10,334 research outputs found
Approximating Local Homology from Samples
Recently, multi-scale notions of local homology (a variant of persistent
homology) have been used to study the local structure of spaces around a given
point from a point cloud sample. Current reconstruction guarantees rely on
constructing embedded complexes which become difficult in high dimensions. We
show that the persistence diagrams used for estimating local homology, can be
approximated using families of Vietoris-Rips complexes, whose simple
constructions are robust in any dimension. To the best of our knowledge, our
results, for the first time, make applications based on local homology, such as
stratification learning, feasible in high dimensions.Comment: 23 pages, 14 figure
Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening
This work introduces a number of algebraic topology approaches, such as
multicomponent persistent homology, multi-level persistent homology and
electrostatic persistence for the representation, characterization, and
description of small molecules and biomolecular complexes. Multicomponent
persistent homology retains critical chemical and biological information during
the topological simplification of biomolecular geometric complexity.
Multi-level persistent homology enables a tailored topological description of
inter- and/or intra-molecular interactions of interest. Electrostatic
persistence incorporates partial charge information into topological
invariants. These topological methods are paired with Wasserstein distance to
characterize similarities between molecules and are further integrated with a
variety of machine learning algorithms, including k-nearest neighbors, ensemble
of trees, and deep convolutional neural networks, to manifest their descriptive
and predictive powers for chemical and biological problems. Extensive numerical
experiments involving more than 4,000 protein-ligand complexes from the PDBBind
database and near 100,000 ligands and decoys in the DUD database are performed
to test respectively the scoring power and the virtual screening power of the
proposed topological approaches. It is demonstrated that the present approaches
outperform the modern machine learning based methods in protein-ligand binding
affinity predictions and ligand-decoy discrimination
Multidimensional persistent homology is stable
Multidimensional persistence studies topological features of shapes by
analyzing the lower level sets of vector-valued functions. The rank invariant
completely determines the multidimensional analogue of persistent homology
groups. We prove that multidimensional rank invariants are stable with respect
to function perturbations. More precisely, we construct a distance between rank
invariants such that small changes of the function imply only small changes of
the rank invariant. This result can be obtained by assuming the function to be
just continuous. Multidimensional stability opens the way to a stable shape
comparison methodology based on multidimensional persistence.Comment: 14 pages, 3 figure
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