To facilitate precision medicine and whole-genome annotation, we developed a machine-learning technique that scores how strongly genetic variants affect RNA splicing, whose alteration contributes to many diseases. Analysis of more than 650,000 intron...
Deep learning (DL) has emerged as a powerful tool to make accurate predictions from complex data such as image, text, or video. However, its ability to predict phenotypic values from molecular data is less well studied. Here, we describe the theoreti...
Progress in biophysics and molecular biology
33961842
Cognition-sensing and responding to the environment-is the unifying principle behind the genetic code, origin of life, evolution, consciousness, artificial intelligence, and cancer. However, the conventional model of biology seems to mistake cause an...
Whether we emphasize the notion of 'sign' or the notion of 'code', either way the main interest of biosemiotics and Code Biology is the same, and we argue that the idea of the lower threshold is what still unifies these two groups. Code Biology conce...
Generative artificial intelligence (AI) is a burgeoning field with widespread applications, including in science. Here, we explore two paradigms that provide insight into the capabilities and limitations of Chat Generative Pre-trained Transformer (Ch...
Degeneracy in the genetic code allows many possible DNA sequences to encode the same protein. Optimizing codon usage within a sequence to meet organism-specific preferences faces combinatorial explosion. Nevertheless, natural sequences optimized thro...
Journal of the American Medical Informatics Association : JAMIA
39998912
OBJECTIVES: The vast and complex nature of human genomic sequencing data presents challenges for effective analysis. This review aims to investigate the application of natural language processing (NLP) techniques, particularly large language models (...