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| Main Authors: | , , , , |
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| Format: | Preprint |
| Published: |
2024
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| Subjects: | |
| Online Access: | https://arxiv.org/abs/2403.03018 |
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| _version_ | 1866909128648032256 |
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| author | Rostami, Mohammad Ghariyazi, Amin Dashti, Hamed Rohban, Mohammad Hossein Rabiee, Hamid R. |
| author_facet | Rostami, Mohammad Ghariyazi, Amin Dashti, Hamed Rohban, Mohammad Hossein Rabiee, Hamid R. |
| contents | Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a gene editing technology that has revolutionized the fields of biology and medicine. However, one of the challenges of using CRISPR is predicting the on-target efficacy and off-target sensitivity of single-guide RNAs (sgRNAs). This is because most existing methods are trained on separate datasets with different genes and cells, which limits their generalizability. In this paper, we propose a novel ensemble learning method for sgRNA design that is accurate and generalizable. Our method combines the predictions of multiple machine learning models to produce a single, more robust prediction. This approach allows us to learn from a wider range of data, which improves the generalizability of our model. We evaluated our method on a benchmark dataset of sgRNA designs and found that it outperformed existing methods in terms of both accuracy and generalizability. Our results suggest that our method can be used to design sgRNAs with high sensitivity and specificity, even for new genes or cells. This could have important implications for the clinical use of CRISPR, as it would allow researchers to design more effective and safer treatments for a variety of diseases. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2403_03018 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | CRISPR: Ensemble Model Rostami, Mohammad Ghariyazi, Amin Dashti, Hamed Rohban, Mohammad Hossein Rabiee, Hamid R. Machine Learning Genomics Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a gene editing technology that has revolutionized the fields of biology and medicine. However, one of the challenges of using CRISPR is predicting the on-target efficacy and off-target sensitivity of single-guide RNAs (sgRNAs). This is because most existing methods are trained on separate datasets with different genes and cells, which limits their generalizability. In this paper, we propose a novel ensemble learning method for sgRNA design that is accurate and generalizable. Our method combines the predictions of multiple machine learning models to produce a single, more robust prediction. This approach allows us to learn from a wider range of data, which improves the generalizability of our model. We evaluated our method on a benchmark dataset of sgRNA designs and found that it outperformed existing methods in terms of both accuracy and generalizability. Our results suggest that our method can be used to design sgRNAs with high sensitivity and specificity, even for new genes or cells. This could have important implications for the clinical use of CRISPR, as it would allow researchers to design more effective and safer treatments for a variety of diseases. |
| title | CRISPR: Ensemble Model |
| topic | Machine Learning Genomics |
| url | https://arxiv.org/abs/2403.03018 |