Uses of Interface
edu.cmu.tetrad.algcomparison.utils.HasParameters

Packages that use HasParameters
  • Uses of HasParameters in edu.cmu.tetrad.algcomparison.algorithm

    Modifier and Type
    Interface
    Description
    interface 
    Interface that algorithm must implement.
    interface 
    Implements an algorithm that takes multiple data sets as input.
    Modifier and Type
    Class
    Description
    class 
    This is a base class for bootstrap algorithms.
    class 
    A base class for bootstrapping multi-dataset algorithms (such as IMaGES), parallel to AbstractBootstrapAlgorithm for single-dataset algorithms.
    class 
    Tags an an algorithm that loads up external graphs for inclusion in reports.
    class 
    First inflection point.
    class 
    Stability selection: runs the wrapped algorithm on resamples of the data and returns the graph containing exactly those edges (with orientation) appearing in more than "percentStability" of the resample graphs.
    class 
    StARS (Stability Approach to Regularization Selection): selects a value for one numeric parameter of a wrapped algorithm by sweeping the parameter over [low, high] in steps of 0.5, measuring the StARS adjacency instability of the algorithm's output over a fixed set of resamples at each value, choosing the value with the largest instability strictly below the cutoff (Params "StARS.cutoff"), and then running the wrapped algorithm on the full data at the chosen value.
  • Uses of HasParameters in edu.cmu.tetrad.algcomparison.algorithm.continuous.dag

    Modifier and Type
    Class
    Description
    class 
    Implements the DAGMA algorithm.
    class 
    Direct LiNGAM.
    class 
    FASK algorithm.
    class 
    Deprecated.
    class 
    ICA-LiNGAM, the former name of LiNGAM.
    class 
    ICA-LiNG-D, the former name of LiNG-D.
    class 
    IcaLingam class implements the Algorithm and ReturnsBootstrapGraphs interface.
    class 
    IcaLingD is an implementation of the Algorithm interface that performs the LiNG-D algorithm for discovering causal models for the linear non-Gaussian case where the underlying model might be cyclic.
  • Uses of HasParameters in edu.cmu.tetrad.algcomparison.algorithm.multi

    Modifier and Type
    Class
    Description
    class 
    Wraps the IMaGES algorithm for continuous variables.
    class 
    Wraps the pooled-FASK multi-dataset algorithm for continuous variables.
    class 
    Wraps the MultiFask algorithm for continuous variables.
    class 
    Runs FCI on multiple datasets using the IOD pooled dataset independence test.
    class 
    Requires that the parameter 'randomSelectionSize' be set to indicate how many datasets should be taken at a time (randomly).
    class 
    Wraps the IMaGES algorithm for continuous variables.
    class 
    Wraps the IMaGES algorithm for continuous variables.
    class 
    Wraps the IMaGES algorithm for continuous variables.
    class 
    Runs the ION (Integration of Overlapping Networks) algorithm on multiple datasets whose variable sets may overlap only partially.
  • Uses of HasParameters in edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag

    Modifier and Type
    Class
    Description
    class 
    BOSS (Best Order Score Search)
    class 
    BOSS + score-based CD-NOD context augmentation.
    class 
    BOSS-TopK (Best Order Score Search, Top K).
    class 
    Deprecated.
    class 
    Represents the CAM algorithm, which is a causal additive model search algorithm.
    class 
    CD-NOD wrapper for algcomparison.
    class 
    Algcomparison wrapper for the CD-NOD-BOSS search (CdnodBoss): a BOSS backbone with constraint-based collider orientation applied only to unshielded triples that BOSS leaves fully undirected, followed by Meek closure.
    class 
    CD-NOD wrapper for algcomparison.
    class 
    Conservative PC (CPC).
    class 
    Cstar class.
    class 
    Fast Adjacency Search (FAS)--i.e., the PC adjacency step, which is used in many algorithms.
    class 
    FGES (the heuristic version).
    class 
    FGES-MB (the heuristic version).
    class 
    FLOP (Fast Learning of Order and Parents).
    class 
    GRaSP (Greedy Relaxations of Sparsest Permutation)
    class 
    IS-FGES (Instance-Specific FGES) wrapper for the algcomparison interface.
    class 
    Peter/Clark algorithm (PC).
    class 
    Peter/Clark algorithm with adjacency-rescue (PcAR): PC augmented with detection, and optionally repair, of cancelled unfaithful-triangle edges.
    class 
    PC.
    class 
    PC-Max.
    class 
    PC.
    class 
    PCMCI wrapper for algcomparison.
    class 
    Implements a restricted version of the BOSS (Best Order Score Search) algorithm that focuses search on a set of target variables and their immediate causes.
    class 
    PC.
    class 
    SP (Sparsest Permutation)
    class 
    Deprecated.
    class 
    Algorithm-comparison wrapper for the Trek-MIMIC search.
    class 
    Deprecated.
  • Uses of HasParameters in edu.cmu.tetrad.algcomparison.algorithm.oracle.pag

