Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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On the δ-service level for demand substitution in inventory control
Buisman, Marjolein ; Haijema, Rene ; Hendrix, Eligius M.T. - \ 2018
IFAC-PapersOnLine 51 (2018)11. - ISSN 2405-8963 - p. 963 - 967.
Green Supply Chain - Inventory control - Mathematical Approaches for Scheduling - Poisson - Service level - Stochastic Processes - Substitution

In retail, it is usual to measure the performance of inventory control by a so-called service level which measures the number of days (probability) that demand is fulfilled for a certain product, i.e. the product is not out of stock. Part of the customers that do not encounter the product in stock will look for a substitute. To measure the performance, we introduce a so-called δ-service level which measures the availability of the substitute. We investigate the effect of safety levels and substitution probability on the δ-service level and illustrate them based on the case of poisson demand.

On solving the Best-Worst Method in multi-criteria decision-making
Beemsterboer, D.J.C. ; Hendrix, E.M.T. ; Claassen, G.D.H. - \ 2018
IFAC-PapersOnLine 51 (2018)11. - ISSN 2405-8963 - p. 1660 - 1665.
Best-worst method - Consistency - Convex optimisation - Linear Programming - Linearization - Mixed-integer linear programming - Model approximation - Multiple-criterion optimisation

Decision-making often refers to ranking alternatives based on many involved criteria. Since the introduction of the Analytic Hierarchy Process (AHP) in 1980, pairwise comparisons of criteria have a long tradition in multi-criteria decision-making. One of the main concerns of the AHP refers to the inconsistency of decision makers in pairwise comparisons. Recently, the Best-Worst Method (BWM) was introduced to reduce the inconsistency by a concept that needs substantially less pairwise comparisons. The BWM includes solving a non-linear model (NLM) to derive the weights from the comparisons. A linear model (LM) was introduced in a follow-up to approximate the original NLM. This paper shows that the optimal weights of the proposed linear model (LM) may differ substantially from the optimal weights of the original NLM model. Moreover, this paper provides an MILP model approximation (MILM) which can be solved by standard optimization software and illustrates that its solution approximates the optimal weights of the original NLM model arbitrarily close. Since consistency in pairwise comparisons is usually not self-evident in practice, using approximation MILM to derive unique solutions of the original NLM, extends the applicability of the Best-Worst Method.

Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study
Hellenkamp, Björn ; Schmid, Sonja ; Doroshenko, Olga ; Opanasyuk, Oleg ; Kühnemuth, Ralf ; Rezaei Adariani, Soheila ; Ambrose, Benjamin ; Aznauryan, Mikayel ; Barth, Anders ; Birkedal, Victoria ; Bowen, Mark E. ; Chen, Hongtao ; Cordes, Thorben ; Eilert, Tobias ; Fijen, Carel ; Gebhardt, Christian ; Götz, Markus ; Gouridis, Giorgos ; Gratton, Enrico ; Ha, Taekjip ; Hao, Pengyu ; Hanke, Christian A. ; Hartmann, Andreas ; Hendrix, Jelle ; Hildebrandt, Lasse L. ; Hirschfeld, Verena ; Hohlbein, Johannes ; Hua, Boyang ; Hübner, Christian G. ; Kallis, Eleni ; Kapanidis, Achillefs N. ; Kim, Jae Yeol ; Krainer, Georg ; Lamb, Don C. ; Lee, Nam Ki ; Lemke, Edward A. ; Levesque, Brié ; Levitus, Marcia ; McCann, James J. ; Naredi-Rainer, Nikolaus ; Nettels, Daniel ; Ngo, Thuy ; Qiu, Ruoyi ; Robb, Nicole C. ; Röcker, Carlheinz ; Sanabria, Hugo ; Schlierf, Michael ; Schröder, Tim ; Schuler, Benjamin ; Seidel, Henning ; Streit, Lisa ; Thurn, Johann ; Tinnefeld, Philip ; Tyagi, Swati ; Vandenberk, Niels ; Vera, Andrés Manuel ; Weninger, Keith R. ; Wünsch, Bettina ; Yanez-Orozco, Inna S. ; Michaelis, Jens ; Seidel, Claus A.M. ; Craggs, Timothy D. ; Hugel, Thorsten - \ 2018
Nature Methods : techniques for life scientists and chemists 15 (2018)9. - ISSN 1548-7091 - p. 669 - 676.

