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Limitations of phylogeny inference and utility of perplexity in BFMs — ARCADIA Knowledge Graph

InferenceChain·arcadia

Limitations of phylogeny inference and utility of perplexity in BFMs

This chain explains how direct phylogenetic inference methods fail to scale with large BFM datasets, suggests information-theoretic approaches like perplexity as alternatives to capture phylogenetic structure, and highlights inherent limits in using phylogeny alone to understand fitness in biological foundation models.

Confidence
80%
◑partialactivecomplexity: mid

Reasoning Steps (3)

Phylogenetic tree inference does not scaleStep 1
Perplexity as proxy for phylogenetic structureStep 2
Disentangling phylogeny and fitness is complexStep 3

Source

Synthesis for current paper

Connections (3)

Biological foundation models learn evolutionary rulesAssociation
Data leakage affects biological foundation modelsAssociation
Training data structure influences performance biasAssociation