Structural Inference Methods in this Benchmark
A collection of the methods in this work.
| Methods | Paper | Official Implementation | Our Implementation |
|---|---|---|---|
| ppcor: An R Package for a Fast Calculation to Semi-partial Correlation Coefficients (ppcor) | Link | Link | /src/models/ppcor |
| TIGRESS: Trustful Inference of Gene REgulation using Stability Selection (TIGRESS) | Link | Link | /src/models/TIGRESS |
| ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context (ARACNe) | Link | Link | /src/models/ARACNE |
| Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles (CLR) | Link | Link | /src/models/CLR |
| Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures (PIDC) | Link | Link | /src/models/PIDC |
| Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe (Scribe) | Link | Link | /src/models/scribe |
| dynGENIE3: dynamical GENIE3 for the inference of gene networks from time series expression data (dynGENIE3) | Link | Link | /src/models/dynGENIE3 |
| Inference of gene regulatory networks based on nonlinear ordinary differential equations (XGBGRN) | Link | Link | /src/models/GRNs_nonlinear_ODEs |
| Neural Relational Inference for Interacting Systems (NRI) | Link | Link | /src/models/NRI |
| Amortized Causal Discovery: Learning to Infer Causal Graphs from Time-Series Data (ACD) | Link | Link | /src/models/ACD |
| Neural Relational Inference with Efficient Message Passing Mechanisms (MPM) | Link | Link | /src/models/MPM |
| Iterative Structural Inference of Directed Graphs (iSIDG) | Link | Link | /src/models/iSIDG |
| Effective and Efficient Structural Inference with Reservoir Computing (RCSI) | Link | Link | /src/models/RCSI |
More details about the methods please visit documentation.