17 research outputs found
Metrics for generalized persistence modules
We consider the question of defining interleaving metrics on generalized
persistence modules over arbitrary preordered sets. Our constructions are
functorial, which implies a form of stability for these metrics. We describe a
large class of examples, inverse-image persistence modules, which occur
whenever a topological space is mapped to a metric space. Several standard
theories of persistence and their stability can be described in this framework.
This includes the classical case of sublevelset persistent homology. We
introduce a distinction between `soft' and `hard' stability theorems. While our
treatment is direct and elementary, the approach can be explained abstractly in
terms of monoidal functors.Comment: Final version; no changes from previous version. Published online Oct
2014 in Foundations of Computational Mathematics. Print version to appea
Categorification of persistent homology
We redevelop persistent homology (topological persistence) from a categorical
point of view. The main objects of study are diagrams, indexed by the poset of
real numbers, in some target category. The set of such diagrams has an
interleaving distance, which we show generalizes the previously-studied
bottleneck distance. To illustrate the utility of this approach, we greatly
generalize previous stability results for persistence, extended persistence,
and kernel, image and cokernel persistence. We give a natural construction of a
category of interleavings of these diagrams, and show that if the target
category is abelian, so is this category of interleavings.Comment: 27 pages, v3: minor changes, to appear in Discrete & Computational
Geometr
TopologyNet: Topology based deep convolutional neural networks for biomolecular property predictions
Although deep learning approaches have had tremendous success in image, video
and audio processing, computer vision, and speech recognition, their
applications to three-dimensional (3D) biomolecular structural data sets have
been hindered by the entangled geometric complexity and biological complexity.
We introduce topology, i.e., element specific persistent homology (ESPH), to
untangle geometric complexity and biological complexity. ESPH represents 3D
complex geometry by one-dimensional (1D) topological invariants and retains
crucial biological information via a multichannel image representation. It is
able to reveal hidden structure-function relationships in biomolecules. We
further integrate ESPH and convolutional neural networks to construct a
multichannel topological neural network (TopologyNet) for the predictions of
protein-ligand binding affinities and protein stability changes upon mutation.
To overcome the limitations to deep learning arising from small and noisy
training sets, we present a multitask topological convolutional neural network
(MT-TCNN). We demonstrate that the present TopologyNet architectures outperform
other state-of-the-art methods in the predictions of protein-ligand binding
affinities, globular protein mutation impacts, and membrane protein mutation
impacts.Comment: 20 pages, 8 figures, 5 table
The Medusa of Spatial Sorting: Topological Construction
We consider the simultaneous movement of finitely many colored points in
space, calling it a spatial sorting process. The name suggests a purpose that
drives the collection to a configuration of increased or decreased order.
Mapping such a process to a subset of space-time, we use persistent homology
measurements of the time function to characterize the process topologically
Alexander Duality for Functions: the Persistent Behavior of Land and Water and Shore
This note contributes to the point calculus of persistent homology by
extending Alexander duality to real-valued functions. Given a perfect Morse
function and a decomposition such
that M = \U \cap V is an -manifold, we prove elementary relationships
between the persistence diagrams of restricted to , to , and to .Comment: Keywords: Algebraic topology, homology, Alexander duality,
Mayer-Vietoris sequences, persistent homology, point calculu
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
Harmonic Persistent Homology
We introduce harmonic persistent homology spaces for filtrations of finite
simplicial complexes. As a result we can associate concrete subspaces of cycles
to each bar of the barcode of the filtration. We prove stability of the
harmonic persistent homology subspaces under small perturbations of functions
defining them. We relate the notion of "essential simplices" introduced in an
earlier work to identify simplices which play a significant role in the birth
of a bar, with that of harmonic persistent homology. We prove that the harmonic
representatives of simple bars maximizes the "relative essential content"
amongst all representatives of the bar, where the relative essential content is
the weight a particular cycle puts on the set of essential simplices.Comment: 35 pages, 5 figures. Comments welcom