Job tasks Genomic sequences are modeled as evolving along binary phylogenetic trees through stochastic string-valued substitution and insertion-deletion (indel) processes. Given a set of present-day sequences, classical inference problems in phylogenetics are: (i) homology inference (ii) tree inference, and (iii) ancestral sequence reconstruction. A central focus of our recent work has been to develop fast frequentist indel-aware approaches to these problems. 
For tractability, the models in most cases must assume that residues evolve independently across sites. In reality, mutation probabilities are influenced by sequence context, including position-specific structural and functional constraints. In recent years, the convergence of computational biology and data-driven methods has led to genomic large language models (gLLMs). These can model sequence context dependences. 
Building on our previous work, our aim is to develop neuro-symbolic methods that retain mechanistic ground...