Gabriele Di Palma

Estimating the frequencies of host-symbiont coevolution events used to require reconstructing a host tree and then reconciling the symbiont tree against it, so tree-inference error propagated into the result. Fox instead uses a transformer to output the relative frequencies of cospeciation, host switching, loss and duplication directly from the host and symbiont multiple sequence alignments and their mapping, paying the simulation cost once at training time and processing each new system in a single forward pass. On the independent simulator treeducken, Fox reached a mean absolute error of 0.060 on the 92 datasets AmoCoala completed, against 0.131 for AmoCoala, while running more than three orders of magnitude faster.

Estimating the frequencies of host-symbiont coevolution events used to require reconstructing a host tree and then reconciling the symbiont tree against it, so tree-inference error propagated into the result. Fox instead uses a transformer to output the relative frequencies of cospeciation, host switching, loss and duplication directly from the host and symbiont multiple sequence alignments and their mapping, paying the simulation cost once at training time and processing each new system in a single forward pass. On the independent simulator treeducken, Fox reached a mean absolute error of 0.060 on the 92 datasets AmoCoala completed, against 0.131 for AmoCoala, while running more than three orders of magnitude faster.