• Rfam

  • Referenced in 33 articles [sw04637]
  • consensus secondary structures and covariance models (CMs). The families in Rfam break down into three ... broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs ... functional RNAs often have a conserved secondary structure which may be better preserved than ... complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously...
  • SOFTSUSY

  • Referenced in 79 articles [sw01415]
  • superparticles in the Minimal Supersymmetric Standard Model (MSSM). The program solves the renormalisation group equations ... with theoretical constraints on soft supersymmetry breaking terms provided by the user. Weak-scale gauge ... breaking. The program can also calculate a measure of fine-tuning. The program structure...
  • GEOCLAW

  • Referenced in 33 articles [sw08626]
  • solvers for modeling floods in rugged terrain: application to the Malpasset dam-break flood (France ... high-resolution finite volume methods and block-structured dynamic adaptive mesh refinement (AMR), is described ... this paper. The efficiency of block-structured AMR makes large-scale problems tractable, and allows ... tested in this context. The difficulties of modeling floods in rugged terrain, and the rationale...
  • Spheno

  • Referenced in 52 articles [sw09544]
  • gauge mediated supersymmetry breaking, anomaly mediated supersymmetry breaking, or string effective field theories. An interface ... exists for an easy implementation of other models. The program solves the renormalization group equations ... incoming electrons/positrons. The program is structured such that it can easily be extend to include...
  • gets

  • Referenced in 4 articles [sw25589]
  • Saturation Methods. Automated General-to-Specific (GETS) modelling of the mean and variance ... methods for detecting and testing for structural breaks in the mean...
  • FlexibleSUSY

  • Referenced in 8 articles [sw20846]
  • superpotential, gauge structure and particle content in a SARAH model file; specific boundary conditions ... defined in a separate FlexibleSUSY model file. From these model files, FlexibleSUSY generates C++ code ... renormalization group equations (RGEs) and electroweak symmetry breaking (EWSB) conditions and combines them with numerical ... model, including loop-corrected pole masses, consistent with user specified boundary conditions. The modular structure...
  • LOOPN++

  • Referenced in 3 articles [sw31033]
  • structuring techniques with the petri net formalism which has proved beneficial in the modelling ... Coloured Petri Nets, in that it breaks away from the traditional approach of viewing ... petri net as a global control structure. The paper presents a textual language for specifying ... oriented petri nets which is convenient for modelling complex concurrent systems. The underlying formalism provides...
  • SUSYGEN

  • Referenced in 6 articles [sw10782]
  • supersymmetry breaking (SUGRA), and gauge mediated supersymmetry breaking (GMSB). The program incorporates the most important ... decays to the gravitino in GMSB models. lnitial state radiation corrections take into account ... effects in the structure function formalism, and an optimized hadronization interface to JETSET 7.4 including...
  • MercuryDPM

  • Referenced in 7 articles [sw26835]
  • simulations of complex interactions such as sintering, breaking, plastic deformation, wet-materials and cohesion ... complex wall generation techniques, that can exactly model real industrial geometries. Additionally, MercuryDPMs’ state ... dimensional continuum fields such as density, velocity, structure and stress tensors, providing information often...
  • chngpt

  • Referenced in 0 articles [sw15887]
  • phase regression, break-point regression, split-point regression, structural change models and threshold regression models...
  • TACO

  • Referenced in 6 articles [sw07668]
  • complex linked data structures. We instrument code analysis with a symmetry-breaking predicate that allows ... tools based on SAT-solving, model checking or SMT-solving...
  • factorcpt

  • Referenced in 8 articles [sw18260]
  • series factor models with multiple change-points in their second-order structure. We operate under ... change-point detection in the second-order structure of a high-dimensional time series, into ... interesting ’spillover’ effect in which substantial breaks in the idiosyncratic components get, naturally enough, identified...
  • EIX

  • Referenced in 1 article [sw35206]
  • Explain Interactions in ’XGBoost’. Structure mining from ’XGBoost’ and ’LightGBM’ models. Key functionalities of this ... package cover: visualisation of tree-based ensembles models, identification of interactions, measuring of variable importance ... interaction importance, explanation of single prediction with break down plots (based on ’xgboostExplainer’ and ’iBreakDown...
  • Ocean

  • Referenced in 1 article [sw18993]
  • waves of infinite depth dynamics and breaking mechanism. Modeling is carried out only ... Longuet-Higgins-Cokelet and Krasilnikov. Software package structure, computational methods and indication functions are described...
  • KGAT

  • Referenced in 1 article [sw32568]
  • recommendation, it is compulsory to go beyond modeling user-item interactions and take side information ... utility of knowledge graph (KG), which breaks down the independent interaction assumption by linking items ... argue that in such a hybrid structure of KG and user-item graph, high-order ... Knowledge Graph Attention Network (KGAT) which explicitly models the high-order connectivities...
  • spBFA

  • Referenced in 1 article [sw31476]
  • prior, the probit stick-breaking process. Areal spatial data is modeled using a conditional autoregressive ... Gaussian process. The response variable can be modeled as Gaussian, probit, Tobit, or Binomial (using ... latent factors through a hierarchical structure and can be specified as exponential or first-order...
  • RecBole

  • Referenced in 1 article [sw37574]
  • including general and extensible data structures, comprehensive benchmark models and datasets, efficient GPU-accelerated execution ... library, such as automatic parameter tuning and break-point resume. Such a framework is useful...
  • PhyloBayes MPI

  • Referenced in 2 articles [sw23042]
  • recent phylogenomics studies, while more refined model structures, more realistic and empirically more fit, have ... PhyloBayes, implementing the Dirichlet process mixture models as well as more classical empirical matrices ... truncated stick-breaking representation for the Dirichlet process prior. The implementation shows close to linear...
  • COBRAS2

  • Referenced in 1 article [sw29065]
  • structure interactions. The paper presents a numerical investigation on the role of air modeling ... phase flows. The (k)-(epsilon) model is adopted to define the Reynolds stress; the polytropic ... track the interface. Simulations of dam-break wave and 1D water piston illustrate the model...
  • OpenCurrent

  • Referenced in 1 article [sw11883]
  • breaks down a PDE into 3 basic objects, “Grids”, “Solvers,” and “Equations.” “Grid” data structures ... array-wide reductions. “Solvers” use these data structures to calculate terms arising from discretizations ... solver that uses a second-order Boussinesq model. This equation solver is fully validated...