Search · four archives
Search · four archives
12 papers · ranked by Valyu relevance
Peter Steffen, Robert Giegerich
Background Dynamic programming is a widely used programming technique in bioinformatics. In sharp contrast to the simplicity of textbook examples, implementing a dynamic programming algorithm for a novel and non-trivial application is a tedious and error prone task. The algebraic dynamic programming approach seeks to…
Christian Höner zu Siederdissen, Sonja J Prohaska, Peter F Stadler
Background Dynamic programming algorithms provide exact solutions to many problems in computational biology, such as sequence alignment, RNA folding, hidden Markov models (HMMs), and scoring of phylogenetic trees. Structurally analogous algorithms compute optimal solutions, evaluate score distributions, and perform…
Cédric Saule, Robert Giegerich
Pareto optimization combines independent objectives by computing the Pareto front of its search space, defined as the set of all solutions for which no other candidate solution scores better under all objectives. This gives, in a precise sense, better information than an artificial amalgamation of different scores into…
Georg Sauthoff, Mathias Möhl, Stefan Janssen, Robert Giegerich
Motivation: Dynamic programming is ubiquitous in bioinformatics. Developing and implementing non-trivial dynamic programming algorithms is often error prone and tedious. Bellman’s GAP is a new programming system, designed to ease the development of bioinformatics tools based on the dynamic programming technique.…
Sungho Shin, Ophelia S. Venturelli, Victor M. Zavala, Qing Nie
We present a nonlinear programming (NLP) framework for the scalable solution of parameter estimation problems that arise in dynamic modeling of biological systems. Such problems are computationally challenging because they often involve highly nonlinear and stiff differential equations as well as many experimental data…
Xiaowei Xing, Dong Eui Chang, Biswanath Samanta
The paper develops the adaptive dynamic programming toolbox (ADPT), which is a MATLAB-based software package and computationally solves optimal control problems for continuous-time control-affine systems. The ADPT produces approximate optimal feedback controls by employing the adaptive dynamic programming technique and…
Mohammad Moradi, Sama Goliaei, Mohammad-Hadi Foroughmand-Araabi, Gareth J. Baxter
'Gareth J. Baxter'] Control problem in a biological system is the problem of finding an interventional policy for changing the state of the biological system from an undesirable state, e.g. disease, into a desirable healthy state. Boolean networks are utilized as a mathematical model for gene regulatory networks. This…
Mateusz Gruzewski, Marek Palkowski, Ramon Antonio Rodriges Zalipynis
In this article, we present an efficient and concise OpenMP implementation of the Nussinov RNA folding algorithm, a well-known representative of non-serial polyadic dynamic programming (NPDP). Our goal is to develop an optimized implementation that can serve as a template for related dynamic programming applications.…
David P. Morton, Oscar Dowson, Bernardo K. Pagnoncelli
We study a class of multi-stage stochastic programs, which incorporate modeling features from Markov decision processes (MDPs). This class includes structured MDPs with continuous action and state spaces. We extend policy graphs to include decision-dependent uncertainty for one-step transition probabilities as well as…
Barouch Matzliach, Irad Ben-Gal, Evgeny Kagan, Gholamreza Anbarjafari
'Gholamreza Anbarjafari'] This paper addresses the problem of detecting multiple static and mobile targets by an autonomous mobile agent acting under uncertainty. It is assumed that the agent is able to detect targets at different distances and that the detection includes errors of the first and second types. The goal…
Steve N'Guyen, Clément Moulin-Frier, Jacques Droulez, Matteo G. A. Paris
'Matteo G. A. Paris'] We propose a new approach for solving a class of discrete decision making problems under uncertainty with positive cost. This issue concerns multiple and diverse fields such as engineering, economics, artificial intelligence, cognitive science and many others. Basically, an agent has to choose a…
Zhanyou Ma, Zhaokai Li, Weijun Li, Yingnan Gao + 2 more
In order to solve the problems in fuzzy computation tree logic model checking with cost operator, we propose a fuzzy decision process computation tree logic model checking method with cost. Firstly, we introduce a fuzzy decision process model with cost, which can not only describe the uncertain choice and transition…