# Enhanced Gene Selection in Single-Cell Genomics: Pre-Filtering Synergy and Reinforced Optimization

arXiv: https://arxiv.org/abs/2406.07418 · HTML: https://mlsanity.com/paper/2406.07418/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 5 of its 52 references that are in the map.
- First posted on arXiv 11 Jun 2024.

## Builds on (most cited first, 5 of 5)

- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Soft Actor-Critic Algorithms and Applications](https://mlsanity.com/paper/1812.05905/) (2018)
- [Prioritized Experience Replay](https://mlsanity.com/paper/1511.05952/) (2015)
- [Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution](https://mlsanity.com/paper/2204.13545/) (2022)
- [Reinforcement-Enhanced Autoregressive Feature Transformation: Gradient-steered Search in Continuous Space for Postfix Expressions](https://mlsanity.com/paper/2309.13618/) (2023)

## Built on by (most cited first, 3 of 3)

- [Revolutionizing Biomarker Discovery: Leveraging Generative AI for Bio-Knowledge-Embedded Continuous Space Exploration](https://mlsanity.com/paper/2409.15612/) (2024)
- [scReader: Prompting Large Language Models to Interpret scRNA-seq Data](https://mlsanity.com/paper/2412.18156/) (2024)
- [GeneSUM: Large Language Model-based Gene Summary Extraction](https://mlsanity.com/paper/2412.18154/) (2024)

## Abstract (arXiv)

Recent advancements in single-cell genomics necessitate precision in gene panel selection to interpret complex biological data effectively. Those methods aim to streamline the analysis of scRNA-seq data by focusing on the most informative genes that contribute significantly to the specific analysis task. Traditional selection methods, which often rely on expert domain knowledge, embedded machine learning models, or heuristic-based iterative optimization, are prone to biases and inefficiencies that may obscure critical genomic signals. Recognizing the limitations of traditional methods, we aim to transcend these constraints with a refined strategy. In this study, we introduce an iterative gene panel selection strategy that is applicable to clustering tasks in single-cell genomics. Our method uniquely integrates results from other gene selection algorithms, providing valuable preliminary boundaries or prior knowledge as initial guides in the search space to enhance the efficiency of our framework. Furthermore, we incorporate the stochastic nature of the exploration process in reinforcement learning (RL) and its capability for continuous optimization through reward-based feedback. This combination mitigates the biases inherent in the initial boundaries and harnesses RL's adaptability to refine and target gene panel selection dynamically. To illustrate the effectiveness of our method, we conducted detailed comparative experiments, case studies, and visualization analysis.