TaxoFormer
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TaxoFormer: Hierarchical Transformer for Predicting the Full Taxonomic Lineage of Protein Sequences
Predicting labels in massive, hierarchically structured output spaces is a core challenge in machine learning. In this work, we use the problem of predicting the full taxonomic lineage of a protein from its sequence as a case study for this challenge. We introduce TaxoFormer, an architecture whose primary contribution is a structured tokenization scheme that losslessly represents the entire NCBI phylogenetic tree, a graph with over 1.3 million nodes using a compact vocabulary of just 15,000...