# DeepFM-Crispr: Prediction of CRISPR On-Target Effects via Deep Learning

arXiv: https://arxiv.org/abs/2409.05938 · HTML: https://mlsanity.com/paper/2409.05938/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 9 of its 36 references that are in the map.
- First posted on arXiv 9 Sep 2024.

## Builds on (most cited first, 9 of 9)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Densely Connected Convolutional Networks](https://mlsanity.com/paper/1608.06993/) (2016)
- [XGBoost: A Scalable Tree Boosting System](https://mlsanity.com/paper/1603.02754/) (2016)
- [Dense-Captioning Events in Videos](https://mlsanity.com/paper/1705.00754/) (2017)
- [MMC: Advancing Multimodal Chart Understanding with Large-scale Instruction Tuning](https://mlsanity.com/paper/2311.10774/) (2023)
- [Mementos: A Comprehensive Benchmark for Multimodal Large Language Model Reasoning over Image Sequences](https://mlsanity.com/paper/2401.10529/) (2024)
- [Towards Understanding In-Context Learning with Contrastive Demonstrations and Saliency Maps](https://mlsanity.com/paper/2307.05052/) (2023)
- [Large Language Models and Causal Inference in Collaboration: A Survey](https://mlsanity.com/paper/2403.09606/) (2024)

## Abstract (arXiv)

Since the advent of CRISPR-Cas9, a groundbreaking gene-editing technology that enables precise genomic modifications via a short RNA guide sequence, there has been a marked increase in the accessibility and application of this technology across various fields. The success of CRISPR-Cas9 has spurred further investment and led to the discovery of additional CRISPR systems, including CRISPR-Cas13. Distinct from Cas9, which targets DNA, Cas13 targets RNA, offering unique advantages for gene modulation. We focus on Cas13d, a variant known for its collateral activity where it non-specifically cleaves adjacent RNA molecules upon activation, a feature critical to its function. We introduce DeepFM-Crispr, a novel deep learning model developed to predict the on-target efficiency and evaluate the off-target effects of Cas13d. This model harnesses a large language model to generate comprehensive representations rich in evolutionary and structural data, thereby enhancing predictions of RNA secondary structures and overall sgRNA efficacy. A transformer-based architecture processes these inputs to produce a predictive efficacy score. Comparative experiments show that DeepFM-Crispr not only surpasses traditional models but also outperforms recent state-of-the-art deep learning methods in terms of prediction accuracy and reliability.