scholarly journals LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search

2019 ◽  
Vol 35 (14) ◽  
pp. i295-i304 ◽  
Author(s):  
Liang Huang ◽  
He Zhang ◽  
Dezhong Deng ◽  
Kai Zhao ◽  
Kaibo Liu ◽  
...  
Keyword(s):  
Dynamic Programming ◽  
Computational Linguistics ◽  
Rna Folding ◽  
Linear Time ◽  
Dynamic Programming Algorithm ◽  
Optimal Solution ◽  
Supplementary Information ◽  
Programming Algorithm ◽  
Time Dynamic ◽  
Approximate Search

Abstract Motivation Predicting the secondary structure of an ribonucleic acid (RNA) sequence is useful in many applications. Existing algorithms [based on dynamic programming] suffer from a major limitation: their runtimes scale cubically with the RNA length, and this slowness limits their use in genome-wide applications. Results We present a novel alternative O(n3)-time dynamic programming algorithm for RNA folding that is amenable to heuristics that make it run in O(n) time and O(n) space, while producing a high-quality approximation to the optimal solution. Inspired by incremental parsing for context-free grammars in computational linguistics, our alternative dynamic programming algorithm scans the sequence in a left-to-right (5′-to-3′) direction rather than in a bottom-up fashion, which allows us to employ the effective beam pruning heuristic. Our work, though inexact, is the first RNA folding algorithm to achieve linear runtime (and linear space) without imposing constraints on the output structure. Surprisingly, our approximate search results in even higher overall accuracy on a diverse database of sequences with known structures. More interestingly, it leads to significantly more accurate predictions on the longest sequence families in that database (16S and 23S Ribosomal RNAs), as well as improved accuracies for long-range base pairs (500+ nucleotides apart), both of which are well known to be challenging for the current models. Availability and implementation Our source code is available at https://github.com/LinearFold/LinearFold, and our webserver is at http://linearfold.org (sequence limit: 100 000nt). Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Folding Polyominoes into (Poly)Cubes

2018 ◽  
Vol 28 (03) ◽  
pp. 197-226 ◽  
Author(s):  
Oswin Aichholzer ◽  
Michael Biro ◽  
Erik D. Demaine ◽  
Martin L. Demaine ◽  
David Eppstein ◽  
...  
Keyword(s):  
Dynamic Programming ◽  
Linear Time ◽  
Dynamic Programming Algorithm ◽  
Unit Cube ◽  
Programming Algorithm ◽  
Regular Tetrahedron ◽  
Time Dynamic ◽  
Constant Size ◽  
Inclusion Relations

We study the problem of folding a polyomino [Formula: see text] into a polycube [Formula: see text], allowing faces of [Formula: see text] to be covered multiple times. First, we define a variety of folding models according to whether the folds (a) must be along grid lines of [Formula: see text] or can divide squares in half (diagonally and/or orthogonally), (b) must be mountain or can be both mountain and valley, (c) can remain flat (forming an angle of [Formula: see text]), and (d) must lie on just the polycube surface or can have interior faces as well. Second, we give all the inclusion relations among all models that fold on the grid lines of [Formula: see text]. Third, we characterize all polyominoes that can fold into a unit cube, in some models. Fourth, we give a linear-time dynamic programming algorithm to fold a tree-shaped polyomino into a constant-size polycube, in some models. Finally, we consider the triangular version of the problem, characterizing which polyiamonds fold into a regular tetrahedron.

scholarly journals A Hybrid Dynamic Programming for Solving Fixed Cost Transportation with Discounted Mechanism

2016 ◽  
Vol 2016 ◽  
pp. 1-9
Author(s):  
Farhad Ghassemi Tari
Keyword(s):  
Dynamic Programming ◽  
Programming Model ◽  
Transportation Network ◽  
Dynamic Programming Algorithm ◽  
Optimal Solution ◽  
Transportation Cost ◽  
Solution Algorithm ◽  
Transportation Costs ◽  
Programming Algorithm ◽  
Fixed Cost

The problem of allocating different types of vehicles for transporting a set of products from a manufacturer to its depots/cross docks, in an existing transportation network, to minimize the total transportation costs, is considered. The distribution network involves a heterogeneous fleet of vehicles, with a variable transportation cost and a fixed cost in which a discount mechanism is applied on the fixed part of the transportation costs. It is assumed that the number of available vehicles is limited for some types. A mathematical programming model in the form of the discrete nonlinear optimization model is proposed. A hybrid dynamic programming algorithm is developed for finding the optimal solution. To increase the computational efficiency of the solution algorithm, several concepts and routines, such as the imbedded state routine, surrogate constraint concept, and bounding schemes, are incorporated in the dynamic programming algorithm. A real world case problem is selected and solved by the proposed solution algorithm, and the optimal solution is obtained.

