Principal components analysis in the space of phylogenetic trees

Phylogenetic analysis of DNA or other data commonly gives rise to a collection or sample of inferred evolutionary trees. Principal Components Analysis (PCA) cannot be applied directly to collections of trees since the space of evolutionary trees on a fixed set of taxa is not a vector space. This paper describes a novel geometrical approach to PCA in tree-space that constructs the first principal path in an analogous way to standard linear Euclidean PCA. Given a data set of phylogenetic trees, a geodesic principal path is sought that maximizes the variance of the data under a form of projection onto the path. Due to the high dimensionality of tree-space and the nonlinear nature of this problem, the computational complexity is potentially very high, so approximate optimization algorithms are used to search for the optimal path. Principal paths identified in this way reveal and quantify the main sources of variation in the original collection of trees in terms of both topology and branch lengths. The approach is illustrated by application to simulated sets of trees and to a set of gene trees from metazoan (animal) species.Comment: Published in at http://dx.doi.org/10.1214/11-AOS915 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

Compression for Smooth Shape Analysis

Most 3D shape analysis methods use triangular meshes to discretize both the shape and functions on it as piecewise linear functions. With this representation, shape analysis requires fine meshes to represent smooth shapes and geometric operators like normals, curvatures, or Laplace-Beltrami eigenfunctions at large computational and memory costs. We avoid this bottleneck with a compression technique that represents a smooth shape as subdivision surfaces and exploits the subdivision scheme to parametrize smooth functions on that shape with a few control parameters. This compression does not affect the accuracy of the Laplace-Beltrami operator and its eigenfunctions and allow us to compute shape descriptors and shape matchings at an accuracy comparable to triangular meshes but a fraction of the computational cost. Our framework can also compress surfaces represented by point clouds to do shape analysis of 3D scanning data

Curvature weighted metrics on shape space of hypersurfaces in nn-space

Let $M$ be a compact connected oriented $n-1$ dimensional manifold without boundary. In this work, shape space is the orbifold of unparametrized immersions from $M$ to $\mathbb R^n$. The results of \cite{Michor118}, where mean curvature weighted metrics were studied, suggest incorporating Gau{\ss} curvature weights in the definition of the metric. This leads us to study metrics on shape space that are induced by metrics on the space of immersions of the form G_f(h,k) = \int_{M} \Phi . \bar g(h, k) \vol(f^*\bar{g}). Here f \in \Imm(M,\R^n) is an immersion of $M$ into $\R^n$ and $h,k\in C^\infty(M,\mathbb R^n)$ are tangent vectors at $f$. $\bar g$ is the standard metric on $\mathbb R^n$, $f^*\bar g$ is the induced metric on $M$, \vol(f^*\bar g) is the induced volume density and $\Phi$ is a suitable smooth function depending on the mean curvature and Gau{\ss} curvature. For these metrics we compute the geodesic equations both on the space of immersions and on shape space and the conserved momenta arising from the obvious symmetries. Numerical experiments illustrate the behavior of these metrics.Comment: 12 pages 3 figure

Barycentric Subspace Analysis on Manifolds

This paper investigates the generalization of Principal Component Analysis (PCA) to Riemannian manifolds. We first propose a new and general type of family of subspaces in manifolds that we call barycentric subspaces. They are implicitly defined as the locus of points which are weighted means of $k+1$ reference points. As this definition relies on points and not on tangent vectors, it can also be extended to geodesic spaces which are not Riemannian. For instance, in stratified spaces, it naturally allows principal subspaces that span several strata, which is impossible in previous generalizations of PCA. We show that barycentric subspaces locally define a submanifold of dimension k which generalizes geodesic subspaces.Second, we rephrase PCA in Euclidean spaces as an optimization on flags of linear subspaces (a hierarchy of properly embedded linear subspaces of increasing dimension). We show that the Euclidean PCA minimizes the Accumulated Unexplained Variances by all the subspaces of the flag (AUV). Barycentric subspaces are naturally nested, allowing the construction of hierarchically nested subspaces. Optimizing the AUV criterion to optimally approximate data points with flags of affine spans in Riemannian manifolds lead to a particularly appealing generalization of PCA on manifolds called Barycentric Subspaces Analysis (BSA).Comment: Annals of Statistics, Institute of Mathematical Statistics, A Para\^itr