Explainable deep learning for stratified medicine in inflammatory bowel disease
Abstract Moving from a one-size-fits-all to an individual approach in precision medicine requires a deeper understanding of disease molecular mechanisms. Especially in heterogeneous complex diseases such as inflammatory bowel disease (IBD), better molecular stratification will help select the correc...
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| Format: | Article |
| Language: | English |
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BMC
2025-07-01
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| Series: | Genome Biology |
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| Online Access: | https://doi.org/10.1186/s13059-025-03692-6 |
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| author | Nora Verplaetse Piero Fariselli Yves Moreau Daniele Raimondi |
| author_facet | Nora Verplaetse Piero Fariselli Yves Moreau Daniele Raimondi |
| author_sort | Nora Verplaetse |
| collection | DOAJ |
| description | Abstract Moving from a one-size-fits-all to an individual approach in precision medicine requires a deeper understanding of disease molecular mechanisms. Especially in heterogeneous complex diseases such as inflammatory bowel disease (IBD), better molecular stratification will help select the correct therapy. For this, we build end-to-end biologically sparsified neural network architectures for IBD subtyping based on whole exome sequence representations with gene-level and variant-level resolution. By moving beyond univariate methods, we capitalize on the model’s ability to extract complex molecular patterns to improve prediction. Model interpretation identifies the most predictive pathways, genes, and variants, uncovering important intestinal barrier, immunological, and microbiome factors. |
| format | Article |
| id | doaj-art-8661329b94ea4f66b11f6f70537b44ff |
| institution | Kabale University |
| issn | 1474-760X |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj-art-8661329b94ea4f66b11f6f70537b44ff2025-08-20T03:42:49ZengBMCGenome Biology1474-760X2025-07-0126113010.1186/s13059-025-03692-6Explainable deep learning for stratified medicine in inflammatory bowel diseaseNora Verplaetse0Piero Fariselli1Yves Moreau2Daniele Raimondi3ESAT-STADIUS, KU LeuvenDepartment of Medical Sciences, University of TorinoESAT-STADIUS, KU LeuvenESAT-STADIUS, KU LeuvenAbstract Moving from a one-size-fits-all to an individual approach in precision medicine requires a deeper understanding of disease molecular mechanisms. Especially in heterogeneous complex diseases such as inflammatory bowel disease (IBD), better molecular stratification will help select the correct therapy. For this, we build end-to-end biologically sparsified neural network architectures for IBD subtyping based on whole exome sequence representations with gene-level and variant-level resolution. By moving beyond univariate methods, we capitalize on the model’s ability to extract complex molecular patterns to improve prediction. Model interpretation identifies the most predictive pathways, genes, and variants, uncovering important intestinal barrier, immunological, and microbiome factors.https://doi.org/10.1186/s13059-025-03692-6Genome interpretationNeural networksMachine learning |
| spellingShingle | Nora Verplaetse Piero Fariselli Yves Moreau Daniele Raimondi Explainable deep learning for stratified medicine in inflammatory bowel disease Genome Biology Genome interpretation Neural networks Machine learning |
| title | Explainable deep learning for stratified medicine in inflammatory bowel disease |
| title_full | Explainable deep learning for stratified medicine in inflammatory bowel disease |
| title_fullStr | Explainable deep learning for stratified medicine in inflammatory bowel disease |
| title_full_unstemmed | Explainable deep learning for stratified medicine in inflammatory bowel disease |
| title_short | Explainable deep learning for stratified medicine in inflammatory bowel disease |
| title_sort | explainable deep learning for stratified medicine in inflammatory bowel disease |
| topic | Genome interpretation Neural networks Machine learning |
| url | https://doi.org/10.1186/s13059-025-03692-6 |
| work_keys_str_mv | AT noraverplaetse explainabledeeplearningforstratifiedmedicineininflammatoryboweldisease AT pierofariselli explainabledeeplearningforstratifiedmedicineininflammatoryboweldisease AT yvesmoreau explainabledeeplearningforstratifiedmedicineininflammatoryboweldisease AT danieleraimondi explainabledeeplearningforstratifiedmedicineininflammatoryboweldisease |