Single-molecule Förster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards to ensure the reproducibility and accuracy of measurements of FRET efficiencies are currently lacking. Here we report the results of a comparative blind study in which 20 labs determined the FRET efficiencies (E) of several dye-labeled DNA duplexes. Using a unified, straightforward method, we obtained FRET efficiencies with s.d. between ±0.02 and ±0.05. We suggest experimental and computational procedures for converting FRET efficiencies into accurate distances, and discuss potential uncertainties in the experiment and the modeling. Our quantitative assessment of the reproducibility of intensity-based smFRET measurements and a unified correction procedure represents an important step toward the validation of distance networks, with the ultimate aim of achieving reliable structural models of biomolecular systems by smFRET-based hybrid methods.

Inventory control for a non-stationary demand perishable product: comparing policies and solution methods
Pauls-Worm, K.G.J. ; Hendrix, E.M.T. - \ 2018
Málaga : Universidad de Málaga - 15 p.
This paper summarizes our findings with respect to order policies for an inventory control problem for a perishable product with a maximum fixed shelf life in a periodic review system, where chance constraints play a role. A Stochastic Programming (SP) problem is presented which models a practical production planning problem over a finite horizon. Perishability, non-stationary demand, fixed ordering cost and a service level (chance) constraint make this problem complex. Inventory control handles this type of models with so-called order policies. We compare three different policies: a) production timing is fixed in advance combined with an orderup- to level, b) production timing is fixed in advance and the production quantity takes the agedistribution into account and c) the decision of the order quantity depends on the age-distribution of the items in stock. Several theoretical properties for the optimal solutions of the policies are presented. In this paper, four different solution approaches from earlier studies are used to derive parameter values for the order policies. For policy a), we use MILP approximations and alternatively the so-called Smoothed Monte Carlo method with sampled demand to optimize values. For policy b), we outline a sample based approach to determine the order quantities. The flexible policy c) is derived by SDP. All policies are compared on feasibility regarding the α-service level, computation time and ease of implementation to support management in the choice for an order policy.
Accelerating an algorithm for perishable inventory control on heterogeneous platforms
Gutierrez-Alcoba, A. ; Ortega, G. ; Hendrix, E.M.T. ; García, I. - \ 2017
Journal of Parallel and Distributed Computing 104 (2017). - ISSN 0743-7315 - p. 12 - 18.
This paper analyses and evaluates parallel implementations of an optimization algorithm for perishable inventory control problems. This iterative algorithm has high computational requirements when solving large problems. Therefore, the use of parallel and distributed computing reduces the execution time and improves the quality of the solutions. This work investigates two implementations on heterogeneous platforms: (1) a MPI-PTHREADS version; and (2) a multi-GPU version. A comparison of these implementations has been carried out. Experimental results show the benefits of using parallel and distributed codes to solve this kind of problems. Furthermore, the distribution of the workload among the available processing elements is a challenging problem. This distribution of tasks can be modelled as a Bin-Packing problem. This implies that the selection of the set of tasks assigned to every processing element requires the design of a heuristic capable of efficiently balancing the workload statically with no significant overhead. This heuristic has been used for the parallel implementations of the optimization for perishable inventory control problem.
A model for optimal fleet composition of vessels for offshore wind farm maintenance
Alcoba, A.G. ; Ortega, G. ; Hendrix, E.M.T. ; Halvorsen-Waere, E.E. ; Haugland, Dag - \ 2017
Procedia Computer Science 108 (2017). - ISSN 1877-0509 - p. 1512 - 1521.
We present a discrete optimisation model that chooses an optimal fleet of vessels to support maintenance operations at Offshore Wind Farms (OFWs). The model is presented as a bi-level problem. On the first (tactical) level, decisions are made on the fleet composition for a certain time horizon. On the second (operational) level, the fleet is used to optimise the schedule of operations needed at the OWF, given events of failures and weather conditions.
