September 23, 2019

Summer of Productivity at OREL

An update on what we did with our Summer at the Orthogonal Research and Education Laboratory. We hosted a study group based on an emerging collaboration to understand how Braitenberg Vehicles can be used as a model to study neural development [1].

We hosted one Google Summer of Code student (Stefan Dvoretskii), and mentored another GSoC student through the OpenWorm Foundation (Vinay Varma). Thanks go to INCF as well for their support. We also hosted the activities of several mentees (Ziyi Gong, Jesse Parent, Ankit Gupta, and Hrishikesh Kulkarni) which is topically diverse and will be featured in future blog posts [2]. Below are three tweets from the OREL Twitter account that show highlights from some of this work (congrats again to Stefan Dvoretskii, Vinay Varma, Jesse Parent, and Hrishikesh Kulkarni for their completed milestones).

Click on image for higher resolution. Click here for links.

 Click on image for higher resolution. Click here for links.

Click on image for higher resolution. Click here for links.

Click on image for higher resolution. Click here for links.

[1] our project repository is located here.

[1] two additional students were hosted through the DevoWorm group: Ujjwal Singh and Asmit Singh, who worked on a project called Digital Bacillaria.

September 2, 2019

Introducing: DevoWormML

This has been cross-posted to The Node blog.

I am pleased to announce a new collaborative interest initiative called DevoWormML, based on work being done in the DevoWorm group. DevoWormML will meet on a weekly basis, and explore the application of machine learning and artificial intelligence to problems in developmental biology. These applications can be geared towards the analysis of imaging data, gaining a better understanding of thought experiments, or anything else relevant to the community.

While "ML" stands for machine learning, participation can include various types of intelligent systems approaches. Our goal is to stimulate interest in new techniques, discover new research domains, and establish new collaborations. Guests are welcome to attend, so if you know an interested colleague, feel free to direct them our way.

Meetings will be Wednesdays at 1pm UTC on Google Meet. Discussions will also take place on the #devowormml channel of OpenWorm Slack (request an invitation). We will discuss organizational details at our first meeting on September 4. If you cannot make this time but are still interested in participating, please contact me. Hope to see you there!

May 31, 2019

Summer of Working Groups

I am happy to announce that this Summer I will be advising/mentoring two research groups of Google Summer of Code (GSoC) students and applicants. Thanks to INCF for sponsoring our applications and applicants again this year. The first group (DevoWorm), based in the OpenWorm Foundation, is interested in image segmentation and Machine Learning. GSoC applicants Asmit Singh and Ujjwal Singh (currently attending IIT Delhi) are working on extracting quantitative data to construct a digital model for organisms in the diatom genus Bacillaria. The GSoC student (Vinay Varma, currently attending Amrita Vishwa Vidyapeetham University) is working on developing a method for Semantic Segmentation based on microscopy of the embryogenetic process, focusing on the biology of Caenorhabditis elegans.

The other group is based in the Orthogonal Research and Education Laboratory, and is focused on creating a methodology for developmental Braitenberg Vehicles. This involves simulating the formation of a brain (neurons and connectome) in a simple body that continuously interacts with its environment. The GSoC student in this group (Stefan Dvoretskii) is developing such a model using Genetic Algorithms and the open-source SimBrain platform. The GSoC applicants (Ziyi Gong, Jesse Parent, and Ankit Gupta) are working on a variety of unique approaches that will aid in our
understanding of this complex system. These alternative approaches range from biologically-inspired (Ziyi) to a cybernetic architecture based on the Every Good Regulator Theorem (Jesse).

The hybrid education/research working group is something I started with last year's Orthogonal Lab GSoC group. There is a good chance that this Summer's discussions and work periods will produce awesome, cutting-edge science. Follow us on Github (DW group, BV group) and YouTube (DW group, BV group) for more!