    Modifier and Type
    Class
    Description
    class 
    Adjusts FGES-FCI to use a permutation algorithm (such as BOSS-Tuck) to do the initial steps of finding adjacencies and unshielded colliders.
    class 
    BFCI-Bryan: BOSS followed by the from-scratch, sepset-map-as-state formulation of the gated StarFCI extra-edge-removal step, with sepset RE-SELECTION (a gate-rejected separating set does not retire the pair; the next separating set is tried) and NO saturating step.
    class 
    BFCI-Bryan-Score: BFCI-Bryan (sepset re-selection under the legality gate) with a scoring step: a legal candidate is committed only if the RICF Gaussian BIC of its MAG strictly improves on the committed model's, following Bryan Andrews's "BFCI-Bryan with scoring" pseudocode.
    class 
    Adjusts FGES-FCI to use a permutation algorithm (such as BOSS-Tuck) to do the initial steps of finding adjacencies and unshielded colliders.
    class 
    Adjusts FGES-FCI to use a permutation algorithm (such as BOSS-Tuck) to do the initial steps of finding adjacencies and unshielded colliders.
    class 
    / Hidden from the interface on 2026-10-21 (no @Algorithm annotation): kept only so that saved sessions
    class 
    BOSS-CCD (Cyclic Causal Discovery with a BOSS adjacency superstructure).
    class 
    BOSS-FCI, the former name of BFCI.
    class 
    BOSS-POD, removed in Tetrad 8.0.0.
    class 
    CCD (Cyclic Causal Discovery)
    class 
    CFCI (Conservative FCI).
    class 
    Implements the CPW (Cyclic Pairwise) algorithm for causal discovery from continuous, causally sufficient observational data.
    class 
    Algorithm-comparison wrapper for the Murray-Watters/Glymour style Detect-Mimic search, DM.
    class 
    DM-FCIT, removed in Tetrad 8.0.0.
    class 
    DM-PC, removed in Tetrad 8.0.0.
    class 
    The Fast Causal Inference (FCI) algorithm.
    class 
    FCI-CPW: Run FCI with internally constructed PW-forbidden knowledge, then orient edges using a pairwise left-right rule on standardized data in cases that are safe under no-selection-bias cyclic semantics: Tail–tail (—) edges Orient per pairwise rule. Tail–circle (—o) edges If pairwise prefers x→y, set x→y (symmetrically, if prefers y→x, set y→x). Circle–circle (o–o) edges If pairwise prefers x→y, set x o→y (symmetrically for y→x).
    class 
    FCI-Max.
    class 
    This class represents the FCI Targeted Testing (FCIT) algorithm, which is variant of the *-FCI algorithm for learning causal structures from observational data using the BOSS algorithm as an initial CPDAG and using all score-based steps afterward.
    class 
    This class represents the FCI Targeted Testing (FCIT) algorithm, which is variant of the *-FCI algorithm for learning causal structures from observational data using the BOSS algorithm as an initial CPDAG and using all score-based steps afterward.
    class 
    This class represents the FCI Targeted Testing (FCIT) algorithm, which is variant of the *-FCI algorithm for learning causal structures from observational data using the BOSS algorithm as an initial CPDAG and using all score-based steps afterward.
    class 
    This class represents the FCI Targeted Testing (FCIT) algorithm, which is variant of the *-FCI algorithm for learning causal structures from observational data using the BOSS algorithm as an initial CPDAG and using all score-based steps afterward.
    class 
    FCIT-SL-Score-Check: the FCIT-SL algorithm with a MAG BIC SCORE CHECK applied to every candidate the search adjudicates.
    class 
    This class represents the FCI Targeted Testing (FCIT) algorithm, which is variant of the *-FCI algorithm for learning causal structures from observational data using the BOSS algorithm as an initial CPDAG and using all score-based steps afterward.
    class 
    The Fges-FCI class represents the Greedy Fast Causal Inference algorithm, adjusted as in *-FCI.
    class 
    The GFCI class represents the Greedy Fast Causal Inference algorithm, adjusted as in *-FCI.
    class 
    GMAS: a latent-variable search that uses no independence tests.
    class 
    GRaSP-FCI, an implentatation of *-FCI using GRaSP.
    class 
    The Iterative Causal Discovery (ICD) algorithm.
    class 
    IS-GFCI (Instance-Specific GFCI) wrapper for the algcomparison interface.
    class 
    Wrapper for LV-BOSS: the fully score-based latent-variable search that embeds a MAG projection inside a BOSS-style search over orders, scored by the exact RICF Gaussian MAG BIC (MagRicfBicScorer).
    class 
    This class represents the FCIT algorithm, which is an implementation of the FGES-FCI algorithm for learning causal structures from observational data using the BOSS algorithm as an initial CPDAG and using all score-based steps afterward.
    class 
    PAG-Sampling-RFCI, the former name of the class now called PagSamplingRfci.
    class 
    Jan 29, 2023 3:45:09 PM
    class 
    RFCI.
    class 
    Runs RFCI-BSC, which is RFCI with bootstrap sampling of PAGs.
    class 
    Adjusts GFCI to use a permutation algorithm (in this case SP) to do the initial steps of finding adjacencies and unshielded colliders.
  • Uses of HasParameters in edu.cmu.tetrad.algcomparison.algorithm.other

