November 18, 2020

Presentations at Neuromatch (NM)3


Neuromatch 3 (NM3) happened a few weeks ago in virtual space, and it was great! There were hundreds of presentations over five days (October 26-30), many of them already archived on YouTube. This version of Neuromatch took the place of Society for Neuroscience (SfN), which was cancelled due to COVID. In this sense, Neuromatch is proving itself to be an improvement on the legacy conference. Between my two research groups (Representational Brains and Phenotypes and DevoWorm), we had five presentations submitted to NM3. Let's go through them one by one.



This presentation was by Krishna Katyal and myself. Krishna is a regular contributor to the DevoWorm group. This presentation demonstrates several contrasts between Biological and Artificial Neural Networks, and how level of abstraction, network structure, and energetics all play a role in distinguishing the information-processing marvels known as biological brains.



Thinking more along the lines of biological development, the next presentation features work done in the Representational Brains and Phenotypes Group. Taking a developmental approach to the classic Braitenberg Vehicle, we demonstrate how embodied developmental principles can be used to shape and guide networks for learning. Topics such as developmental contingency and the difference between morphogenesis and learning during the development of an artificial nervous system were also discussed.



Are the advantages of cognitive information processing limited to organisms with a brain? This seems like a strange question, but can actually help us understand what a brain does and why it is important for coordinating the behavior of complex multicellular systems. In this presentation, which includes contributors to both the Representational Brains and Phenotypes and DevoWorm groups, we reconsider a model of Diatom movement as cognitive information processing. We also propose a series of potential scenarios in which this information processing occurs as well as Psychophysical-like measures to quantify these phenomena.



This abstract was submitted by Jesse Parent and Anson Lim, two regular contributors to the Orthogonal Research and Education Lab. Jesse is also a group leader and community manager in the lab. While they were not able to present during the scheduled time, they continue to work on this topic under the new and emerging Cognition Futures project.



The final talk was by Akshara Gopi (a regular contributor to the Orthogonal Research and Education Lab), along with myself and Ashwin Irungovel. This presentation was on convergence insufficiency in human vision, a topical specialty of Akshara and Ashwin. My contribution was to propose an agent-based model for this phenomenon. 

Check out all of the great talks at NM3, including one by Rishabh Chakrabarty (regular research contributor to the Orthogonal Lab) and his co-author called "Seeing through the Mind’s Eye: reconstruction of the visual stimuli using 3D Generative-Adversarial Modeling". This intriguingly titled talk features research that combines Neuroimaging data with Deep Learning.

If you are interested in these topics and want to be involved in this research, join us at our weekly research meetings (Saturday Morning NeuroSim and DevoWorm group), or watch them on YouTube! I also invite you to join the Orthogonal Research and Education Lab Slack or OpenWorm Slack (DevoWorm) for continued discussion. Hope to see everyone at Neuromatch 4!

October 20, 2020

ASAPBio Session on the "Past, Present, and Future of Preprints"

For Open Access Week 2020, Synthetic Daisies will feature an exciting panel discussion on preprints. On Monday (19th), I was part of a panel called "Past, Present, and Future of Preprints", hosted by ASAPBio. I live tweeted the event from the Orthogonal Research and Education Lab Twitter account. If you were not able to attend in person, the recording is on YouTube! The session started with a short introduction from each of our participants: Antonis Rokas, Soumya Swaminathan, Richard Sever, Ross Mounce, and Anjana Badrinarayan.


Yamini Ravichandran and Marco Fumasoni started us off with a short introductory presentation, followed by an introduction by each of our panelists. This part of the session culminated with Marco posing an initial question to the panel.

It turns out that there are many contributing factors to preprint adoption. Some of them involve legacy patterns from manuscript submissions and publications. But preprints also democratizes access to both the production and consumption of scientific literature. It turns out that cultural traditions (within fields and countries), researcher agency, and community incentives are also quite important.

The theme of research culture came up time and time again. But research culture is not only a motivating factor; pro-preprint behaviors can lead to other virtuous practices. For example, Ross Mounce suggests that preprints can encourage a culture of versioning, where different versions of a paper are viewed as important steps in the research process rather than simply being erratum.


There was also a discussion of the role traditional journals play in the research dissemination process. One future direction of preprint culture is to decouple papers from journals. Towards the end of our session, we heard a choice quote from Antonis Rokas and the Rokas Lab.

This combines nicely with observations earlier in the session regarding citation metrics: with the movement towards iteratively-developed preprints with multiple supporting components (open data sets, supplemental figures and notes), there will be a need to distinguish article quality from journal quality. Altmetrics are one path forward, but a more robust system is needed. 

Thanks to everyone for participating! Thanks also go to Sarah Stryeck, Jessica Polka, and of course Iratxe Puebla for being a great community manager! Happy Open Access Week



UPDATE (11/3): A recording of the session is now on YouTube!

October 14, 2020

Hacktoberfest now live!

Welcome to Hacktoberfest! Check out our DevoLearn repositories and our DevoLearn AI resources. Contribute from now until the end of October. Make five commits during the course of October, and Github [1] has something for you!

Want to participate in Hacktoberfest @ DevoWorm? Look at our issue board for Group Meetings, or look at the contribution guidelines for DevoLearn and contribute a Data Science demo

Select issues on the Group Meetings issue board (DevoWorm) and the Community Board for DevoLearn are also marked with the "Hacktoberfest" label. Once you decide where to contribute, issue a pull request or communicate your interest as a comment in the issue you want to address!

Thanks to Mauyukh Deb and Ujjwal Singh for their administration efforts, and Github users AbtahaJainal09RaviKarriRudRajit1729Joel-Hansonshreyraj2002Malvi-Mkrishnakatyal, and jesparent for their commits so far!


[1] Github offers a T-shirt as incentive for contributing. Offer only applies to labeled repositories (most of the DevoLearn repositories are eligible).

October 8, 2020

Multidimensional Chess Convoluted to a Pretty Picture

At last Monday's DevoWorm Group meeting, I gave a short lecture on ways to interpret multidimensional data using PCA, tSNE, and UMAP.  Here are the slides (below) and the YouTube link. The focus here is on Developmental Molecular Biology, but are generally useful, particularly for comparing methods. Here are the slides with a bonus from Leland McInnes, one of the originators of the UMAP technique!

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September 30, 2020

OpenWorm Annual Meeting -- DevoWorm Slides

Today we held the OpenWorm Annual Meeting, which is a time for the Board of Directors and Senior Contributors to meet and discuss the latest developments within the foundation (in this case, activities over the past 1.5 years). Overall, a very inspiring meeting! Here are the slides I presented on progress and the latest activities in the DevoWorm group. If anything looks interesting to you, and you would like to contribute, please let me know.



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