Software Benchmark—Classification Tree Algorithms for Cell Atlases Annotation Using Single-Cell RNA-Sequencing Data
| dc.contributor.author | Alaqeeli, O. | |
| dc.contributor.author | Xing, L. | |
| dc.contributor.author | Zhang, Xuekui | |
| dc.date.accessioned | 2021-08-18T17:18:27Z | |
| dc.date.available | 2021-08-18T17:18:27Z | |
| dc.date.copyright | 2021 | en_US |
| dc.date.issued | 2021 | |
| dc.description.abstract | Classification tree is a widely used machine learning method. It has multiple implementations as R packages; rpart, ctree, evtree, tree and C5.0. The details of these implementations are not the same, and hence their performances differ from one application to another. We are interested in their performance in the classification of cells using the single-cell RNA-Sequencing data. In this paper, we conducted a benchmark study using 22 Single-Cell RNA-sequencing data sets. Using cross-validation, we compare packages’ prediction performances based on their Precision, Recall, F1-score, Area Under the Curve (AUC).We also compared the Complexity and Run-time of these R packages. Our study shows that rpart and evtree have the best Precision; evtree is the best in Recall, F1-score and AUC; C5.0 prefers more complex trees; tree is consistently much faster than others, although its complexity is often higher than others. | en_US |
| dc.description.reviewstatus | Reviewed | en_US |
| dc.description.scholarlevel | Faculty | en_US |
| dc.description.sponsorship | The research was funded by the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grants (LX and XZ) and Canada Research Chair Grant (XZ). This research was enabled in part by support provided by WestGrid (www.westgrid.ca, accessed on 6 April 2021) and Compute Canada (www.computecanada.ca, accessed on 6 April 2021). | en_US |
| dc.identifier.citation | Alaqeeli, O., Xing, L., Zhang, X. (2021). Software benchmark—Classification tree algorithms for cell atlases annotation using single-cell RNA-sequencing data. Microbiology Research, 12, 317-334. https://doi.org/10.3390/microbiolres12020022 | en_US |
| dc.identifier.uri | https://doi.org/10.3390/microbiolres12020022 | |
| dc.identifier.uri | http://hdl.handle.net/1828/13272 | |
| dc.language.iso | en | en_US |
| dc.publisher | Microbiology Research | en_US |
| dc.subject | classification tree | en_US |
| dc.subject | single-cell RNA-sequencing | en_US |
| dc.subject | benchmark | en_US |
| dc.subject | precision | en_US |
| dc.subject | recall | en_US |
| dc.subject | F1-score | en_US |
| dc.subject | complexity | en_US |
| dc.subject | area under the curve | en_US |
| dc.subject | run-time | en_US |
| dc.title | Software Benchmark—Classification Tree Algorithms for Cell Atlases Annotation Using Single-Cell RNA-Sequencing Data | en_US |
| dc.type | Article | en_US |