    Modifier and Type
    Class
    Description
    class 
    Factor analysis.
    class 
    GLASSO.
    class 
    Mimbuild Bollen.
    class 
    Mimbuild PCA.
    class 
    Deprecated.
    class 
    Wrapper for the RLCD algorithm (Rank-based Latent Causal Discovery; Dong et al., ICLR 2024), which learns a graph over the observed variables and newly introduced latent variables from rank constraints on the covariance matrix.
  • Uses of HasParameters in edu.cmu.tetrad.algcomparison.algorithm.pairwise

    Modifier and Type
    Class
    Description
    class 
    FASK-PW (pairwise).
    class 
    R1.
    class 
    R2.
    class 
    R3.
    class 
    RSkew.
    class 
    RSkewE.
    class 
    Skew.
    class 
    SkewE.
    class 
    Tanh.
  • Uses of HasParameters in edu.cmu.tetrad.algcomparison.independence

    Modifier and Type
    Interface
    Description
    interface 
    An interface that extends functionality of the IndependenceWrapper and HasParameters interfaces by adding support for block-specific configuration in independence testing.
    interface 
    Interface that algorithm must implement.
    Modifier and Type
    Class
    Description
    class 
    Wrapper for BE-GCM (Basis-Expanded Generalised Covariance Measure Test).
    class 
    Wrapper for BF-Blocks-Test.
    class 
    Wrapper for BF-LRT (Basis Function Likelihood Ratio Test).
    class 
    Deprecated.
    class 
    Deprecated.
    class 
    Wrapper for BF-Blocks-Test.
    class 
    Wrapper for Daudin Conditional Independence test.
    class 
    Wrapper for Fisher Z test.
    class 
    An IndependenceWrapper that runs the Fisher Z conditional independence test implemented in the Python causal-learn library, bridging it into Tetrad's IndependenceTest framework.
    class 
    An IndependenceWrapper that runs the Kernel-based Conditional Independence (KCI) test implemented in the Python causal-learn library, bridging it into Tetrad's IndependenceTest framework.
    class 
    An IndependenceWrapper that runs the Randomized Conditional Independence Test (RCIT) implemented in the Python causal-learn library, bridging it into Tetrad's IndependenceTest framework.
    class 
    Wrapper for Fisher Z test.
    class 
    Wrapper for the CORD conditional independence test backed by Eric's engine (IndTestCordEric): an omnibus, orthogonal rank-score test of Y ⊥ Z | X that is sensitive to higher-moment, tail, and co-volatility dependence which a covariance-based test (e.g., Fisher Z) cannot see.
    class 
    Wrapper for DG LRT.
    class 
    The SemBicTest class implements the IndependenceWrapper interface and represents a test for independence based on SEM BIC algorithm.
    class 
    Wrapper for the equivalence (TOST) test on the Fisher Z partial correlation.
    class 
    Wrapper for FFCI test with a reduced parameter set.
    class 
    Wrapper for FF-CI-Continuous test.
    class 
    Wrapper for Fisher Z test.
    class 
    Wrapper for KCI test.
    class 
    Wrapper for GIN (Generalized Independent Noise) residual-independence test.
    class 
    Wrapper for Fisher Z test.
    class 
    Wrapper for KCI test.
    class 
    Wrapper for Minimax binning test.
    class 
    Wrapper for M-separation test.
    class 
    Wrapper for Fisher Z test.
    class 
    Deprecated.
    class 
    The SemBicTest class implements the IndependenceWrapper interface and represents a test for independence based on SEM BIC algorithm.
    class 
    Dec 17, 2018 3:44:46 PM
    class 
    Deprecated.
    class 
    Rank Independence Test TS, the former name of the test now called Rank Independence Test TS Singletons.
