The effect of non-linear signal in classification problems using gene expression.
Those building predictive models from transcriptomic data are faced with two conflicting perspectives. The first, based on the inherent high dimensionality of biological systems, supposes that complex non-linear models such as neural networks will better match complex biological systems. The second,...
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Public Library of Science (PLoS)
2023-03-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010984&type=printable |
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| author | Benjamin J Heil Jake Crawford Casey S Greene |
| author_facet | Benjamin J Heil Jake Crawford Casey S Greene |
| author_sort | Benjamin J Heil |
| collection | DOAJ |
| description | Those building predictive models from transcriptomic data are faced with two conflicting perspectives. The first, based on the inherent high dimensionality of biological systems, supposes that complex non-linear models such as neural networks will better match complex biological systems. The second, imagining that complex systems will still be well predicted by simple dividing lines prefers linear models that are easier to interpret. We compare multi-layer neural networks and logistic regression across multiple prediction tasks on GTEx and Recount3 datasets and find evidence in favor of both possibilities. We verified the presence of non-linear signal when predicting tissue and metadata sex labels from expression data by removing the predictive linear signal with Limma, and showed the removal ablated the performance of linear methods but not non-linear ones. However, we also found that the presence of non-linear signal was not necessarily sufficient for neural networks to outperform logistic regression. Our results demonstrate that while multi-layer neural networks may be useful for making predictions from gene expression data, including a linear baseline model is critical because while biological systems are high-dimensional, effective dividing lines for predictive models may not be. |
| format | Article |
| id | doaj-art-1a94026c384a4ba5bca5cb2647c9c2bd |
| institution | DOAJ |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2023-03-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-1a94026c384a4ba5bca5cb2647c9c2bd2025-08-20T02:49:29ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582023-03-01193e101098410.1371/journal.pcbi.1010984The effect of non-linear signal in classification problems using gene expression.Benjamin J HeilJake CrawfordCasey S GreeneThose building predictive models from transcriptomic data are faced with two conflicting perspectives. The first, based on the inherent high dimensionality of biological systems, supposes that complex non-linear models such as neural networks will better match complex biological systems. The second, imagining that complex systems will still be well predicted by simple dividing lines prefers linear models that are easier to interpret. We compare multi-layer neural networks and logistic regression across multiple prediction tasks on GTEx and Recount3 datasets and find evidence in favor of both possibilities. We verified the presence of non-linear signal when predicting tissue and metadata sex labels from expression data by removing the predictive linear signal with Limma, and showed the removal ablated the performance of linear methods but not non-linear ones. However, we also found that the presence of non-linear signal was not necessarily sufficient for neural networks to outperform logistic regression. Our results demonstrate that while multi-layer neural networks may be useful for making predictions from gene expression data, including a linear baseline model is critical because while biological systems are high-dimensional, effective dividing lines for predictive models may not be.https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010984&type=printable |
| spellingShingle | Benjamin J Heil Jake Crawford Casey S Greene The effect of non-linear signal in classification problems using gene expression. PLoS Computational Biology |
| title | The effect of non-linear signal in classification problems using gene expression. |
| title_full | The effect of non-linear signal in classification problems using gene expression. |
| title_fullStr | The effect of non-linear signal in classification problems using gene expression. |
| title_full_unstemmed | The effect of non-linear signal in classification problems using gene expression. |
| title_short | The effect of non-linear signal in classification problems using gene expression. |
| title_sort | effect of non linear signal in classification problems using gene expression |
| url | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010984&type=printable |
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