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⬐ anthony_bak

Hey. That's me. On hackernews :)

Happy to answer questions here regarding TDA but am no longer with Ayasdi so won't comment on company specific stuff.

The material in the video is dated but still relevant - I now have a better understanding of how to use "Shape" to improve Machine Learning models in an operational setting.

⬐ gavazzy

Any new talks, videos, or papers to recommend?

⬐ anthony_bak

Sure. Gunnar's "Topology and Data" paper (already linked to by another poster) is the first place to go for an overview of TDA (although it's getting dated). A more updated version (but behind paywall) is "Topological pattern recognition for point cloud data" ( http://dx.doi.org/10.1017/S0962492914000051 )

Robert Ghrist has another take on TDA ( https://www.math.upenn.edu/~ghrist/preprints.html ) that is more "engineering" focused and also uses a different mathematical tool set than the above (eg. Sheaves/Co-Sheaves). I particularly like the sensor coverage results.

Rob Ghrist and John Harer ( http://fds.duke.edu/db/aas/math/faculty/john.harer/publicati... )both have textbooks available if you want to get into the fundamentals in the field.

Jose Perea has some nice results using ideas from TDA in a variety of contexts. eg texture classification ( https://www.math.msu.edu/user_content/docs/KleinBottleTextur... ) and signal processing ( https://www.math.msu.edu/user_content/docs/Sw1Pes_Theory2015... )

Here's a talk I gave at ICERM last summer using persistent homology as a feature generating method for drug discovery:

https://icerm.brown.edu/video_archive/#/play/726

(slides available for download if you poke around on the icerm web site).

This is my "part two" of the video linked to in the parent article:

https://www.youtube.com/watch?v=3Z73Wd2T1xE

⬐ fitzwatermellow

Thanks for the updated list, Anthony!

On the practical side, what packages are you guys using? I'm familiar with JavaPlex for Matlab:

http://appliedtopology.github.io/javaplex/

⬐ anthony_bak

For Mapper consider using PythonMapper by Daniel Müllner ( http://danifold.net/mapper/ ). The UI is touchy - I use it mostly via scripts only. Mapper is pretty simple to implement (just a series of well understood pieces - the magic is in the interpretation/understanding what you've done). As an example consider the kepler-mapper project ( https://github.com/MLWave/kepler-mapper ). More lines of code are used for calling out to the d3 visualization than implementing the core mapper algorithm.

For my persistent homology calculations I always use Dionysus ( http://www.mrzv.org/software/dionysus/ ). Rumor has it a much improved parallelized version will be released soon.

⬐ irickt

Papers are available on Ayasdi's site: http://www.ayasdi.com/approach/data-scientist/

⬐ lsprack

There's also a very nice open-source R implementation of some of the TDA mapper functionality that I played with a while back:

https://github.com/paultpearson/TDAmapper/

⬐ fitzwatermellow

Interesting background on Ayasdi (literally, “to seek,” in Cherokee, perhaps sparking the newest trend in startup names deriving from indigenous languages) and its DARPA roots:

http://bits.blogs.nytimes.com/2013/01/16/ayasdi-a-big-data-s...

And a link to founder and Stanford Math Prof. Gunnar Carlsson's seminal AMS paper on "Topology and Data":

http://www.ams.org/journals/bull/2009-46-02/S0273-0979-09-01...