    class 
    Deprecated.
    class 
    Deprecated.
    class 
    Wrapper for RCIT test.
    class 
    The SemBicTest class implements the IndependenceWrapper interface and represents a test for independence based on SEM BIC algorithm.
    class 
    Wrapper for the stratified (domain-pooled) rank conditional independence test, IndTestStratifiedRank -- the Phase 1 test of LCD-NOD (Dong, Dai, Ng, Spirtes, and Zhang, ICML 2026).
    class 
    Wrapper for Rank independence test.
    final class 
    Wrapper for the TRFF likelihood-ratio CI test built on TRffBicScore.
  • Uses of HasParameters in edu.cmu.tetrad.algcomparison.score

    Modifier and Type
    Interface
    Description
    interface 
    Represents an interface for scoring data models using predefined block structures.
    interface 
    Interface that algorithm must implement.
    Modifier and Type
    Class
    Description
    class 
    Wrapper for BF-BGe, the BGe (Normal-Wishart marginal likelihood) score over the basis-function embedding that BF-BIC uses.
    class 
    Wrapper for Basis Function BIC Score (Basis-BIC) version.
    class 
    Wrapper for the full-sample (tabular) Basis Function BIC Score, delegating to BasisFunctionBicScoreFullSample.
    class 
    Wrapper for Fisher Z test.
    class 
    Wrapper for Blocks BIC Score (Blocks-BIC) version.
    class 
    Wrapper for the BGe (Bayesian Gaussian equivalent) score, the Gaussian analog of BDeu: the local score is the exact log marginal likelihood of a family under a Normal-Wishart prior rather than a BIC-penalized maximum likelihood.
    class 
    Wrapper for Blocks BIC Score (Blocks-BIC) version.
    class 
    Wrapper for Fisher Z test.
    class 
    Wrapper for DG-BGe, the BGe (Normal-Wishart marginal likelihood) score over the degenerate Gaussian indicator embedding that DG-BIC uses.
    class 
    Wrapper for degenerate Gaussian BIC score
    class 
    Wrapper for Discrete BIC test.
    class 
    Wrapper for linear, Gaussian Extended BIC score (Chen and Chen).
    class 
    Wrapper for FF-ML MIxed Marginal Likelihood Score.
    class 
    Wrapper for FF Marginal Likelihood Score.
    class 
    The GicScores class is an implementation of the ScoreWrapper interface that calculates the Generalized Information Criterion (GIC) scores for a given data model.
    class 
    Wrapper for linear, Gaussian SEM BIC score.
    class 
    // * Wrapper for Huang Marginal Likelihood Score.
    final class 
    Wrapper for InstanceAugmentedSemBicScore that: - pulls the testing DataSet from Params.TESTING_DATA (injected by the algorithm wrapper), - takes the instance row from Params.INSTANCE_ROW, - aligns columns by training variable names, - uses alpha from Params.IS_ALPHA (default 1.0).
    final class 
    Wrapper for ISBDeuScore (discrete).
    class 
    Wrapper for KVC BIC score.
    class 
    Wrapper for Kernel Marginal Likelihood Score.
    class 
    Wrapper for degenerate Gaussian BIC score
    class 
    Wrapper for Fisher Z test.
    class 
    Deprecated.
    class 
    Wrapper for the Poisson prior score (Bryan)
    class 
    Wrapper for linear, Gaussian SEM BIC score.
    class 
    Wrapper for linear, Gaussian SEM BIC score.
    class 
    Wrapper for linear, Gaussian SEM BIC score.
    class 
    The TRffBicScore class is a scoring mechanism designed to evaluate the fit and complexity of a data model.
    class 
    Wrapper for linear, Gaussian Extended BIC score (Chen and Chen).
  • Uses of HasParameters in edu.cmu.tetrad.algcomparison.simulation

