Recent Developments in Persistent Homology

Jeremy Kun
University of Illinois at Chicago Department of Mathematics, Statistics, and Computer Science

27-4-2013

Big Picture

Compute qualitative information about high-dimensional data,

Big Picture Compute qualitative information about high-dimensional data. for the purpose of creating more accurate models. .

The Story of Miller-Reaven Why is qualitative information important? .

In short Assume the data is sampled from a manifold with noise. “A barcode shape descriptor for curve point cloud data” About 50-60 papers published since then. and robustly compute the underlying topological features in all dimensions and at all resolutions.History First paper 2004: Carlsson et al. .

Vietoris-Rips. .. Witness.) depending on some parameter ε.. .Outline Pick a functorial method to turn data points into a simplicial complex (Cech.

Outline Pick a functorial method to turn data points into a simplicial complex (Cech..) depending on some parameter ε. . from which we pick a finite sub-complex.. Implicitly this defines a filtration of complexes {Xε }. . Vietoris-Rips. Witness.

. Vietoris-Rips. Witness. Implicitly this defines a filtration of complexes {Xε }.Outline Pick a functorial method to turn data points into a simplicial complex (Cech. from which we pick a finite sub-complex. Compute homology of the resulting complex (decompose into “barcodes”). .) depending on some parameter ε...

Persistence Complex .

Persistence Barcodes .

Image Analysis .

Image Analysis What persistent homology provided: .

Image Analysis Additional analysis: Space of patches is densely concentrated around a two-dimensional manifold in 8-dimensional space. 50% of the data occupies 9% of the total volume of the data. Persistent homology computations suggest this manifold is the Klein bottle. .

Klein Bottle Model .

Texture Classification Using the Klein Bottle Model Perea & Carlsson (2012). “On the local behavior of spaces of natural images” . Zomorodian (2008). de Silva. Ishkhanov. “A Klein-Bottle-Based Dictionary for Texture Representation” Carlsson.

Tumor Detection .

Tumor Detection Using 3d radiological imaging. higher-density areas show up as clusters of points. .

higher-density areas show up as clusters of points.Tumor Detection Using 3d radiological imaging. . Blood vessels show up as “tubes” Tumors show up as “balls” We can differentiate them with persistent homology.

(2011) “Topology based data analysis identifies a subgroup of breast cancers with a unique mutational profile and excellent survival” Adcock. et al. Carlsson (2012). et al (2010). “Applications of computational homology to the analysis of treatment response in breast cancer patients” Nicolau. Rubin. “Classification of Hepatic Lesions using the Matching Metric” .Tumor Detection Some papers in this area: DeWoskin.

molecular dynamics. et al (2009). et al (2008). “Topological methods for exploring low-density states in biomolecular folding pathways” Bowman. “Persistent Topology and Metastable State in Conformational Dynamics” Yao. Chang. et al (2013). “Topological analysis of population activity in visual cortex” .Biological/Chemical Applications Protein folding. “Structural insight into RNA Hairpin Folding Intermediates” Singh. brain scan analysis. et al (2008).

clustering. “Cloud detection and characterization using topological data analysis” Navigation: Ghrist. and computer hardware. et al (2012). “A New Text Representation for Natural Language Processing” Climatology: Guiang. “Topological landmark-based navigation and mapping” Others include signal processing. Levine (2012).Other Applications Sensor Networks: de Silva. Ghrist (2005). “Coverage in sensor networks via persistent homology” NLP: Zhu (2013). .

com . http://jeremykun.End.

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