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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DELAY OF GERMINATION 1-LIKE 4 acts as an inducer of seed reserve accumulation
Sall, Khadidiatou ; Dekkers, Bas J.W. ; Nonogaki, Mariko ; Katsuragawa, Yoshihiko ; Koyari, Ryosuke ; Hendrix, David ; Willems, Leo A.J. ; Bentsink, Leónie ; Nonogaki, Hiroyuki - \ 2019
The Plant Journal 100 (2019)1. - ISSN 0960-7412 - p. 7 - 19.
abscisic acid - dormancy - hormone - seed development - seed maturation - storage proteins

More than 70% of global food supply depends on seeds. The major seed reserves, such as proteins, lipids, and polysaccharides, are produced during seed maturation. Here, we report that DELAY OF GERMINATION 1-LIKE 4 (DOGL4) is a major inducer of reserve accumulation during seed maturation. The DOGL family proteins are plant-specific proteins of largely unknown biochemical function. DOGL4 shares only limited homology in amino acid sequence with DOG1, a major regulator of seed dormancy. DOGL4 was identified as one of the outstanding abscisic acid (ABA)-induced genes in our RNA sequencing analysis, whereas DOG1 was not induced by ABA. Induction of DOGL4 caused the expression of 70 seed maturation-specific genes, even in germinating seeds, including the major seed reserves ALBUMIN, CRUCIFERIN and OLEOSIN. Although DOG1 affects the expression of many seed maturation genes, the major seed reserve genes induced by DOGL4 are not altered by the dog1 mutation. Furthermore, the reduced dormancy and longevity phenotypes observed in the dog1 seeds were not observed in the dogl4 mutants, suggesting that these two genes have limited functional overlap. Taken together, these results suggest that DOGL4 is a central factor mediating reserve accumulation in seeds, and that the two DOG1 family proteins have diverged over the course of evolution into independent regulators of seed maturation, but retain some overlapping function.

Who to genotype to improve crossbred performance: Purebreds or Crossbreds?
Wientjes, Yvonne - \ 2019
A CUDA approach to compute perishable inventory control policies using value iteration
Ortega, G. ; Hendrix, E.M.T. ; García, I. - \ 2019
Journal of Supercomputing 75 (2019)3. - ISSN 0920-8542 - p. 1580 - 1593.
CUDA - GPU - Inventory control - Value iteration

Dynamic programming (DP) approaches, in particular value iteration, is often seen as a method to derive optimal policies in inventory management. The challenge in this approach is to deal with an increasing state space when handling realistic problems. As a large part of world food production is thrown out due to its perishable character, a motivation exists to have a good look at order policies in retail. Recently, investigation has been introduced to consider substitution of one product by another, when one is out of stock. Taking this tendency into account in a policy requires an increasing state space. Therefore, we investigate the potential of using GPU platforms in order to derive optimal policies when the number of products taken into account simultaneously is increasing. First results show the potential of the GPU approach to accelerate computation in value iteration for DP.