    Modifier and Type
    Interface
    Description
    interface 
    The interface that simulations must implement.
    Modifier and Type
    Class
    Description
    class 
    This class represents a Causal Perceptron Network.
    class 
    Bayes net simulation.
    class 
    A simulation method based on the conditional Gaussian assumption.
    class 
    Implements the DAG-adaptation of the Onion (DaO) simulation method for generating linear data from a DAG, with exogenous errors drawn from one of the reference implementation's five variance-matched families (Gaussian by default; Exponential, Gumbel, Laplace, or Uniform via daoErrorDistribution), as described in:
    class 
    Simulates data with the anatomy of a designed physical experiment (the archetype is the NASA Airfoil Self-Noise dataset), in contrast to an observational sample.
    class 
    Wrapper for the neural-net Generalized Additive Model (GAM) simulator.
    class 
    This class represents a Causal Perceptron Network.
    class 
    The GeneralSemSimulation class represents a simulation using a generalized structural equation model (SEM).
    class 
    This was used for a simulation to test the FTFC and FOFC algorithm and contains some carefully selected functions to test nonlinearity and non-Gaussianity.
    class 
    NL SEM simulation.
    class 
    This class represents a Simulation using Structural Equation Modeling (SEM).
    class 
    A version of the Lee and Hastic simulation.
    class 
    This class represents a continuous MNAR simulation.
    class 
    Linear Fisher Model.
    class 
    A simulation method based on the mixed variable polynomial assumption.
    class 
    A linear SEM simulation whose exogenous noises are drawn independently from the distribution given by the customNoiseExpression parameter (default Exp(1)) rather than from Gaussians.
    class 
    This class represents a nonlinear functions of linear simulation.
    class 
    Simulates data with the anatomy of a real observational scientific dataset (the archetype is the Algerian Forest Fires dataset, but with all complications defaulted off this is a plain mixed-data cross-sectional study).
    class 
    This class represents a post-nonlinear SEM model.
    class 
    This class represents a Simulation using Structural Equation Modeling (SEM).
    class 
    SEM the discretize.
    class 
    A Simulation implementation that returns a single supplied data set.
    class 
    Standardized SEM simulation.
    class 
    Time series SEM simulation.
    class 
    Trained DAG model.
  • Uses of HasParameters in edu.cmu.tetrad.algcomparison.utils

    Modifier and Type
    Interface
    Description
    interface 
    A score wrapper that can construct its per-data-set scores jointly, coordinating any data-dependent representation choices across the data sets.
    Modifier and Type
    Class
    Description
    final class 
    The test-side counterpart of PooledScoreWrapper: builds the inner test on each pooled data set and combines them with IndTestMulti using Fisher's method (default) or Tippett's method on the per-data-set p-values, per Params.POOLED_TEST_METHOD (data sets are assumed independent of one another, e.g.
    final class 
    A score wrapper that pools several data sets into one IMaGES score built from an inner score wrapper.
  • Uses of HasParameters in edu.cmu.tetrad.data.simulation

    Modifier and Type
    Class
    Description
    class 
    Load data sets and graphs from a directory.
    class 
    Load data sets and graphs from a directory.
    class 
    Load data sets and graphs from a directory.
    class 
    Load data sets and graphs from a directory.
    class 
    Load data sets and graphs from a directory.