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Constrained Shape Analysis with Applications to RNA Structure
Authors:
Kanti V. Mardia,
Benjamin Eltzner,
Stephan F. Huckemann
Abstract:
In many applications of shape analysis, lengths between some landmarks are constrained. For instance, biomolecules often have some bond lengths and some bond angles constrained, and variation occurs only along unconstrained bonds and constrained bonds' torsions where the latter are conveniently modelled by dihedral angles. Our work has been motivated by low resolution biomolecular chain RNA where…
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In many applications of shape analysis, lengths between some landmarks are constrained. For instance, biomolecules often have some bond lengths and some bond angles constrained, and variation occurs only along unconstrained bonds and constrained bonds' torsions where the latter are conveniently modelled by dihedral angles. Our work has been motivated by low resolution biomolecular chain RNA where only some prominent atomic bonds can be well identified. Here, we propose a new modelling strategy for such constrained shape analysis starting with a product of polar coordinates (polypolars), where, due to constraints, for example, some radial coordinates should be omitted, leaving products of spheres (polyspheres). We give insight into these coordinates for particular cases such as five landmarks which are motivated by a practical RNA application. We also discuss distributions for polypolar coordinates and give a specific methodology with illustration when the constrained size-and-shape variables are concentrated. There are applications of this in clustering and we give some insight into a modified version of the MINT-AGE algorithm.
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Submitted 22 February, 2025;
originally announced February 2025.
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Generalized Intersection Algorithms with Fixpoints for Image Decomposition Learning
Authors:
Robin Richter,
Duy H. Thai,
Stephan F. Huckemann
Abstract:
In image processing, classical methods minimize a suitable functional that balances between computational feasibility (convexity of the functional is ideal) and suitable penalties reflecting the desired image decomposition. The fact that algorithms derived from such minimization problems can be used to construct (deep) learning architectures has spurred the development of algorithms that can be tr…
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In image processing, classical methods minimize a suitable functional that balances between computational feasibility (convexity of the functional is ideal) and suitable penalties reflecting the desired image decomposition. The fact that algorithms derived from such minimization problems can be used to construct (deep) learning architectures has spurred the development of algorithms that can be trained for a specifically desired image decomposition, e.g. into cartoon and texture. While many such methods are very successful, theoretical guarantees are only scarcely available. To this end, in this contribution, we formalize a general class of intersection point problems encompassing a wide range of (learned) image decomposition models, and we give an existence result for a large subclass of such problems, i.e. giving the existence of a fixpoint of the corresponding algorithm. This class generalizes classical model-based variational problems, such as the TV-l2 -model or the more general TV-Hilbert model. To illustrate the potential for learned algorithms, novel (non learned) choices within our class show comparable results in denoising and texture removal.
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Submitted 16 October, 2020;
originally announced October 2020.
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Information geometry for phylogenetic trees
Authors:
Maryam K. Garba,
Tom M. W. Nye,
Jonas Lueg,
Stephan F. Huckemann
Abstract:
We propose a new space of phylogenetic trees which we call wald space. The motivation is to develop a space suitable for statistical analysis of phylogenies, but with a geometry based on more biologically principled assumptions than existing spaces: in wald space, trees are close if they induce similar distributions on genetic sequence data. As a point set, wald space contains the previously devel…
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We propose a new space of phylogenetic trees which we call wald space. The motivation is to develop a space suitable for statistical analysis of phylogenies, but with a geometry based on more biologically principled assumptions than existing spaces: in wald space, trees are close if they induce similar distributions on genetic sequence data. As a point set, wald space contains the previously developed Billera-Holmes-Vogtmann (BHV) tree space; it also contains disconnected forests, like the edge-product (EP) space but without certain singularities of the EP space. We investigate two related geometries on wald space. The first is the geometry of the Fisher information metric of character distributions induced by the two-state symmetric Markov substitution process on each tree. Infinitesimally, the metric is proportional to the Kullback-Leibler divergence, or equivalently, as we show, any to f -divergence. The second geometry is obtained analogously but using a related continuous-valued Gaussian process on each tree, and it can be viewed as the trace metric of the affine-invariant metric for covariance matrices. We derive a gradient descent algorithm to project from the ambient space of covariance matrices to wald space. For both geometries we derive computational methods to compute geodesics in polynomial time and show numerically that the two information geometries (discrete and continuous) are very similar. In particular geodesics are approximated extrinsically. Comparison with the BHV geometry shows that our canonical and biologically motivated space is substantially different.
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Submitted 17 September, 2020; v1 submitted 29 March, 2020;
originally announced March 2020.