Detecting Spatial Dependence in Transcriptomics Data using Vectorised Persistence Diagrams
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arXiv
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| Format: | Preprint |
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2024
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| _version_ | 1866912389865144320 |
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| author | Limbeck, Katharina Rieck, Bastian |
| author_facet | Limbeck, Katharina Rieck, Bastian |
| contents | Evaluating spatial patterns in data is an integral task across various domains, including geostatistics, astronomy, and spatial tissue biology. The analysis of transcriptomics data in particular relies on methods for detecting spatially-dependent features that exhibit significant spatial patterns for both explanatory analysis and feature selection. However, given the complex and high-dimensional nature of these data, there is a need for robust, stable, and reliable descriptors of spatial dependence. We leverage the stability and multiscale properties of persistent homology to address this task. To this end, we introduce a novel framework using functional topological summaries, such as Betti curves and persistence landscapes, for identifying and describing non-random patterns in spatial data. In particular, we propose a non-parametric one-sample permutation test for spatial dependence and investigate its utility across both simulated and real spatial omics data. Our vectorised approach outperforms baseline methods at accurately detecting spatial dependence. Further, we find that our method is more robust to outliers than alternative tests using Moran's I. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2409_03575 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Detecting Spatial Dependence in Transcriptomics Data using Vectorised Persistence Diagrams Limbeck, Katharina Rieck, Bastian Methodology Computational Geometry Evaluating spatial patterns in data is an integral task across various domains, including geostatistics, astronomy, and spatial tissue biology. The analysis of transcriptomics data in particular relies on methods for detecting spatially-dependent features that exhibit significant spatial patterns for both explanatory analysis and feature selection. However, given the complex and high-dimensional nature of these data, there is a need for robust, stable, and reliable descriptors of spatial dependence. We leverage the stability and multiscale properties of persistent homology to address this task. To this end, we introduce a novel framework using functional topological summaries, such as Betti curves and persistence landscapes, for identifying and describing non-random patterns in spatial data. In particular, we propose a non-parametric one-sample permutation test for spatial dependence and investigate its utility across both simulated and real spatial omics data. Our vectorised approach outperforms baseline methods at accurately detecting spatial dependence. Further, we find that our method is more robust to outliers than alternative tests using Moran's I. |
| title | Detecting Spatial Dependence in Transcriptomics Data using Vectorised Persistence Diagrams |
| topic | Methodology Computational Geometry |
| url | https://arxiv.org/abs/2409.03575 |