The shape of worm behavior

"Topological data analysis of C. elegans locomotion and behavior" by Ashleigh Thomas, Kathleen Bates, Alex Elchesen, Iryna Hartsock, Hang Lu, and Peter Bubenik.

[preprint, more details]

Given a video of a worm moving around its environment, we can look at, say, 20 consecutive frames of the video and record the worm's posture for each frame. This sequence of 20 postures is a "movement" of length 20. A collection of all the movements of length 20 from a ~13 second video of a worm are shown at left. We analyze the shape of this "movement space" to compare worm behaviors across various biological experiments.

More details ...

Topological data analysis of cell patterning data

with Peter Bubenik, Daniel Cruz, Elena Dimitrova, Alex Elchesen, Iryna Hartsock, Melissa Kemp, Eunbi Park, and Jack Toppen.

Primary decomposition distance for (multi)persistence modules

with Ezra Miller.

[thesis ch. 4]

Multirank: an invariant for statistical multiparameter persistent homology

[slides, poster, thesis ch. 3]

Multiparameter persistent homology for morphology of fly wings

with Ezra Miller and Surabhi Beriwal.

[thesis ch. 5]

Active sound localization in a symmetric environment

Jordan Brindza, Ashleigh Thomas, Spencer Lee, William McDermid, Yizheng He, and Daniel D. Lee.

International Journal of Advanced Robotic Systems (2013).

[pdf of paper, publisher link]

Humanoid robots can fall down, get pushed over or in a new direction, or lose track of where they are. If they do that in an environment is that has rotational symmetry -- like some buildings, hallways, or rooms; or places that have very few landmarks -- they can get "turned around" and fail to identify which direction they were facing before being disrupted. We propose a method for using teams of robots to collectively break environmental rotational symmetry so robots can re-localize correctly after disruption.

A room is rotationally symmetric if you can stand in the middle of the room and not be able to tell the difference between what you see when looking in two different directions. You might have experienced this when coming out of a room in a building you've never visited before; you come out of the room and don't remember which end of the hallway you walked in from. Both directions look the same and to leave the building you need to either find more clues (was there a water fountain near where you walked in?) or just pick a direction, try to exit that direction, and either find your way out of find out the other direction was the correct one.

The method we propose for solving this problem is essentially to bring a friend with you to your meeting. If, when you enter the building, your friend waits at the end of the hallway from which you entered, then when you come out of the room after your meeting, your friend can call your name and point you towards this door. Your friend is breaking the symmetry of the hallway and communicating and enough information so that you can easily figure out which direction is "out."

Video encoding

  • Internship at Immedia Semiconductor

  • Independently created data visualizer for data exploration and debugging.

  • Developed novel video encoding algorithms in collaboration with team lead and integrated them into a large, existing code base. Written in C++.