Decomposition-based Inner- and Outer-Refinement Algorithms for Global Optimization
Nowak, Ivo ; Breitfeld, Norman ; Hendrix, E.M.T. ; Njacheun-Njanzoua, Grégoire - \ 2018
Journal of Global Optimization 72 (2018)2. - ISSN 0925-5001 - p. 305 - 321.
Global optimization - Decomposition method - MINLP - Successive approximation - Column generation
Traditional deterministic global optimization methods are often based on a Branch-and-Bound (BB) search tree, which may grow rapidly, preventing the method to find a good solution. Motivated by decomposition-based inner approximation (column generation) methods for solving transport scheduling problems with over 100 million variables, we present a new deterministic decomposition-based successive approximation method for general modular and/or sparse MINLPs. The new method, called Decomposition-based Inner- and Outer-Refinement, is based on a block-separable reformulation of the model into sub-models. It generates inner- and outer-approximations using column generation, which are successively refined by solving many easier MINLP and MIP subproblems in parallel (using BB), instead of searching over one (global) BB search tree. We present preliminary numerical results with Decogo (Decomposition-based Global Optimizer), a new parallel decomposition MINLP solver implemented in Python and Pyomo.
Parallel algorithms for computing the smallest binary tree size in unit simplex refinement
Aparicio, G. ; Salmerón, J.M.G. ; Casado, L.G. ; Asenjo, R. ; Hendrix, E.M.T. - \ 2018
Journal of Parallel and Distributed Computing 112 (2018). - ISSN 0743-7315 - p. 166 - 178.
Regular simplex - Longest edge bisection - Binary tree - TBB - Pthreads - Dynamic number of threads - Shared memory
Refinement of the unit simplex by iterative longest edge bisection (LEB) up to sub-simplices have a size smaller or equal to a given accuracy, generates a binary tree. For a dimension higher than three, the size of the generated tree depends on the bisected LE. There may exist more than one selection sequence of LE that solves the Smallest Binary Tree Size Problem (SBTSP). Solving SBTSP by full enumeration requires considering every possible LE bisection in each sub-simplex. This is an irregular Combinatorial Optimization problem with an increasing computational burden in the dimension and the stopping criterion. Therefore, parallel computing is appealing to find the minimum size for hard instances in a reasonable time.

The aim of this study is to develop and compare threaded algorithms running on multicore systems to solve the SBTS problem. Versions running on multicore systems with a static number of threads using TBB, and a dynamic number of threads using Pthread are compared. Interestingly, TBB scales better than the Pthread implementations for lower dimensional problems. However, when the problem dimension is higher than six, the Pthread approach with a dynamic number of threads finds a solution, where the TBB version fails. This is caused by the smaller memory footprint of the Pthread version, as it traverses deeper branches of the tree than the TBB work-stealing approach.
Order policies for a perishable product in retail
Pauls-Worm, K.G.J. ; Hendrix, E.M.T. - \ 2018
Retail - Order policy - perishable product - non-stationary demand - service level constraint
A challenge of inventory control of perishable products in retail is that in general the age distribution of the items in stock is not known. Only the total numbers of items delivered and sold are recorded, resulting in an estimate of the total items in stock. The exact number may be different from the inventory status according to the checkout system due to damaged items and more waste than expected. We investigate order policies for a product with a maximum shelf life of 3 days at delivery. Demand is non-stationary during the week, but stationary over the weeks. Lead time is one day.
For planning purposes in the supermarket, we search for order policies with fixed reorder days during the week, so we order at least 3 times a week, and at most every day. It is likely to have items of different ages in stock. Customers can pick the items in front of the shelf (FIFO), as preferred and stimulated by the store, or search for the freshest items (LIFO). The store has a target α-service level to meet demand.
A Stochastic Programming (SP) model is presented of the situation in the retailer practice. Several policies to determine the order quantity are studied and compared to a policy from literature. The base is a YS order policy where the reorder days Y are fixed and order-up-to levels S are used, with parameter values generated by an MILP approximation of the SP model. Numerical experiments compare the effectiveness of the policies with respect to costs and reached service levels.
Erratum to: Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study
Hellenkamp, Björn ; Schmid, Sonja ; Doroshenko, Olga ; Opanasyuk, Oleg ; Kühnemuth, Ralf ; Adariani, Soheila Rezaei ; 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 - \ 2018
Nature Methods : techniques for life scientists and chemists 15 (2018)11. - ISSN 1548-7091 - p. 984 - 984.
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: Markov Decision Processes in Practice Springer New York LLC (International Series in Operations Research and Management Science ) - ISBN 9783319477640 - 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 / Boucherie, Richard J., van Dijk, Nico M., Springer New York LLC (International Series in Operations Research and Management Science ) - ISBN 9783319477640 - 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.
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
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