scholarly journals Comparison of Dynamic Programming Algorithm and Greedy Algorithm on Integer Knapsack Problem in Freight Transportation

2018 ◽  
Vol 5 (1) ◽  
pp. 49 ◽  
Author(s):  
Global Ilham Sampurno ◽  
Endang Sugiharti ◽  
Alamsyah Alamsyah
Keyword(s):  
Dynamic Programming ◽  
Greedy Algorithm ◽  
Knapsack Problem ◽  
Dynamic Programming Algorithm ◽  
Optimal Solution ◽  
Freight Transportation ◽  
Total Weight ◽  
Knapsack Problems ◽  
Programming Algorithm ◽  
Selection Of

At this time the delivery of goods to be familiar because the use of delivery of goods services greatly facilitate customers. PT Post Indonesia is one of the delivery of goods. On the delivery of goods, we often encounter the selection of goods which entered first into the transportation and  held from the delivery. At the time of the selection, there are Knapsack problems that require optimal selection of solutions. Knapsack is a place used as a means of storing or inserting an object. The purpose of this research is to know how to get optimal solution result in solving Integer Knapsack problem on freight transportation by using Dynamic Programming Algorithm and Greedy Algorithm at PT Post Indonesia Semarang. This also knowing the results of the implementation of Greedy Algorithm with Dynamic Programming Algorithm on Integer Knapsack problems on the selection of goods transport in PT Post Indonesia Semarang by applying on the mobile application. The results of this research are made from the results obtained by the Dynamic Programming Algorithm with total weight 5022 kg in 7 days. While the calculation result obtained by Greedy Algorithm, that is total weight of delivery equal to 4496 kg in 7 days. It can be concluded that the calculation results obtained by Dynamic Programming Algorithm in 7 days has a total weight of 526 kg is greater when compared with Greedy Algorithm.

scholarly journals Dynamic Programming and Heuristic for Stochastic Uncapacitated Lot-Sizing Problems with Incremental Quantity Discount

2012 ◽  
Vol 2012 ◽  
pp. 1-21 ◽  
Author(s):  
Yuli Zhang ◽  
Shiji Song ◽  
Cheng Wu ◽  
Wenjun Yin
Keyword(s):  
Dynamic Programming ◽  
Lot Sizing ◽  
Dynamic Programming Algorithm ◽  
Optimal Solution ◽  
Mixed Integer ◽  
Programming Algorithm ◽  
Quantity Discount ◽  
Path Property ◽  
Commercial Solver

The stochastic uncapacitated lot-sizing problems with incremental quantity discount have been studied in this paper. First, a multistage stochastic mixed integer model is established by the scenario analysis approach and an equivalent reformulation is obtained through proper relaxation under the decreasing unit order price assumption. The proposed reformulation allows us to extend the production-path property to this framework, and furthermore we provide a more accurate characterization of the optimal solution. Then, a backward dynamic programming algorithm is developed to obtain the optimal solution and considering its exponential computation complexity in term of time stages, we design a new rolling horizon heuristic based on the proposed property. Comparisons with the commercial solver CPLEX and other heuristics indicate better performance of our proposed algorithms in both quality of solution and run time.

Optimal Bus Stop Spacing Through Dynamic Programming and Geographic Modeling

2000 ◽  
Vol 1731 (1) ◽  
pp. 15-22 ◽  
Author(s):  
Peter G. Furth ◽  
Adam B. Rahbee
Keyword(s):  
Dynamic Programming ◽  
Operating Cost ◽  
Dynamic Programming Algorithm ◽  
Optimal Solution ◽  
Programming Algorithm ◽  
Demand Distribution ◽  
Bus Stop ◽  
Geographic Modeling ◽  
Bus Stop Spacing ◽  
Stop Spacing

