoc.2017.0764}, url = {https://doi.org/10.1287/ijoc.2017.0764}, author = {Ahat, Bet{\"u}l and Ekim, Tinaz and Z C Ta{\c s}k{\i}n} } @article {1488, title = {A parallel machine lot-sizing and scheduling problem with a secondary resource and cumulative demand}, journal = {International Journal of Production Research}, volume = {56}, year = {2018}, pages = {3344-3357}, abstract = {

We investigate a parallel machine multi-item lot-sizing and scheduling problem with a secondary resource, in which demands are given for the entire planning horizon rather than for every single period. All-or-nothing assumption of the discrete lot-sizing and scheduling problem is valid so that a machine is either idle or works at full capacity in a period. The objective is to minimise the number of setups and teardowns. We prove that the problem is NP-hard and present two equivalent formulations. We show some properties of the optimal objective value, give optimality conditions and suggest a heuristic algorithm. We discuss and formulate two possible extensions related to real-life applications. Finally, we carry out computational experiments to compare the two formulations, to determine the effect of our proposed modeling improvements on solution performance, and to test the quality of our heuristic.

}, doi = {10.1080/00207543.2017.1406675}, url = {https://doi.org/10.1080/00207543.2017.1406675}, author = {Murat G{\"u}ng{\"o}r and Ali Tamer {\"U}nal and Z C Ta{\c s}k{\i}n} } @article {1130, title = {Branch-cut-price algorithms for solving a class of search problems on general graphs}, journal = {Networks}, volume = {70}, year = {2017}, pages = {4-18}, doi = {http://doi.org/10.1002/net.21740}, author = {Z C Ta{\c s}k{\i}n and J. Cole Smith} } @article {1164, title = {Designing distribution systems with reverse flows}, journal = {Journal of Remanufacturing}, volume = {7}, year = {2017}, pages = {113{\textendash}137}, author = {Tombu{\c s}, Ay{\c s}e Cilac{\i} and Necati Aras and Verter, Vedat} } @article {1090, title = {Employee Scheduling in Service Industries with Flexible Employee Availability and Demand}, journal = {Omega}, volume = {66}, year = {2017}, pages = {159-169}, doi = {http://dx.doi.org/10.1016/j.omega.2016.03.001}, author = {Semra A{\u g}ral{\i} and Z C Ta{\c s}k{\i}n and Ali Tamer {\"U}nal} } @conference {1185, title = {Linear-Time Generation of Random Chordal Graphs}, booktitle = {International Conference on Algorithms and Complexity}, year = {2017}, publisher = {Springer}, organization = {Springer}, author = {Oylum {\c S}eker and Pinar Heggernes and Ekim, Tinaz and Z. Caner Ta{\c s}k{\i}n} } @proceedings {1190, title = {Modeling the Long Term Dynamics of Obesity as a Societal Epidemic}, journal = {34th International Conference of the System Dynamics Society}, year = {2016}, address = {Delft, the Netherlands}, author = {Akta{\c s}, Gizem and Nefel Tellio{\u g}lu and Yaman Barlas and Hakan Ya{\c s}arcan} } @article {1171, title = {Optimal berth allocation, time-variant quay crane assignment and scheduling with crane setups in container terminals}, journal = {European Journal of Operational Research}, volume = {254}, year = {2016}, pages = {985{\textendash}1001}, author = {T{\"u}rko{\u g}ullar{\i}, Yavuz B and Z. Caner Ta{\c s}k{\i}n and Necati Aras and I. Kuban Altinel} } @article {1089, title = {Optimal Berth Allocation, Time-variant Quay Crane Assignment and Scheduling with Crane Setups in Container Terminals}, journal = {European Journal of Operational Research}, volume = {254}, year = {2016}, pages = {985-1001}, doi = {http://dx.doi.org/10.1016/j.ejor.2016.04.022}, author = {Yavuz Boga{\c c} T{\"u}rkogullari and Z C Ta{\c s}k{\i}n and Necati Aras and I. Kuban Altinel} } @article {785, title = {A column generation approach for evaluating delivery efficiencies of collimator technologies in IMRT treatment planning}, journal = {Physics in Medicine and Biology}, volume = {60}, year = {2015}, pages = {1989-2004}, author = {Merve G{\"o}ren and Z C Ta{\c s}k{\i}n} } @article {786, title = {Mathematical Programming-Based Sales and Operations Planning at Vestel Electronics}, journal = {Interfaces}, volume = {45}, year = {2015}, pages = {325-340}, doi = {http://dx.doi.org/10.1287/inte.2015.0793}, author = {Z C Ta{\c s}k{\i}n and Semra A{\u g}ral{\i} and Ali Tamer {\"U}nal and Vahdet Belada and Filiz G{\"o}kten-Y{\i}lmaz} } @article {908, title = {Metabolic connectivity as index of verbal working memory}, journal = {Journal of cerebral blood flow and metabolism}, volume = {35}, year = {2015}, month = {July}, pages = {1122{\textemdash}1126}, issn = {0271-678X}, doi = {10.1038/jcbfm.2015.40}, url = {http://dx.doi.org/10.1038/jcbfm.2015.40}, author = {Zou, Na and Chetelat, Gael and Mustafa Gokce Baydogan and Li, Jing and Fischer, Florian U and Titov, Dmitry and Dukart, Juergen and Fellgiebel, Andreas and Schreckenberger, Mathias and Yakushev, Igor} } @article {1511, title = {On some applications of the selective graph coloring problem}, journal = {European Journal of Operational Research}, volume = {240}, year = {2015}, pages = {307-314}, abstract = {

In this paper we present the Selective Graph Coloring Problem, a generalization of the standard graph coloring problem as well as several of its possible applications. Given a graph with a partition of its vertex set into several clusters, we want to select one vertex per cluster such that the chromatic number of the subgraph induced by the selected vertices is minimum. This problem appeared in the literature under different names for specific models and its complexity has recently been studied for different classes of graphs. Here, we describe different models {\textendash} some already discussed in previous papers and some new ones {\textendash} in very different contexts under a unified framework based on this graph problem. We point out similarities between these models, offering a new approach to solve them, and show some generic situations where the selective graph coloring problem may be used. We focus on specific graph classes motivated by each model, and we briefly discuss the complexity of the selective graph coloring problem in each one of these graph classes and point out interesting future research directions.

}, keywords = {Combinatorial optimization, Computational complexity, Graph theory, partition coloring, Selective coloring}, issn = {0377-2217}, doi = {https://doi.org/10.1016/j.ejor.2014.05.011}, url = {https://www.sciencedirect.com/science/article/pii/S0377221714004184}, author = {Marc Demange and Ekim, Tinaz and Bernard Ries and Cerasela Tanasescu} } @article {671, title = {An Integer Programming-Based Search Technique for Error-Prone Substructures of LDPC Codes}, journal = {AEU - International Journal of Electronics and Communications}, volume = {68}, year = {2014}, pages = {1097-1105}, doi = {10.1016/j.aeue.2014.05.012}, author = {Abdullah Sar{\i}duman and Ali Emre Pusane and Z C Ta{\c s}k{\i}n} } @article {TurkogullariEtAl2014, title = {Optimal berth allocation and time-invariant quay crane assignment in container terminals}, journal = {European Journal of Operational Research}, volume = {235}, number = {1}, year = {2014}, pages = {88{\textendash}101}, doi = {http://dx.doi.org/10.1016/j.ejor.2013.10.015}, author = {Yavuz Boga{\c c} T{\"u}rkogullari and Z C Ta{\c s}k{\i}n and Necati Aras and I. Kuban Altinel} } @inbook {aras2014simultaneous, title = {Simultaneous Optimization of Berth Allocation, Quay Crane Assignment and Quay Crane Scheduling Problems in Container Terminals}, booktitle = {Operations Research Proceedings 2012}, year = {2014}, pages = {101{\textendash}107}, publisher = {Springer International Publishing}, organization = {Springer International Publishing}, author = {Necati Aras and T{\"u}rko{\u g}ullar{\i}, Yavuz and Z C Ta{\c s}k{\i}n and I. Kuban Altinel} } @article {33, title = {A Bag-of-Features Framework to Classify Time Series}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, volume = {35}, year = {2013}, pages = {2796-2802}, abstract = {

Time series classification is an important task with many challenging applications. A nearest neighbor (NN) classifier with dynamic time warping (DTW) distance is a strong solution in this context. On the other hand, feature-based approaches have been proposed as both classifiers and to provide insight into the series, but these approaches have problems handling translations and dilations in local patterns. Considering these shortcomings, we present a framework to classify time series based on a bag-of-features representation (TSBF). Multiple subsequences selected from random locations and of random lengths are partitioned into shorter intervals to capture the local information. Consequently, features computed from these subsequences measure properties at different locations and dilations when viewed from the original series. This provides a feature-based approach that can handle warping (although differently from DTW). Moreover, a supervised learner (that handles mixed data types, different units, etc.) integrates location information into a compact codebook through class probability estimates. Additionally, relevant global features can easily supplement the codebook. TSBF is compared to NN classifiers and other alternatives (bag-of-words strategies, sparse spatial sample kernels, shapelets). Our experimental results show that TSBF provides better results than competitive methods on benchmark datasets from the UCR time series database.

