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한빛사논문
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Brief. Bioinform., Jan 22 2024, 25 (2) bbae004 | https://doi.org/10.1093/bib/bbae004
Species-agnostic transfer learning for cross-species transcriptomics data integration without gene orthology
Youngjun Park 1,2, Nils P Muttray 3, Anne-Christin Hauschild 1,4
1Department of Medical Informatics, University Medical Center Göttingen, Göttingen, Germany.
2International Max Planck Research Schools for Genome Science, Georg-August-Universität Göttingen Göttingen, Germany.
3Applied Statistics, Georg-August-Universität Göttingen Göttingen, Germany.
4Campus-Institute Data Science (CIDAS), Georg-August-Universität Göttingen Göttingen, Germany.
Corresponding author : Anne-Christin Hauschild
Abstract
Novel hypotheses in biomedical research are often developed or validated in model organisms such as mice and zebrafish and thus play a crucial role. However, due to biological differences between species, translating these findings into human applications remains challenging. Moreover, commonly used orthologous gene information is often incomplete and entails a significant information loss during gene-id conversion. To address these issues, we present a novel methodology for species-agnostic transfer learning with heterogeneous domain adaptation. We extended the cross-domain structure-preserving projection toward out-of-sample prediction. Our approach not only allows knowledge integration and translation across various species without relying on gene orthology but also identifies similar GO among the most influential genes composing the latent space for integration. Subsequently, during the alignment of latent spaces, each composed of species-specific genes, it is possible to identify functional annotations of genes missing from public orthology databases. We evaluated our approach with four different single-cell sequencing datasets focusing on cell-type prediction and compared it against related machine-learning approaches. In summary, the developed model outperforms related methods working without prior knowledge when predicting unseen cell types based on other species' data. The results demonstrate that our novel approach allows knowledge transfer beyond species barriers without the dependency on known gene orthology but utilizing the entire gene sets.
논문정보
- Research article
- 2024년 01월 (BRIC 등록일 2024-02-16)
- 국외 연구진
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