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FenTechSolutions / CausalDiscoveryToolbox

Package for causal inference in graphs and in the pairwise settings. Tools for graph structure recovery and dependencies are included.
https://fentechsolutions.github.io/CausalDiscoveryToolbox/html/index.html
MIT License
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[BUG] cdt.data.load_dataset('sachs') + one of the returned objects, 'target', is inconsistent with the paper(Sachs,etc 2005) #143

Open xwbxxx opened 2 years ago

xwbxxx commented 2 years ago

The CDT version is 0.6.0 (as you can see in the first line of the output)

Problem: When I viewed the target, I found there exists a loop among PIP2, PIP3 and plcg（The top 3 nodes in my screenshot）. image

As far as I know, Sachs Dataset should be a DAG, so I checked the paper where the graph came from, Causal-Protein-Signaling-Networks-Derived-from-Multiparameter-Single-Cell-Data(Sachs,etc 2005) to make sure. According to the paper, PIP3 should point to PIP2 . Moreover, there are a total of 20 edges in the diagram of the paper, but the function, _cdt.data.loaddataset('sachs'), outputs a graph with only 18 edges. So I would like to know if the Sachs dataset is updated or if there are errors and missing edges in the graph from this function.

image

diviyank commented 2 years ago

Hello ! Thanks for the feedback ! I know that this dataset does have multiple versions (and revisions) ; I'll check and get back to you ! My version could be out-of-date

Best, Diviyan