}, keywords = {codebook, feature extraction, supervised learning}, issn = {0162-8828}, doi = {http://doi.ieeecomputersociety.org/10.1109/TPAMI.2013.72}, author = {Mustafa Gokce Baydogan and George Runger and Eugene Tuv} } @article {TaskinCevik2013, title = {Combinatorial Benders Cuts for Decomposing IMRT Fluence Maps Using Rectangular Apertures}, journal = {Computers and Operations Research}, volume = {40(9)}, year = {2013}, pages = {2178{\textendash}2186}, doi = {http://dx.doi.org/10.1016/j.cor.2011.07.005}, author = {Z C Ta{\c s}k{\i}n and Mucahit Cevik} } @article {BodurEtAl2013, title = {Decomposition Algorithms for Solving the Minimum Weight Maximal Matching Problem}, journal = {Networks}, volume = {62}, number = {4}, year = {2013}, pages = {273{\textendash}287}, doi = {http://dx.doi.org/10.1002/net.21516}, author = {Merve Bodur and Ekim, Tinaz and Z C Ta{\c s}k{\i}n} } @article {demange2013hardness, title = {Hardness and approximation of minimum maximal matchings}, journal = {International Journal of Computer Mathematics}, number = {ahead-of-print}, year = {2013}, pages = {1{\textendash}20}, publisher = {Taylor \& Francis}, author = {Demange, Marc and Ekim, Tinaz and Tanasescu, Cerasela} } @conference {tanyolacc2012control, title = {Control Heuristics for Soft Landing Problem}, booktitle = {The 30th International System Dynamics Conference, St. Gallen, Switzerland}, year = {2012}, publisher = {System Dynamics Society (http://www.systemdynamics.org/conferences/2012/index.html)}, organization = {System Dynamics Society (http://www.systemdynamics.org/conferences/2012/index.html)}, author = {Tanyola{\c c}, Togay and Yasarcan, Hakan} } @article {AgraliEtAl2012, title = {A Facility Location Model with Safety Stock Costs: Analysis of the Cost of Single-Sourcing Requirements}, journal = {Journal of Global Optimization}, volume = {54(3)}, year = {2012}, pages = {551-581}, doi = {http://dx.doi.org/10.1007/s10898-011-9777-z}, author = {Semra A{\u g}ral{\i} and Joseph Geunes and Z C Ta{\c s}k{\i}n} } @article {TaskinEkim2012, title = {Integer Programming Formulations for the Minimum Weighted Maximal Matching Problem}, journal = {Optimization Letters}, volume = {6(6)}, year = {2012}, pages = {1161-1171}, doi = {http://dx.doi.org/10.1007/s11590-011-0351-x}, author = {Z C Ta{\c s}k{\i}n and Ekim, Tinaz} } @article {TaskinEtAl2012, title = {Mixed-Integer Programming Techniques for Decomposing IMRT Fluence Maps Using Rectangular Apertures}, journal = {Annals of Operations Research}, volume = {196(1)}, year = {2012}, pages = {799-818}, doi = {http://dx.doi.org/10.1007/s10479-010-0767-1}, author = {Z C Ta{\c s}k{\i}n and J. Cole Smith and H. Edwin Romeijn} } @conference {yasarcan2012soft, title = {A Soft Landing Model and an Experimental Platform as an Introductory Control Design Tool}, booktitle = {The 30th International System Dynamics Conference, St. Gallen, Switzerland}, year = {2012}, publisher = {System Dynamics Society (http://www.systemdynamics.org/conferences/2012/index.html)}, organization = {System Dynamics Society (http://www.systemdynamics.org/conferences/2012/index.html)}, author = {Yasarcan, Hakan and Tanyola{\c c}, Togay} } @article {aras2011selective, title = {Selective multi-depot vehicle routing problem with pricing}, journal = {Transportation Research Part C: Emerging Technologies}, volume = {19}, number = {5}, year = {2011}, pages = {866{\textendash}884}, publisher = {Elsevier}, author = {Necati Aras and Aksen, Deniz and Tu{\u g}rul Tekin, Mehmet} } @conference {tanyolacc2011soft, title = {A Soft Landing Model and a Mass Spring Damper Based Control Heuristic}, booktitle = {The 29th International System Dynamics Conference, Washington, DC, USA}, year = {2011}, publisher = {System Dynamics Society (http://www.systemdynamics.org/conferences/2011/index.htm)}, organization = {System Dynamics Society (http://www.systemdynamics.org/conferences/2011/index.htm)}, author = {Tanyola{\c c}, Togay and Yasarcan, Hakan} } @article {13998331, title = {{A column generation based heuristic for sensor placement, activity scheduling and data routing in wireless sensor networks}}, journal = {European Journal of Operational Research}, volume = {207}, year = {2010}, pages = {1014{\textendash}1026}, doi = {10.1016/j.ejor.2010.05.020}, author = {Yavuz Boga{\c c} T{\"u}rkogullari and Necati Aras and I. Kuban Altinel and Cem Ersoy} } @article {13288019, title = {{An efficient heuristic for placement, scheduling and routing in wireless sensor networks}}, journal = {Ad Hoc Networks}, volume = {8}, year = {2010}, pages = {654{\textendash}667}, doi = {10.1016/j.adhoc.2010.01.005}, author = {Yavuz Boga{\c c} T{\"u}rkogullari and Necati Aras and I. Kuban Altinel and Cem Ersoy} } @conference {aras2010location, title = {Location and selective routing problem with pricing for the collection of used products}, booktitle = {Computers and Industrial Engineering (CIE), 2010 40th International Conference on}, year = {2010}, pages = {1{\textendash}6}, publisher = {IEEE}, organization = {IEEE}, author = {Necati Aras and Aksen, Deniz and Tekin, Tugrul} } @article {TaskinEtAl2010a, title = {Optimal Multileaf Collimator Leaf Sequencing in IMRT Treatment Planning}, journal = {Operations Research}, volume = {58}, number = {3}, year = {2010}, pages = {674{\textendash}690}, doi = {http://dx.doi.org/10.1287/opre.1090.0759}, author = {Z C Ta{\c s}k{\i}n and J. Cole Smith and H. Edwin Romeijn and James F. Dempsey} } @article {turkougullari2010optimal, title = {Optimal placement, scheduling, and routing to maximize lifetime in sensor networks}, journal = {Journal of the Operational Research Society}, volume = {61}, number = {6}, year = {2010}, pages = {1000{\textendash}1012}, publisher = {Nature Publishing Group}, author = {T{\"u}rko{\u g}ullar{\i}, YB and Necati Aras and I. Kuban Altinel and Ersoy, Cem} } @article {TaskinEtAl2009a, title = {Cutting Plane Algorithms for Solving a Stochastic Edge-Partition Problem}, journal = {Discrete Optimization}, volume = {6}, number = {4}, year = {2009}, pages = {420-435}, doi = {http://dx.doi.org/10.1016/j.disopt.2009.05.004}, author = {Z C Ta{\c s}k{\i}n and J. Cole Smith and Shabbir Ahmed and Andrew J. Schaefer} } @article {TaskinUnal2009, title = {Tactical Level Planning in Float Glass Manufacturing with Co-Production, Random Yields and Substitutable Products}, journal = {European Journal of Operational Research}, volume = {199}, number = {1}, year = {2009}, pages = {252-261}, doi = {http://dx.doi.org/10.1016/j.ejor.2008.11.024}, author = {Z C Ta{\c s}k{\i}n and Ali Tamer {\"U}nal} } @conference {50713928, title = {{An efficient heuristic for placement, scheduling and routing in wireless sensor networks}}, booktitle = {International Symposium