It is unclear if this forum is frequented as much as it used to be. Let’s see if this post goes off echoing into the abyss. Is anyone out there knowledgeable and / or working on the following topics?
Accounting for co-evolution in phylogenetic models. It is my (naive) understanding that phylogenetic models are built on the core assumption of mutational independence. Recent work built on the assumption that some mutations are co-dependent (co-evolution) has resulted in significant progress in protein structure modeling from sequences alone (https://science.sciencemag.org/content/355/6322/294.abstract). Said differently, how is co-evolution (within a protein family, between protein families, between nucleotides / amino acids / codons / etc) being taken into consideration in phylogenetic models nowadays?
VAE hyperbolic Poincaré embeddings via VAE for phylogeny. Surely, some of you in this crowd encountered this recent paper from DeepMind (https://deepmind.com/research/publications/hierarchical-representations-poincare-variational-auto-encoders). I attended NeurIPs recently and was informed that as enticing as Figure 1 is, it is apparently only applicable to phylogenetic tree construction if the ancestral nodes are part of the dataset as well… Anybody else thinking about this!?
"Ground truths" for phylogenetic trees. As a newcomer to this field - please forgive me if this is already an obvious answer… - but it is unclear if there exist empirical benchmarks by which phylogenetic tree models can be compared against. I imagine there are sub-topic and / or niche “positive controls” for phylogenetic tree construction but unlike the protein world, which has a biannual protein structure prediction competition (CASP), a field-wide benchmark / metric / competition for phylogeny seems to be absent…
Dylan (email: firstname.lastname@example.org)