A simple heuristic for perishable inventory control under non-stationary stochastic demand
Alcoba, A.G. ; Rossi, R. ; Martin-Barragan, B. ; Hendrix, E.M.T. - \ 2017
International Journal of Production Research 55 (2017)7. - ISSN 0020-7543 - p. 1885 - 1897.
In this paper, we study the single-item single-stocking location non-stationary stochastic lot sizing problem for a perishable product. We consider fixed and proportional ordering cost, holding cost and penalty cost. The item features a limited shelf life, therefore we also take into account a variable cost of disposal. We derive exact analytical expressions to determine the expected value of the inventory of different ages. We also discuss a good approximation for the case in which the shelf-life is limited. To tackle this problem, we introduce two new heuristics that extend Silver’s heuristic and compare them to an optimal Stochastic Dynamic Programming policy in the context of a numerical study. Our results demonstrate the effectiveness of our approach.
On grid aware refinement of the unit hypercube and simplex: Focus on the complete tree size
Casado, L.G. ; Hendrix, E.M.T. ; Salmerón, J.M.G. ; Tóth, B.G. ; García, I. - \ 2017
In: Computational Science and Its Applications - ICCSA 2017. - Cham : Springer (Lecture Notes in Computer Science (LNCS) ) - ISBN 9783319623979 - p. 165 - 180.
Branch and bound (BnB) Global Optimization algorithms can be used to find the global optimum (minimum) of a multiextremal function over the unit hypercube and unit simplex with a guaranteed accuracy. Subdivision strategies can take the information of the evaluated points into account leading to irregular shaped subsets. This study focuses on the passive generation of spatial subdivisions aiming at evaluating points on a predefined grid. The efficiency measure is in terms of the complete tree size, or worst case BnB scenario, with a termination criterion on the subset size. Longest edge bisection is used as a benchmark. It is shown that taking the grid for a given termination tolerance into account, other general partitions exist that improve the BnB upper bound on the number of evaluated points and subsets.
H2O2 as a candidate bottleneck for MnP activity during cultivation of Agaricus bisporus in compost
Vos, Aurin M. ; Jurak, E. ; Pelkmans, Jordi F. ; Herman, Koen ; Pels, Gill ; Baars, J.J.P. ; Hendrix, E.A.H.J. ; Kabel, M.A. ; Lugones, Luis G. ; Wösten, Han A.B. - \ 2017
AMB Express 7 (2017). - ISSN 2191-0855
Degradation of lignin by fungi enhances availability of cellulose and hemicellulose in plant waste and thereby increases the amount of carbon source available to these microorganisms. The button mushroom Agaricus bisporus
degrades only about half of the lignin in compost and about 40% of the carbohydrates remain unutilized during mushroom cultivation. Here it was assessed whether over-expression of the manganese peroxidase gene mnp1
improves lignin degradation and, as a consequence, carbohydrate breakdown by A. bisporus. Transformants expressing mnp1 under the control of actin regulatory sequences produced MnP activity in malt extract medium, while the
parental strain A15 did not. MnP activity was increased 0.3- and 3-fold at casing and after the 2nd flush of a semicommercial cultivation, respectively, when compared to strain A15. Pyrolysis-GC–MS showed that overexpression of
MnP decreased phenylmethane and phenylethane type lignin relative to the phenylpropane type after the 2nd flush.
However, it neither affected the syringyl/guaiacyl derived residue ratio nor the ratio of oxidized to non-oxidized lignin residues. Moreover, the carbohydrate content and accessibility was not affected in compost. Notably, the capacity
of compost extract to consume the MnP co-factor H2O2 was 4- to 8-fold higher than its production. This may well explain why over-expression of mnp1 did not improve carbohydrate degradation in compost. In fact, availability of
H2O2 may limit lignin degradation by wild-type A. bisporus.
On parallel Branch and Bound frameworks for Global Optimization
Herrera, Juan F.R. ; Salmerón, José M.G. ; Hendrix, Eligius M.T. ; Asenjo, Rafael ; Casado, Leocadio G. - \ 2017
Journal of Global Optimization 69 (2017)3. - ISSN 0925-5001 - p. 547 - 560.
Branch-and-Bound - Framework - Load balancing - Shared-memory - TBB