on Computer and Information Sciences}, year = {2008}, doi = {10.1109/ISCIS.2008.4717856}, author = {Yavuz Boga{\c c} T{\"u}rkogullari and Necati Aras and I. Kuban Altinel and Cem Ersoy} } @article {Aras2008, title = {Locating collection centers for incentive-dependent returns under a pick-up policy with capacitated vehicles}, journal = {European Journal of Operational Research}, volume = {191}, number = {3}, year = {2008}, pages = {1223{\textendash}1240}, publisher = {Elsevier}, author = {Necati Aras and Aksen, Deniz and G{\"o}n{\"u}l Tanu{\u g}ur, Ay{\c s}e} } @article {MenEtAl2007, title = {An Exact Approach to Direct Aperture Optimization in IMRT Treatment Planning}, journal = {Physics in Medicine and Biology}, volume = {52}, number = {24}, year = {2007}, pages = {7333-7352}, doi = {http://dx.doi.org/10.1088/0031-9155/52/24/009}, author = {Chunhua Men and H. Edwin Romeijn and Z C Ta{\c s}k{\i}n and James F. Dempsey} } @conference {50632893, title = {{Optimal placement and activity scheduling to maximize coverage lifetime in wireless sensor networks}}, booktitle = {International Symposium on Computer and Information Sciences}, year = {2007}, doi = {10.1109/ISCIS.2007.4456874}, author = {Yavuz Boga{\c c} T{\"u}rkogullari and Necati Aras and I. Kuban Altinel and Cem Ersoy} } @article {Tirler;etal:2004a, title = {An Error in the {Kinderman-Ramage} Method and How to Fix It}, journal = {Computational Statistics and Data Analysis}, volume = {47}, number = {3}, year = {2004}, pages = {433{\textendash}440}, author = {Tirler, G{\"u}nter and Dalgaard, Peter and Wolfgang H{\"o}rmann and Leydold, Josef} } @article {Leydold;etal:2003a, title = {An Automatic Code Generator for Nonuniform Random Variate Generation}, journal = {Mathematics and Computers in Simulation}, volume = {62}, number = {3{\textendash}6}, year = {2003}, pages = {405{\textendash}412}, author = {Leydold, Josef and Derflinger, Gerhard and Tirler, G{\"u}nter and Wolfgang H{\"o}rmann} } @article {bilge1997agv, title = {AGV systems with multi-load carriers: basic issues and potential benefits}, journal = {Journal of manufacturing systems}, volume = {16}, number = {3}, year = {1997}, pages = {159{\textendash}174}, publisher = {Elsevier}, author = {{\"U}mit Bilge and Tanchoco, JMA} } @article {eksioglu1997predicting, title = {Predicting peak pinch strength: Artificial neural networks vs. regression}, journal = {Occupational Health and Industrial Medicine}, volume = {1}, number = {36}, year = {1997}, pages = {5}, author = {Mahmut Ek{\c s}io{\u g}lu and Fernandez, JE and Twomey, JM} } @article {eksioglu1996predicting, title = {Predicting peak pinch strength: artificial neural networks vs. regression}, journal = {International Journal of Industrial Ergonomics}, volume = {18}, number = {5}, year = {1996}, pages = {431{\textendash}441}, publisher = {Elsevier}, author = {Mahmut Ek{\c s}io{\u g}lu and Fernandez, Jeffrey E and Twomey, Janet M} } @conference {ekcsiouglu1995artificial, title = {An artificial neural network (ANN)}, booktitle = {Advances in Industrial Ergonomics and Safety VII (Proceedings of the Tenth Annual International Industrial Ergonomics and Safety Conference)}, year = {1995}, pages = {577{\textendash}584}, publisher = {Taylor \& Francis}, organization = {Taylor \& Francis}, author = {Mahmut Ek{\c s}io{\u g}lu and Fernandez, Jeffrey E and Twomey, Janet M} }