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SabbaghCodes authored Jun 14, 2024
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Expand Up @@ -85,7 +85,7 @@ Papers that utilize Transformer models to analyze single-cell genomic data.
### Benchmarking Papers
| 📄 Paper | 💻 Code | 🧠 Benchmarking Models | 🌟 Main Focus | 📝 Results & Insights |
|---------------------------------------------------|----------------------|----------------------------------|----------------------------------------|-----------------------|
| [x](#) | [x](#) | [x](#) | x | x |
| [Evaluating the Utilities of Foundation Models in Single-cell Data Analysis](https://www.biorxiv.org/content/10.1101/2023.09.08.555192v5). Tianyu Liu et al. _bioRxiv_ (2024) | [GitHub Repository](https://github.com/HelloWorldLTY/scEval) | scGPT, scFoundation, tGPT, GeneCompass, SCimilarity, UCE, and CellPLM | This paper evaluates the performance of foundation models (FMs) in single-cell sequencing data analysis, comparing them to task-specific methods across eight downstream tasks and proposing a systematic evaluation framework (scEval) for training and fine-tuning single-cell FMs. The study highlights that while single-cell FMs may not always outperform task-specific methods, they show promise in cross-species/cross-modality transfer learning and possess unique emergent abilities. | Open-source single-cell FMs generally outperform closed-source ones due to their accessibility and the community feedback they receive; pre-training significantly enhances model performance in tasks like Cell-type Annotation and Gene Function Prediction. However, the study also found limitations in the stability and performance of single-cell FMs across certain tasks, suggesting the need for more nuanced training and fine-tuning processes, and indicating substantial room for improvement in their development. |

### Review/Perspective Papers
| 📄 Paper | 💻 Code | 🌟 Highlights/Main Focus | 📝 Remarks & Conclusion |
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