BEM: Mining Coregulation Patterns in Transcriptomics via Boolean Matrix Factorization

Lifan Liang, Kunju Zhu, Songjian Lu. BEM: Mining Coregulation Patterns in Transcriptomics via Boolean Matrix Factorization.

Bioinformatics 2020 Jan 8. pii: btz977. doi: 10.1093/bioinformatics/btz977



The matrix factorization is an important way to analyze co-regulation patterns in transcriptomic data, which can reveal the tumor signal perturbation status and subtype classification. However, current matrix factorization methods do not provide clear bicluster structure. Furthermore, these algorithms are based on the assumption of linear combination, which may not be sufficient to capture the coregulation patterns.


We presented a new algorithm for Boolean matrix factorization via expectation maximization (BEM). BEM is more aligned with the molecular mechanism of transcriptomic coregulation and can scale to matrix with over 100 million data points. Synthetic experiments showed that BEM outperformed other Boolean matrix factorization methods in terms of reconstruction error. Real world application demonstrated that BEM is applicable to all kinds of transcriptomic data, including bulk RNAseq, single cell RNAseq, and spatial transcriptomic datasets. Given appropriate binarization, BEM was able to extract coregulation patterns consistent with disease subtypes, cell types, or spatial anatomy.

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Lifan Liang, Kunju Zhu, Songjian Lu.
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