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v2.11.0 (#138)
* Adding bips_tpc: This version introduces the bips_tpc module, based on the temporal PC (tPC) and the micd package. It enables causal discovery through the PC algorithm allowing for Edge constraints, mixed data, and missing data handling. * Updating basic conf example. Updating example for MVPC.
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‎VERSION‎

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2.10.0
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2.11.0

‎config/config.json‎

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{
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"benchmark_setup": [
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{
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"title": "example_config",
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"data": [
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{
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"graph_id": "avneigs4_p20",
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"graph_true_plots": true,
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"graph_true_stats": true,
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"ggally_ggpairs": true,
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"graph_plots": [
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"fges-sem-bic",
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"tabu-bge",
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"itsearch-bge",
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"pc-gaussCItest"
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],
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"graph_estimation": {
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"ids": [
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"fges-sem-bic",
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"tabu-bge",
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"itsearch-bge",
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"pc-gaussCItest"
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],
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"convert_to": [],
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"graphs": true,
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"adjmats": true,
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"diffplots": true,
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"csvs": true,
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"graphvizcompare": true
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},
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"mcmc_traj_plots": [],
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"mcmc_heatmaps": [],
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"mcmc_autocorr_plots": []
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},
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"title": "config"
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}
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}
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],
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"resources": {

‎config/paper_er_bin.json‎

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"path": true,
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"text": false,
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"ids": [
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"gobnilp-bde",
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"grasp-bdeu",
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"boss-bdeu",
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"asobs-bdeu",

‎config/paper_er_sem.json‎

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"path": true,
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"text": false,
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"ids": [
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"gobnilp-bge",
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"boss-sem-bic",
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"grasp-sem-bic",
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"notears-l2",

‎config/paper_er_sem_small.json‎

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"path": true,
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"text": false,
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"ids": [
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"gobnilp-bge",
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"boss-sem-bic",
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"grasp-sem-bic",
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"notears-l2",

‎config/paper_hepar2_bin.json‎

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"path": true,
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"text": false,
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"ids": [
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"gobnilp-bde",
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"grasp-bdeu",
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"boss-bdeu",
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"asobs-bdeu",

‎config/paper_hepar2_sem.json‎

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"path": true,
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"text": false,
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"ids": [
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"gobnilp-bge",
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"boss-sem-bic",
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"grasp-sem-bic",
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"notears-l2",

‎config/paper_sachs.json‎

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"path": true,
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"text": false,
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"ids": [
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"gobnilp-bge",
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"boss-sem-bic",
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"grasp-sem-bic",
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"notears-l2",

‎docs/source/available_background_knowledge.rst‎

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---------------------------------------
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Benchpress allows users to incorporate edge constraints to guide structure learning algorithms in several packages:
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**pcalg**, **mvpc**, **bnlearn**, **tetrad**, **gobnilp**, and **bidag**. These constraints enable the inclusion of prior knowledge to refine
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**pcalg**, **bips_tpc**, **mvpc**, **bnlearn**, **tetrad**, **gobnilp**, and **bidag**. These constraints enable the inclusion of prior knowledge to refine
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the search space of causal graphs, improving the reliability of the inferred relationships. Users can specify **forbidden or
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required edges**, **tiers for temporal ordering**, and **group-based constraints**.
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The edge constraints should be defined in a JSON file located within the ``resources/constraints`` folder.
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.. rubric:: Supported Constraints
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+-------------+---------------------+--------------------+-----------+----------------------+---------------------+
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| **Package** | **forbidden_edges** | **required_edges** | **tiers** | **forbidden_groups** | **required_groups** |
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+=============+=====================+====================+===========+======================+=====================+
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| mvpc | X | X | N/A | N/A | N/A |
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+-------------+---------------------+--------------------+-----------+----------------------+---------------------+
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| pcalg | X | X | N/A | N/A | N/A |
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+-------------+---------------------+--------------------+-----------+----------------------+---------------------+
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| bnlearn | X | X | X | X | X |
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+-------------+---------------------+--------------------+-----------+----------------------+---------------------+
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| tetrad | X | X | X | X | X |
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+-------------+---------------------+--------------------+-----------+----------------------+---------------------+
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| gobnilp | X | X | X | X | X |
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+-------------+---------------------+--------------------+-----------+----------------------+---------------------+
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| bidag | X | N/A | N/A | X | N/A |
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+-------------+---------------------+--------------------+-----------+----------------------+---------------------+
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+-------------+---------------------+--------------------+-----------+----------------------+---------------------+-----------------+------------------+------------------+
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| **Package** | **forbidden_edges** | **required_edges** | **tiers** | **forbidden_groups** | **required_groups** | **context_all** | **context_tier** | **source_nodes** |
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+=============+=====================+====================+===========+======================+=====================+=================+==================+==================+
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| bips_tpc | X | N/A | X | X | N/A | X | X | X |
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+-------------+---------------------+--------------------+-----------+----------------------+---------------------+-----------------+------------------+------------------+
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| mvpc | X | X | N/A | N/A | N/A | N/A | N/A | N/A |
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+-------------+---------------------+--------------------+-----------+----------------------+---------------------+-----------------+------------------+------------------+
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| pcalg | X | X | N/A | N/A | N/A | N/A | N/A | N/A |
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+-------------+---------------------+--------------------+-----------+----------------------+---------------------+-----------------+------------------+------------------+
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| bnlearn | X | X | X | X | X | N/A | N/A | N/A |
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+-------------+---------------------+--------------------+-----------+----------------------+---------------------+-----------------+------------------+------------------+
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| tetrad | X | X | X | X | X | N/A | N/A | N/A |
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+-------------+---------------------+--------------------+-----------+----------------------+---------------------+-----------------+------------------+------------------+
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| gobnilp | X | X | X | X | X | N/A | N/A | N/A |
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+-------------+---------------------+--------------------+-----------+----------------------+---------------------+-----------------+------------------+------------------+
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| bidag | X | N/A | N/A | X | N/A | N/A | N/A | N/A |
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+-------------+---------------------+--------------------+-----------+----------------------+---------------------+-----------------+------------------+------------------+
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.. rubric:: Description
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- ``forbidden_edges``: A list of directed edges that are explicitly prohibited from existing between specific nodes. Each edge is defined as a pair of nodes, where the first node cannot directly cause the second node.
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- ``required_edges``: A list of directed edges that are enforced between specific nodes. Each edge is defined as a pair of nodes, where the first node must directly cause the second node.
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- *Note: For algorithms in the* **pcalg** and **mvpc** *package, the above attributes only specify the presence or absence of edges and do not control their directionality.*
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- ``tiers``: Defines a temporal ordering of nodes across multiple levels (or) tiers. Nodes in one tier are constrained from causing nodes in any of the preceding tiers.
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- ``tier_settings``:
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- ``forbidden_within_tiers``: If set to `true`, prevents edges between nodes that reside within the same tier.
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- ``can_only_cause_next_tier``: If set to `true`, restricts nodes in one tier to only influence or cause nodes in the immediate next tier.
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- ``Groups``: Defines relationships between sets of nodes, grouping them for the purpose of controlling edge behavior across multiple nodes at once. Each group is defined by a collection of "cause" nodes and "effect" nodes.
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- *Groups*: Defines relationships between sets of nodes, grouping them for the purpose of controlling edge behavior across multiple nodes at once. Each group is defined by a collection of "cause" nodes and "effect" nodes.
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- ``forbidden_groups``: A set of constraints that prohibits directed edges between specified groups of nodes.
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- ``required_groups``: A set of requirements that enforces directed edges between specified groups of nodes.
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- ``context_all``: If set to `true`, edges added from this node to all other nodes.
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- ``context_tier``: If set to `true`, edges added from this node to all nodes within the same tier.
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- ``source_nodes``: A list of nodes that are restricted to have no parents.
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.. note::
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For algorithms in the **pcalg** and **mvpc** *package, the above attributes only specify the presence or absence of edges and do not control their directionality.*
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.. rubric:: Example JSON
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"cause": ["22"],
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"effect": ["23"]
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}
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]
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],
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"context_all": ["1"],
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"context_tier": ["3"],
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"source_nodes": ["11"]
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}
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‎docs/source/available_structure_learning_algorithms.rst‎

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structure_learning_algorithms/bidag_itsearch
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structure_learning_algorithms/bidag_order_mcmc
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structure_learning_algorithms/bidag_partition_mcmc
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structure_learning_algorithms/bips_tpc
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structure_learning_algorithms/bnlearn_fastiamb
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structure_learning_algorithms/bnlearn_gs
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structure_learning_algorithms/bnlearn_h2pc
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structure_learning_algorithms/bnlearn_sihitonpc
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structure_learning_algorithms/bnlearn_tabu
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structure_learning_algorithms/causaldag_gsp
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structure_learning_algorithms/causallearn_ges
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structure_learning_algorithms/causallearn_grasp
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structure_learning_algorithms/corr_thresh
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structure_learning_algorithms/dualpc
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- `DAG <https://en.wikipedia.org/wiki/Directed_acyclic_graph>`__, `CPDAG <https://search.r-project.org/CRAN/refmans/pcalg/html/dag2cpdag.html>`__
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- `BiDAG <https://cran.r-project.org/web/packages/BiDAG/index.html>`__
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- :ref:`bidag_partition_mcmc`
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* - tPC
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- `CPDAG <https://search.r-project.org/CRAN/refmans/pcalg/html/dag2cpdag.html>`__
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- `tpc <https://github.com/bips-hb/tpc>`__
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- :ref:`bips_tpc`
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* - Fast IAMB
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- `DAG <https://en.wikipedia.org/wiki/Directed_acyclic_graph>`__
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- `bnlearn <https://www.bnlearn.com/>`__
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- `UDG <https://arxiv.org/pdf/2210.00822.pdf#subsection.2.2>`__
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- `gues <https://pypi.org/project/gues/>`__
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- :ref:`grues`
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* - Graphical lasso
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* - GLasso
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- `UG <https://en.wikipedia.org/wiki/Graph_(discrete_mathematics)#Graph>`__
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- `huge <https://cran.r-project.org/web/packages/huge/index.html>`__
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- :ref:`huge_glasso`

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