• bnlearn

  • Referenced in 68 articles [sw08265]
  • structure learning algorithms for both discrete and Gaussian networks, along with many score functions...
  • GRAPPA

  • Referenced in 12 articles [sw17255]
  • because the running time of its scoring algorithm grows exponentially with the number of genes ... compute a tight lower bound on the score of a given tree, using...
  • brglm2

  • Referenced in 10 articles [sw19510]
  • takes place via a quasi Fisher scoring algorithm, and S3 methods for the construction...
  • PROC LOGISTIC

  • Referenced in 10 articles [sw12078]
  • carried out with either the Fisher scoring algorithm or the Newton-Raphson algorithm...
  • TM-align

  • Referenced in 14 articles [sw22248]
  • align: a protein structure alignment algorithm based on TM-score. We have developed TM-align ... combines the TM-score rotation matrix and Dynamic Programming (DP). The algorithm is ∼4 times ... distinct folds are found when a TM-score threshold of 0.5 is used. We also...
  • DASSOC

  • Referenced in 8 articles [sw27806]
  • DASSOC program uses the modified Newton-Raphson algorithm for association models described in the Haberman ... Currently available procedures based on the scoring algorithm for constrained maximum likelihood are relatively unreliable...
  • PSI-BLAST

  • Referenced in 233 articles [sw17324]
  • protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution ... produced by BLAST into a position-specific score matrix, and searching the database using this...
  • CCASat

  • Referenced in 12 articles [sw12924]
  • strategy results in a simple local search algorithm for SAT called Swcc, which shows promising ... forbids flipping those variables even with great scores, if they do not satisfy ... heuristic leads to an improved algorithm called Swcca, which exhibits state-of-the-art performance ... flipping have the same score. The resulting algorithm CCAsubscore is very efficient for solving random...
  • MUSCLE

  • Referenced in 73 articles [sw13193]
  • alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting ... profile function we call the log‐expectation score, and refinement using tree‐dependent restricted partitioning...
  • PhyME

  • Referenced in 9 articles [sw35645]
  • other species. Results: We propose an algorithm that integrates two important aspects of a motif ... cross-species conservation – into one probabilistic score. The algorithm allows the input orthologous sequences...
  • mcglm

  • Referenced in 5 articles [sw23203]
  • fitted using an efficient Newton scoring algorithm based on quasi-likelihood and Pearson estimating functions...
  • Sentilo

  • Referenced in 3 articles [sw26847]
  • Anyone can plug its own opinion scoring algorithm to compute scores of opinion expressing words ... come up with a combined scoring algorithm for each identified entities and the overall sentence...
  • CatBoost

  • Referenced in 4 articles [sw31560]
  • algorithm and a CPU implementation of scoring algorithm, which are significantly faster than other gradient...
  • SATzilla

  • Referenced in 93 articles [sw06281]
  • automated approach for constructing per-instance algorithm portfolios for SAT that use so-called empirical ... mean runtime, percent of instances solved, or score in a competition). The excellent performance...
  • GraphBase

  • Referenced in 133 articles [sw01555]
  • data useful for testing and comparing combinatorial algorithms. The programs generate a large number ... statistics of the US economy, college football scores, computational logic circuits, the Mona Lisa...
  • SCGLR

  • Referenced in 4 articles [sw12061]
  • Component Generalized Linear Regression. The Fisher Scoring Algorithm is extended so as to combine Partial...
  • GASTS

  • Referenced in 5 articles [sw29624]
  • GASTS: parsimony scoring under rearrangements. The accumulation of whole-genome data has renewed interest ... cancer research all require models and algorithms to elucidate the mechanisms, history, and consequences ... main contribution is GASTS, an algorithm for scoring a fixed phylogenetic tree: given a tree ... algorithm also returns much better scores. In simulations, our tree scores stay within...
  • IsoRankN

  • Referenced in 11 articles [sw08325]
  • induced graph of pairwise alignment scores. IsoRankN outperforms existing algorithms for global network alignment...
  • SEGID

  • Referenced in 9 articles [sw35743]
  • number is the alignment score of a column. Three algorithms are used to identify regions...
  • CLUSTAL

  • Referenced in 18 articles [sw12750]
  • pairwise sequence similarity scores, obtained using a fast pairwise alignment algorithm. Then the multiple alignment...