First day of CCEM's annual workshop 2023 featured engaging discussions and six exciting talks on phenotypic and morphological analyses, evolutionary modelling of shape data, phylogenetic root estimation and species tree inference. #VillumFoundation

CCEM Annual Workshop 2023 was concluded by inspiring talks by Kyle Copas on GBIF – Global Biodiversity Information Facility, by Guojie Zhang on the B10K bird genome project and by Gavin Thomas on the Mark My Bird project. Thank you to all for great discussions! #VillumFoundation

Come join us for a postdoc in Copenhagen aimed at developing computational methods to map genotype-phenotype interactions in birds. candidate.hr-manager.net/ApplicationIni…

CCEM's PhD student Michael Severinsen is currently on a research stay at UC Berkeley - pictured here in front of dog skulls affected by artifical selection in California Academy of Sciences which is one of the foci of the research during his stay #VillumFoundation

Hyperiax: Tree traversals using JAX github.com/ComputationalE… Developed by the team at Centre for Computational Evolutionary Morphometry, initially for applications in phylogenetic analysis of morphological data, but Hyperiax has evolved into a general tree traversal, message passing and edge/node computation framework.

Our notebook github.com/ComputationalE… implements fast estimation of inner nodes of a phylogenetic tree - a simple application of our new tree traversal framework Hyperiax! We also show how Hyperiax can be used for fast simulation of trees under a Brownian Motion model. Centre for Computational Evolutionary Morphometry

Our notebook, github.com/ComputationalE… ..., implements a fast estimation of shape in inner nodes in a phylogenetic tree. Hyperiax is used here to estimate the intermediate shape(in blue) between two different species of butterflies! Centre for Computational Evolutionary Morphometry

Our notebook Upwaards LDDMM utilizing the Hyperiax framework github.com/ComputationalE…… ..., is used here to estimate the ancestral shape (in blue) and two intermediate shapes (in green) for four different butterfly species belonging to Papilionoidea. Centre for Computational Evolutionary Morphometry

Frank van der Meulen Moritz Schauer Coming soon will be other examples from the above references, and later on SDE cases and inference in SDE models for shapes. A major focus at Centre for Computational Evolutionary Morphometry is to make inference in infinite dimensional models of shape variation along phylogenetic trees possible. The above notebooks

Simulating infinite-dimensional nonlinear diffusion bridges w/ Gf Yang Libby Michael Baand Christy Hipsley We merge score matching with neural operators to simulate infinite dimensional non-linear diffusion bridges, e.g. bridges between shapes, ... 1/

Hyperiax and JaxGeometry, talk by Gf Yang at CIRM Luminy

Conditioning shape processes is not restricted to finite configurations of landmarks - we can lift to infinite dimensions and condition nonlinear processes using Doob's h-transform, talk today by Libby at CIRM Luminy

Second-order differential operators, stochastic differential equations and Brownian motions on embedded manifolds w/ Du Nguyen TH TRADING

We welcome our new postdoc Ricardo Ely, PhD, cosupervised with Rasmus Nielsen as part of our Villum Fonden project Stochastic Morphometry. Ricardo will study bird beak evolution (like in this kākāpō) using methods developed by our Centre for Computational Evolutionary Morphometry team.

Score matching for bridges can be learned without time-reversal arxiv.org/abs/2407.15455 w/ Libby Moritz Schauer We learn grad log p(t,x; T,y) for a target y directly without reversing time by combining score matching with adjoint diffusions (Milstein 2004) that give the

Kicking off Geometric Morphometrics workshop at University of Copenhagen Research and Dominika Bujnakova teaching 3D landmarking!!! 🐺

Hyperiax 2.0 is out! Marcus and the rest of the Hyperiax team have done an amazing job at revising the interface and in using Jax much more efficiently for tree computations. Hyperiax now traverses trees with >500 mill. nodes in <50 ms.

Du TH TRADING and I have a new preprint on arxiv: Parallel transport on matrix manifolds and Exponential Action arxiv.org/abs/2408.06054