Multiple Testing under Dependence via Semiparametric Graphical Models
Authors: Jie Liu, Chunming Zhang, Elizabeth Burnside, David Page
ICML 2014 | Conference PDF | Archive PDF | Plain Text | LLM Run Details
| Reproducibility Variable | Result | LLM Response |
|---|---|---|
| Research Type | Experimental | A variety of simulations show that our semiparametric approach outperforms classical procedures which assume independence and the parametric approaches which capture dependence. |
| Researcher Affiliation | Academia | Jie Liu JIELIU@CS.WISC.EDU Department of Computer Sciences, University of Wisconsin-Madison Chunming Zhang CMZHANG@STAT.WISC.EDU Department of Statistics, University of Wisconsin-Madison Elizabeth Burnside EBURNSIDE@UWHEALTH.ORG Department of Radiology, University of Wisconsin-Madison David Page PAGE@BIOSTAT.WISC.EDU Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison |
| Pseudocode | No | The paper describes the algorithmic steps and modifications in narrative text, but it does not include a formally labeled 'Pseudocode' or 'Algorithm' block. |
| Open Source Code | No | The paper does not provide any explicit statements or links indicating that the source code for the described methodology is publicly available. |
| Open Datasets | Yes | We apply our procedure to a real-world GWAS on breast cancer (Hunter et al., 2007) which involves 528,173 SNPs for 1,145 cases and 1,142 controls. |
| Dataset Splits | No | The paper mentions using simulated data for experiments and 'a second cohort to validate the 18 SNPs' in the real-world application, but it does not specify explicit training/validation/test dataset splits with percentages or sample counts for a single dataset. |
| Hardware Specification | Yes | In the chain-structure simulations, it took our data-driven procedure about 10 hours to finish the 500 replications sequentially (for one µ value in (10)) on one 3GHz CPU. In the grid-structure simulations, it took our procedure around 30 hours to finish the 500 replications sequentially (for one µ value in (10)) on one 3GHz CPU. |
| Software Dependencies | No | The paper does not specify any software dependencies with version numbers (e.g., programming languages, libraries, or frameworks). |
| Experiment Setup | Yes | We consider two dependence structures, namely a chain structure and a grid structure. For the chain structure, we choose the number of hypotheses m=10,000. For the grid structure, we choose a 100 × 100 grid, which also yields 10,000 hypotheses. We test two levels of dependence strength, i.e. φ=0.8 and φ=0.6. We set π to be 0.4. We set λ=0.8, and the value of p0 is estimated to be 0.978. |