To resist thermodynamic disorder, living systems maintain low entropy genomic configurations through selection. We propose pseudo-perplexity, the per position surprisal of a masked language model, as an estimator of this biological functional information. Using a unified framework, we demonstrate that transformer deriv...
Tyler D. Myers, Se-Jin Song, A. Bartko· IEEE Symposium on Artificial...· 0 citations
Bladder carcinoma in situ (CIS) is a multifocal, non–muscle-invasive disease with a high risk of progression to muscle-invasive cancer. Current management strategies are often guided by genomic profiling of single tumor samples, which incompletely capture tumor heterogeneity and may contribute to treatment failure. In...
Tyler D. Myers, A. Salmasi, M. Meagher et al.· bioRxiv· 0 citations
Joint Robust Principal Component Analysis (Joint-RPCA), a method designed with these statistical properties in mind and broadly applicable to multi-omics settings with similar challenges, reveals replicable and interpretable multi-omic patterns.
Bianca Cordazzo Vargas, C. Martino, A. Dilmore et al.· Molecular Systems Biology· 1 citation
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