Branch and Bound (B&B) algorithms are known to exhibit an irregularity of the search tree. Therefore, developing a parallel approach for this kind of algorithms is a challenge. The efficiency of a B&B algorithm depends on the chosen Branching, Bounding, Selection, Rejection, and Termination rules. The question we investigate is how the chosen platform consisting of programming language, used libraries, or skeletons influences programming effort and algorithm performance. Selection rule and data management structures are usually hidden to programmers for frameworks with a high level of abstraction, as well as the load balancing strategy, when the algorithm is run in parallel. We investigate the question by implementing a multidimensional Global Optimization B&B algorithm with the help of three frameworks with a different level of abstraction (from more to less): Bobpp, Threading Building Blocks (TBB), and a customized Pthread implementation. The following has been found. The Bobpp implementation is easy to code, but exhibits the poorest scalability. On the contrast, the TBB and Pthread implementations scale almost linearly on the used platform. The TBB approach shows a slightly better productivity.
Dynamic control of traffic lights
Haijema, Rene ; Hendrix, Eligius M.T. ; Wal, J. van der - \ 2017
In: International Series in Operations Research and Management Science Springer New York LLC (International Series in Operations Research and Management Science ) - p. 371 - 386.
Traffic lights are put in place to dynamically change priority between traffic participants. Commonly, the duration of green intervals and the grouping, and ordering in which traffic flows are served are pre-fixed. In this chapter, the problem of minimizing vehicle delay at isolated intersections is formulated as a Markov Decision Process (MDP). Solving the MDP is hampered by a large multi-dimensional state space that contains information on the traffic lights and on the queue lengths. For a single intersection, an approximate solution is provided that is based on policy iteration (PI) and decomposition of the state space. The approach starts with a Markov chain analysis of a pre-timed control policy, called Fixed Cycle (FC). The computation of relative states values for FC can be done fast, since, under FC, the multi-dimensional state space can be decomposed into sub-spaces per traffic flow. The policy obtained by executing a single iteration of Policy Iteration (PI) using relative values is called RV 1. RV1 is compared for two intersections by simulation with FC, a few dynamic (vehicle actuated) policies, and an optimal MDP policy (if tractable). RV1, approximately solves the MDP, and compared to FC, it shows less delay of vehicles, shorter queues, and is robust to changes in traffic volumes. The approach shows very short computation times, which allows the application to networks of intersections, and the inclusion of estimated arrival times of vehicles approaching the intersection.
Optimal fishery policies
Hendrix, Eligius M.T. ; Haijema, Rene ; Dijk, Diana van - \ 2017
In: International Series in Operations Research and Management Science Springer New York LLC (International Series in Operations Research and Management Science ) - p. 425 - 438.
Continuous state space - Discretization - Dynamic programming - Fishery - Stochastic programming
This paper describes and analyses a bi-level Markov Decision Problem (MDP). The model has been used to study questions on the setting of fisheries quota. The problem extends earlier models in literature and describes fish stock and economic dynamics. At the first level, an authority decides on the quota to be fished keeping in mind long term revenues. At the second level, fishermen react on the quota set as well as on the current states of fish stock and fleet capacity by deciding on their investment and fishery effort. An analysis of the behaviour of the model is given and used to decide on how to discretize the state space. The aim is to derive optimum quota settings based on value iteration. This chapter illustrates how aMDP with continuous state and action space can be solved by truncation and discretization of the state space and applying interpolation in the value iteration.
Analysing a MDP model for fisheries policies
Hendrix, E.M.T. ; Haijema, R. ; Dijk, Diana van - \ 2017
In: Markov Decision Processes in Practice / Boucherie, R., van Dijk, N.M., Springer (International Series in Operations Research & Management Science ) - ISBN 9783319477640
MDP for controlling traffic lights
Haijema, R. ; Hendrix, E.M.T. - \ 2017
In: Markov Decision Processes in Practice / Boucherie, Richard, van Dijk, Nico. M., Springer International Publishing (International Series in Operations Research & Management Science ) - ISBN 9783319477640
A Minimax Regret Analysis of Flood Risk Management Strategies Under Climate Change Uncertainty and Emerging Information
Pol, T.D. van der; Gabbert, S. ; Weikard, H.P. ; Ierland, E.C. van; Hendrix, E.M.T. - \ 2017
Environmental and Resource Economics 68 (2017)4. - ISSN 0924-6460 - p. 1087 - 1109.
Adaptive management - Climate change - Flexibility - Flood risk - Learning - Minimax regret - Robust optimisation

