• PSI-BLAST

  • Referenced in 233 articles [sw17324]
  • heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three ... speed of the original. In addition, a method is introduced for automatically combining statistically significant...
  • SPARSE-QR

  • Referenced in 17 articles [sw05215]
  • instead solved by the augmented system method. The accuracy in computed solutions is strongly dependent ... therefore be approximated by a simple heuristic. We describe a multifrontal method for sparse...
  • Algorithm 39

  • Referenced in 42 articles [sw20048]
  • combinatorial problem of clusterwise discrete linear approximation is defined as finding a given number ... minimum. The FORTRAN implementation of a heuristic solution method and a numerical example are given...
  • SchurRings

  • Referenced in 4 articles [sw11785]
  • application, we implement a heuristic method for approximating equivariant resolutions of modules over polynomial rings...
  • SCIP-SDP

  • Referenced in 12 articles [sw15618]
  • presolve routines, primal heuristics, a dual fixing method, and an linear approximation procedure for MISDPs...
  • CCLS

  • Referenced in 18 articles [sw36049]
  • very large, which calls for efficient approximate methods, mainly stochastic local search (SLS) ones. However ... this paper, we propose a new heuristic called CCM for weighted...
  • SpeedHap

  • Referenced in 2 articles [sw35353]
  • this paper we propose a new heuristic method for the problem of haplotype reconstruction ... also hard to approximate with guarantees. Therefore fast heuristics have been proposed. In this ... paper we describe SpeedHap, a new heuristic method that is able to tackle the case...
  • GANSO

  • Referenced in 6 articles [sw00319]
  • Rubinov [Abstract convexity and global approximation (2000; Zbl 0098.90074)], in the programming library GANSO. GANSO ... derivative-free bundle method, the extended cutting angle method, dynamical system-based optimization and their ... various combinations and heuristics. We outline the main ideas behind each method, and report...
  • NCVX

  • Referenced in 4 articles [sw24075]
  • convex sets. We describe general heuristics to approximately solve a wide variety of problems with ... heuristics, which employ convex relaxations, convex restrictions, local neighbour search methods, and the alternating direction ... tuning. We describe an implementation of these methods in a package called NCVX ... that our general purpose heuristics are effective in finding approximate solutions to a wide variety...
  • NeMa

  • Referenced in 4 articles [sw18899]
  • also hard to approximate. (3) We propose a heuristic algorithm for solving the problem based ... techniques to improve the efficiency of our method. (4) We empirically verify that NeMa...
  • ANewDsc

  • Referenced in 10 articles [sw19984]
  • convergence against clusters of roots, and approximate computation to decrease the required precision. It achieves ... method for computing all complex roots and improving upon the complexity of other subdivision methods ... highly efficient realization of the classical Descartes method and currently serves as the default real ... performance of ANewDsc over other subdivision methods also transfers into practice. These experiments also show...
  • fastSTRUCTURE

  • Referenced in 4 articles [sw25207]
  • challenges. Here, we develop efficient algorithms for approximate inference of the model underlying the STRUCTURE ... program using a variational Bayesian framework. Variational methods pose the problem of computing relevant posterior ... inference tools. In addition, we propose useful heuristic scores to identify the number of populations...
  • StarFLIP

  • Referenced in 3 articles [sw04739]
  • typically too complex to solve with exact methods. Additionally, the problems often have to observe ... combination of approximate reasoning based constraints and iterative optimization based heuristics that help to model...
  • sccf

  • Referenced in 2 articles [sw37297]
  • some heuristics for approximately solving instances of these problems. These heuristics can be used ... tractable lower bounds. We illustrate our heuristic methods by applying them to various examples...
  • IPknot

  • Referenced in 3 articles [sw17124]
  • Results: We propose IPknot, a novel computational method for predicting RNA secondary structures with pseudoknots ... pseudoknot-free substructures and approximates a base-pairing probability distribution that considers pseudoknots, leading ... quite fast. In addition, we propose a heuristic algorithm for refining base-paring probabilities ... time as compared with several competitive prediction methods. Availability: The program of IPknot is available...
  • MDVRPTW

  • Referenced in 3 articles [sw02974]
  • this problem class, two-step approximation methods of the type `cluster first, route second’ seem ... distances are added to two assignment heuristics, that previously only used distance to evaluate proximity...
  • Pylogeny

  • Referenced in 1 article [sw28977]
  • such as FastTree and RAxML to acquire approximate ML trees. The following tasks are capable ... phylogenetic tree landscapes. Construct and analyse heuristic methods to search these spaces. Build and rearrange...
  • FEMB

  • Referenced in 3 articles [sw19499]
  • supplementary material for the book Approximation and Modeling with B-Splines (OT132). . The programs ... illustrating the methods described in the SIAM book Finite Element Methods with B-Splines ... which to some extent are based on heuristic strategies, has been emphasized. As a consequence...
  • VOROPACK-D

  • Referenced in 2 articles [sw40483]
  • moderate sizes. Here we introduce a heuristic algorithm which finds sufficiently good solutions in realtime ... property of Voronoi diagram and finds an approximate solution of DPP in O(nlog ... size, thus called a big-disk-first method. The location of a placement is determined...
  • ODEA

  • Referenced in 3 articles [sw07671]
  • polynomial time algorithms as well as heuristic approximation schemes. There is an apparent lack ... this book describes in detail the methods developed for encoding in our software. We devise...