Large-Scale Differentiable Causal Discovery of Factor Graphs
Authors: Romain Lopez, Jan-Christian Huetter, Jonathan Pritchard, Aviv Regev
NeurIPS 2022 | Conference PDF | Archive PDF | Plain Text | LLM Run Details
| Reproducibility Variable | Result | LLM Response |
|---|---|---|
| Research Type | Experimental | DCD-FG uses a Gaussian non-linear low-rank structural equation model and shows significant improvements compared to state-of-the-art methods in both simulations as well as a recent large-scale single-cell RNA sequencing data set with hundreds of genetic interventions. |
| Researcher Affiliation | Collaboration | 1 Division of Research and Early Development, Genentech {lopez.romain, huettej1, regeva}@gene.com 2 Department of Genetics, Stanford University pritch@stanford.edu 3 Department of Biology, Stanford University |
| Pseudocode | No | The paper does not contain any sections or figures explicitly labeled as 'Pseudocode' or 'Algorithm'. |
| Open Source Code | Yes | 3. If you ran experiments... (a) Did you include the code, data, and instructions needed to reproduce the main experimental results (either in the supplemental material or as a URL)? [Yes] (Appendix) |
| Open Datasets | Yes | We focus on a recent Perturb-CITE-seq experiment [14] that contains expression profiles from 218,331 melanoma (cancer) cells, after interventions targeting each of 249 genes. and the citation: [14] Chris J Frangieh, Johannes C Melms, Pratiksha I Thakore, Kathryn R Geiger-Schuller, Patricia Ho, Adrienne M Luoma, Brian Cleary, Livnat Jerby-Arnon, Shruti Malu, Michael S Cuoco, et al. Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion. Nature Genetics, 53(3):332 341, 2021. |
| Dataset Splits | Yes | For every model, we performed a hyperparameter search using a goodness of fit metric on a small validation set. |
| Hardware Specification | Yes | on one NVIDIA Tesla T4 GPU with 15Gb of RAM |
| Software Dependencies | No | The paper mentions 'Python 3.8' and packages like 'PyTorch and SciPy' and 'Scanpy [63]' but does not provide specific version numbers for the libraries/packages used. |
| Experiment Setup | No | We provide further details on all experiments, including the grids used for hyperparameter search, as well as supplementary experiments, in Appendix F. |