This paper studies the dynamic application of the minimax regret (MR) decision criterion to identify robust flood risk management strategies under climate change uncertainty and emerging information. An MR method is developed that uses multiple learning scenarios, for example about sea level rise or river peak flow development, to analyse effects of changes in information on optimal investment in flood protection. To illustrate the method, optimal dike height and floodplain development are studied in a conceptual model, and conventional and adaptive MR solutions are compared. A dynamic application of the MR decision criterion allows investments to be changed after new information on climate change impacts, which has an effect on today’s optimal investments. The results suggest that adaptive MR solutions are more robust than the solutions obtained from a conventional MR analysis of investments in flood protection. Moreover, adaptive MR analysis with multiple learning scenarios is more general and contains conventional MR analysis as a special case.

An Adjustment Restriction on Fish Quota : Resource Rents, Overcapacity and Recovery of Fish Stock
Dijk, Diana van; Hendrix, E.M.T. ; Haijema, Rene ; Groeneveld, R.A. ; Ierland, E.C. van - \ 2017
Environmental and Resource Economics 67 (2017)2. - ISSN 0924-6460 - p. 203 - 230.
Fisheries management - Investment behavior - Quota adjustment restriction - Stochastic dynamic programming

Management objectives of the European Union for North Sea fish stocks are shifting towards considering both biological sustainability and economic benefits. As part of multiannual management plans, an adjustment restriction on fish quota has been introduced. Its objective is to obtain an efficient fish stock and to reduce overcapacity for the fishing industry. We develop and apply a bi-level stochastic dynamic programming model to study the effect of a quota adjustment restriction on the net present value of resource rents, overcapacity and fish stock, when the system is recovering from a downward environmental shock. At level one, a policy maker sets the quota, considering fishermen behavior, stochastic fish stock dynamics, capital stock dynamics and a quota adjustment restriction. At level two, fishermen harvest myopically and make long-term investment decisions, assuming that fish stock and quota do not change over time. The two levels are linked by the quota, which is optimized by the policy maker at level one and becomes a restriction for myopic harvest and long-term investment decisions of fishermen at level two. Our analysis suggests that in the long run, overcapacity can be reduced by 54 % at modest costs, namely at a 1 % reduction in the net present value of resource rents. Long and short run sustainability of the fish stock is not affected.

Generating a smallest binary tree by proper selection of the longest edges to bisect in a unit simplex refinement
Salmerón, J.M.G. ; Aparicio, G. ; Casado, L.G. ; García, I. ; Hendrix, E.M.T. ; Tóth, B.G. - \ 2017
Journal of Combinatorial Optimization 33 (2017)2. - ISSN 1382-6905 - p. 389 - 402.
Bisection sequence - Branch-and-bound - Combinatorial optimization - Longest edge bisection - Regular simplex

In several areas like global optimization using branch-and-bound methods for mixture design, the unit n-simplex is refined by longest edge bisection (LEB). This process provides a binary search tree. For (Formula presented.), simplices appearing during the refinement process can have more than one longest edge (LE). The size of the resulting binary tree depends on the specific sequence of bisected longest edges. The questions are how to calculate the size of one of the smallest binary trees generated by LEB and how to find the corresponding sequence of LEs to bisect, which can be represented by a set of LE indices. Algorithms answering these questions are presented here. We focus on sets of LE indices that are repeated at a level of the binary tree. A set of LEs was presented in Aparicio et al. (Informatica 26(1):17–32, 2015), for (Formula presented.). An additional question is whether this set is the best one under the so-called (Formula presented.)-valid condition.

Fixing the reorder days in retail: order policies for a perishable product
Pauls-Worm, K.G.J. ; Hendrix, E.M.T. - \ 2016
Fixed reorder days for a perishable product in retail
Pauls-Worm, K.G.J. ; Hendrix, E.M.T. - \ 2016
In: Book of Abstracts, 19th International Symposium on Inventories, ISIR 2016. - International Society for Inventory Research (ISIR) - p. 120 - 120.
On B&B Algorithms in Greenhouse Climate Control
Hermelink, Marleen ; Hendrix, E.M.T. ; Haijema, R. - \ 2016
In: Proceedings of the XIII Global Optimization Workshop. - Braga : - ISBN 9789892067643 - p. 77 - 88.
Climate control is essential for managing the production of horticulture in greenhouses. One of the traditional ways to control the climate in the greenhouse is Model Predictive Control (MPC). This paper studies the potential of using branch and bound algorithms in order to effectively reach the best control in MPC.
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