A discrete approach was used to model the impacts of changing bus-stop spacing on a bus route. Among the impacts were delays to through riders, increased operating cost because of stopping delays, and shorter walking times perpendicular to the route. Every intersection along the route was treated as a candidate stop location. A simple geographic model was used to distribute the demand observed at existing stops to cross-streets and parallel streets in the route service area, resulting in a demand distribution that included concentrated and distributed demands. An efficient, dynamic programming algorithm was used to determine the optimal bus-stop locations. The model was compared with the continuum approach used in previous studies. A bus route in Boston was modeled, in which the optimal solution was an average stop spacing of 400 m (4 stops/mi), in sharp contrast to the existing average spacing of 200 m (8 stops/mi). The model may also be used to evaluate the impacts of adding, removing, or relocating selected stops.

scholarly journals On the exact separation of cover inequalities of maximum-depth

2021 ◽  
Author(s):  
Daniele Catanzaro ◽  
Stefano Coniglio ◽  
Fabio Furini
Keyword(s):  
Dynamic Programming ◽  
Knapsack Problem ◽  
Dynamic Programming Algorithm ◽  
Maximum Depth ◽  
Knapsack Problems ◽  
Programming Algorithm ◽  
Separation Problem ◽  
Time Dynamic ◽  
Cover Inequalities ◽  
Exact Separation

AbstractWe investigate the problem of separating cover inequalities of maximum-depth exactly. We propose a pseudopolynomial-time dynamic-programming algorithm for its solution, thanks to which we show that this problem is weakly $${\mathcal {N}}{\mathcal {P}}$$ N P -hard (similarly to the problem of separating cover inequalities of maximum violation). We carry out extensive computational experiments on instances of the knapsack and the multi-dimensional knapsack problems with and without conflict constraints. The results show that, with a cutting-plane generation method based on the maximum-depth criterion, we can optimize over the cover-inequality closure by generating a number of cuts smaller than when adopting the standard maximum-violation criterion. We also introduce the Point-to-Hyperplane Distance Knapsack Problem (PHD-KP), a problem closely related to the separation problem for maximum-depth cover inequalities, and show how the proposed dynamic programming algorithm can be adapted for effectively solving the PHD-KP as well.

scholarly journals Diversity of Solutions: An Exploration Through the Lens of Fixed-Parameter Tractability Theory

2020 ◽  
Author(s):  
Julien Baste ◽  
Michael R. Fellows ◽  
Lars Jaffke ◽  
Tomáš Masařík ◽  
Mateus de Oliveira Oliveira ◽  
...  
Keyword(s):  
Dynamic Programming ◽  
Dynamic Programming Algorithm ◽  
Practical Interest ◽  
Optimal Solution ◽  
Combinatorial Problem ◽  
Combinatorial Problems ◽  
Point Of View ◽  
Programming Algorithm ◽  
Fixed Parameter Tractability ◽  
Fixed Parameter

When modeling an application of practical relevance as an instance of a combinatorial problem X, we are often interested not merely in finding one optimal solution for that instance, but in finding a sufficiently diverse collection of good solutions. In this work we initiate a systematic study of diversity from the point of view of fixed-parameter tractability theory. We consider an intuitive notion of diversity of a collection of solutions which suits a large variety of combinatorial problems of practical interest. Our main contribution is an algorithmic framework which --automatically-- converts a tree-decomposition-based dynamic programming algorithm for a given combinatorial problem X into a dynamic programming algorithm for the diverse version of X. Surprisingly, our algorithm has a polynomial dependence on the diversity parameter.

scholarly journals An improved heuristic-dynamic programming algorithm for rectangular cutting problem

2020 ◽  
Vol 17 (3) ◽  
pp. 717-735
Author(s):  
Aihua Yin ◽  
Chong Chen ◽  
Dongping Hu ◽  
Jianghai Huang ◽  
Fan Yang
Keyword(s):  
Dynamic Programming ◽  
Dynamic Programming Algorithm ◽  
Optimal Solution ◽  
Computation Time ◽  
Programming Algorithm ◽  
Recursive Method ◽  
Two Dimensional ◽  
One Dimensional ◽  
Block Width ◽  
Cutting Problem

In this paper, the two-dimensional cutting problem with defects is discussed. The objective is to cut some rectangles in a given shape and direction without overlapping the defects from the rectangular plate and maximize some profit associated. An Improved Heuristic-Dynamic Program (IHDP) is presented to solve the problem. In this algorithm, the discrete set contains not only the solution of one-dimensional knapsack problem with small rectangular block width and height, but also the cutting positions of one unit outside four boundaries of each defect. In addition, the denormalization recursive method is used to further decompose the sub problem with defects. The algorithm computes thousands of typical instances. The computational experimental results show that IHDP obtains most of the optimal solution of these instances, and its computation time is less than that of the latest literature algorithms.

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