Papers › Causal Discovery Toolbox: Uncover causal relationships in Python

Causal Discovery Toolbox: Uncover causal relationships in Python

6 Mar 2019arXiv:1903.02278archive 2025-07-28

Diviyan Kalainathan, Olivier Goudet

This paper presents a new open source Python framework for causal discovery from observational data and domain background knowledge, aimed at causal graph and causal mechanism modeling. The 'cdt' package implements the end-to-end approach, recovering the direct dependencies (the skeleton of the causal graph) and the causal relationships between variables. It includes algorithms from the 'Bnlearn' and 'Pcalg' packages, together with algorithms for pairwise causal discovery such as ANM. 'cdt' is available under the MIT License at https://github.com/Diviyan-Kalainathan/CausalDiscoveryToolbox.

PaperPDFCodeCode Syntology ran

In Syntology Open this paper in Syntology's Atlas, the map of the papers in Syntology's graph and their citations.

For agents, Syntology's MCP tool lists every function and class Syntology harvested from this paper and whether it ran (how to connect): get_harvested_code_for_paper(arxiv_id="1903.02278")

Code

Syntology Ran 5 of 19 code samples harvested from 2 repositories linked to this paper; 14 have no recorded run. Of those that ran: 1 ran · honoured contract; 1 ran · our draft was wrong; 2 ran · fixture could not drive it; 1 ran with no contract checked.

By repository: community (archive-listed): 19 samples from 2 repositories, 5 ran. The run record, sample by sample. “Ran” means executed on a synthesized input, not that the code is correct or reproduces the paper.

FenTechSolutions/CausalDiscoveryToolbox mentioned on GitHubpytorch report
GoudetOlivier/CGNN mentioned on GitHubtf report
elementai/causal_discovery_toolbox mentioned on GitHubpytorchMIT report

Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.

Code Syntology ran Syntology

19 samples harvested; 5 ran; 1 honoured the contract we drafted; 14 have no recorded run. Read from Syntology's graph 2026-09-24; that is when this build read the record, not when the samples ran.

1ran · honoured contract
1ran · our draft was wrong
2ran · fixture could not drive it
1ran
14unverified

Licence: 0 of the 19 samples are pointer only, meaning Syntology does not serve that copy's text. This page shows no code text for any sample; each one links to its file in the repository.

Harvested from 2 repositories linked to this paper, official or community; each sample names its own and says which. “Ran” means the sample executed on a synthesized input. It does not mean the output is correct, and nothing here reproduces the paper's results. “Honoured” and “violated” refer to a contract Syntology drafted from the code itself; “our draft was wrong” and “fixture could not drive it” are failures of Syntology's instrument, not of the code.

Each sample ends with its code_sha256, Syntology's identity for that exact code. An agent fetches the stored sample with Syntology's MCP tool get_code(code_sha256="…") (how to connect); click an identity to copy that call.

Repository labels, per sample. official repository: The archive marks this repository official for the paper. named in the paper: The archive records that the paper mentions this repository; it is not marked official. community (archive-listed): In the archive's code links for this paper, not marked official and not recorded as mentioned in the paper. found in paper text by Syntology: Syntology found this repository in the paper's own text; whether it is the authors' implementation is not asserted. community: Not in the archive's code links for this paper; a community repository Syntology harvested. Samples from a repository marked official are listed first. Licence labels name the repository's licence as recorded at harvest. “Pointer only” means Syntology does not serve that copy's text, for one of four reasons: no licence file was found; the licence was not identified; the licence is recorded as permissive but that copy's record is not marked cleared; or the licence is outside the permissive list Syntology serves text under (MIT, Apache-2.0, BSD and similar). Some licences outside that list permit redistribution, such as WTFPL, and GPL-3.0 under its conditions; they are simply not on the list. Hover a licence label for the reason. File links open the file on GitHub at the default branch, which may have changed since the harvest.

FastHsicTestGamma FenTechSolutions/CausalDiscoveryToolbox/cdt/causality/pairwise/ANM.py community (archive-listed) ran · fixture could not drive it fingerprinted MIT (permissive) · 3cb1654fab9536d9 · report
message_warning FenTechSolutions/CausalDiscoveryToolbox/cdt/causality/graph/CAM.py community (archive-listed) ran · our draft was wrong MIT (permissive) · 99d91b2cc3c8aef8 · report
rbf_dot FenTechSolutions/CausalDiscoveryToolbox/cdt/causality/pairwise/ANM.py community (archive-listed) ran · fixture could not drive it fingerprinted MIT (permissive) · bdd354350f93fb34 · report
rbf_dot2 FenTechSolutions/CausalDiscoveryToolbox/cdt/causality/pairwise/ANM.py community (archive-listed) ran · honoured contract fingerprinted MIT (permissive) · 4957512edbf23259 · report
retrieve_adjacency_matrix elementai/causal_discovery_toolbox/cdt/metrics.py community (archive-listed) ran MIT (permissive) · 91007bd87b2f9f18 · report
aracne elementai/causal_discovery_toolbox/cdt/utils/graph.py community (archive-listed) unverified MIT (permissive) · 33b84bc94c3cb38b · report
clr elementai/causal_discovery_toolbox/cdt/utils/graph.py community (archive-listed) unverified MIT (permissive) · 4f4929f021d62838 · report
functional_linear3d elementai/causal_discovery_toolbox/cdt/utils/torch.py community (archive-listed) unverified MIT (permissive) · 6938344c3e48f119 · report
get_CPDAG elementai/causal_discovery_toolbox/cdt/metrics.py community (archive-listed) unverified MIT (permissive) · 1504b06f9ca60dbf · report
gumbel_sigmoid elementai/causal_discovery_toolbox/cdt/utils/torch.py community (archive-listed) unverified MIT (permissive) · 1189b0c4307ca015 · report
gumbel_softmax elementai/causal_discovery_toolbox/cdt/utils/torch.py community (archive-listed) unverified MIT (permissive) · 8db23fb76184682b · report
network_deconvolution elementai/causal_discovery_toolbox/cdt/utils/graph.py community (archive-listed) unverified MIT (permissive) · 7e57718538f6e61b · report
notears_constr elementai/causal_discovery_toolbox/cdt/utils/loss.py community (archive-listed) unverified MIT (permissive) · 49362e8478f9c3ba · report
parallel_run elementai/causal_discovery_toolbox/cdt/utils/parallel.py community (archive-listed) unverified MIT (permissive) · 52b85406b3bd7ad8 · report
parallel_run_generator elementai/causal_discovery_toolbox/cdt/utils/parallel.py community (archive-listed) unverified MIT (permissive) · 16630bfa95f2df9c · report
precision_recall elementai/causal_discovery_toolbox/cdt/metrics.py community (archive-listed) unverified MIT (permissive) · 4dbd7430a7f9466a · report
read_adjacency_matrix elementai/causal_discovery_toolbox/cdt/utils/io.py community (archive-listed) unverified MIT (permissive) · 10b87773546bfd0c · report
read_causal_pairs elementai/causal_discovery_toolbox/cdt/utils/io.py community (archive-listed) unverified MIT (permissive) · 5fd171c5bda38854 · report
read_list_edges elementai/causal_discovery_toolbox/cdt/utils/io.py community (archive-listed) unverified MIT (permissive) · efe29062ce865244 · report

Tasks

Causal Discovery

Results from the paper archive 2025-07-28

No leaderboard rows for this paper in the archive.

Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections