Orthogonal Lab Annual Report for 2024

Another year of the Orthogonal Research and Education Laboratory (2024). We have had a great year! I posted a summary video on YouTube that covers activities related to Saturday Morning NeuroSim, our Open Science/Open-source interest group, the Computational Developmental Systems interest group, the Representational Brains and Phenotypes interest group, and the Cybernetics interest group. I also discuss our educational initiatives and conference/publication activities.

The seminal activity of the lab is the Saturday Morning NeuroSim meeting, which happens on Saturdays at 10AM ET (North America). This is based on the Saturday Morning Physics educational events, which originated in Germany and are popular in Physics departments and US National Labs. We had 45 meetings in 2024, and covered all manner of intersections between computational, neuroscience, social science, molecular biology, and complexity theory. 

The Computational Developmental Systems interest group can best be described as Neuro-Devo-Psych. This combines our work on Computational Critical Periods and Computational Developmental Biology (DevoWorm-associated). This also intersects with work in the Representational Brains and Phenotypes interest group and the Developmental Neurosimulation approach. 

Our Open Science/Open-source interest group sponsors Google Summer of Code participation in addition to assorted activities in the research practice and open-source project management spheres. The rejuvenation of our Cybernetics interest group features a reading group and other academic activities. 

Google Summer of Code 2024

 

Welcome to the new Google Summer of Code scholars for 2024! INCF is sponsoring four students for which I (Bradly Alicea) am acting as mentor: two students for the DevoWorm group (via the OpenWorm Foundation community) and two students for the Orthogonal Research and Education Laboratory. 

D-GNNs (sponsored by the DevoWorm group)

Congratulations to Pakhi Banchalia and Mehul Arora for being accepted to work on the Developmental Graph Neural Networks (D-GNNs) project. Pakhi will be working on incorporating Neural Developmental Programs (NDPs) into GNN models. Mehul will be working on hypergraph techniques for developmental lineage trees and embryogenesis [1]. Himanshu Chougule (Google Summer of Code scholar) is a co-mentor for this project.

Virtual Reality for Research and Open-source Sustainability (sponsored by the Orthogonal Research and Education Lab)

Congratulations to Sarrah Bastawala for being accepted to work on the Open-source Sustainability project [2]. Sarrah is incorporating Large Language Models (LLMs) into the collection of agent-based approaches for this project. Jesse Parent is a co-mentor for this project.

We also have two Open-source Development scholars for Summer 2024: Adama Koita and Shubham Soni. They will be participating in the Orthogonal Lab's open-source weekly meetings in addition to projects based around Virtual Reality and Open-source Sustainability, respectively. 

Google Summer of Code 2023

Welcome to the new Google Summer of Code scholars for 2023! INCF is sponsoring four students for which I (Bradly Alicea) am acting as mentor: two students for the DevoWorm group (via the OpenWorm Foundation community) and two students for the Orthogonal Research and Education Laboratory. These four students are pursuing three projects.

D-GNNs and DevoLearn (sponsored by the DevoWorm group)

Congratulations to Himanshu Chougule and Sushmanth Reddy Mereddy for being accepted to work on the Developmental Graph Neural Networks (D-GNNs) project. Sushmanth has been contributing to the DevoLearn platform for quite some time and will spend this summer working on improving the image segmentation to GNN embedding pipeline. Himanshu was a part of last Summer's GSoC cohort in the Orthogonal Research and Education Laboratory, working on the Open-source Sustainability project. His work resulted in developing Agent-based Model-Reinforcement Learning hybrid models. This year, he will be working on building Topological Data Analytic capabilities into the D-GNN pipeline. 

Mayukh Deb and Jiahang Li are co-mentors for this project.

Virtual Reality for Research and Open-source Sustainability (sponsored by the Orthogonal Research and Education Lab)

Congratulations to Vrushali Nandurkar and R.V. Rajagopalan for being accepted to work on the projects Virtual Reality for Research and Open-source Sustainability, respectively. Vrushali is enthusiastic about working on creating open-source virtual world assets for scientific research and educational initiatives. R.V. will be working on a continuation of the Open-source Sustainability project, helping to augment the existing models and web interface.

Jesse Parent is a co-mentor for both projects, while Brian McCorkle is a co-mentor for the Open-source Sustainability project. 

OAWeek 2022: Managing Virtual and Hybrid Meetings

Welcome to International Open Access Week, 2022 edition! Last year, we discussed the vision of a distributed research organization. This year, we will explore this theme a bit further. One aspect of distributed organizations is the need to work both synchronously and asynchronously. This brings the real-world experience closer to the collaborator without the travel, carbon emissions, or expense of being at a centralized institute. As our collaborators live in many time zones and have different lifestyles, it is important to capture their full attention in different ways. 

One way this is done is through the live attendance and replay of group meetings. The Orthogonal Research and Education Lab (OREL) offers a number of regular topical meetings, in addition to a general meeting on Saturdays, that engages collaborators from all over the world using a number of different pedagogical and technological techniques. 

An example of a virtual distributed meeting with collaborators dropping in from different parts of the globe.

An open meeting has a number of moving parts that need to be thoughtfully considered to ensure success. The first of these is choosing a meeting platform. OREL has found success with Jitsi, as it is lightweight and free to use (open source). While Jitsi can be used as a service, installing it on your own server opens up its many customizable features. Jitsi even works with Virtual Reality, with interactions between the 2-D meeting world and immersive 3-D being available in the Wolvic browser and Meta Quest casting option.

Sample scenes from screensharing within Meta Quest and the casting option.

Secondly, programming the meeting is a non-trivial detail that can make the most of your time. For our Saturday Morning NeuroSim meetings, we have settled on the following format: updates, light features, discussion, open collaboration, and finally, papers of the week. Agenda-setting should be flexible with respect to your attendee's availability. Not everyone can make an entire meeting, so allowing them to "drop into" participation is encouraged. 

Notetaking and live feeds are also good for augmenting our meetings. The OREL Lab Manager (Jesse Parent) We use notetaking tools such as Obsidian and Notion with allied feeds (Slack and Discord) for coordinating the various fragments of ideas and themes that emerge during meeting time. Feed technology is also good for sharing papers, and the vision of a stream feed is key to realizing the multimedia aspect of real-time meeting immersion, even when attendees are asynchronous.     

Different types of notetaking and stream feeding within a meeting (from the Cognition Futures Reading Group).

As a tool for participatory engagement, this can be done in a number of different ways. Lead by Daniel Ari Friedman and Bleu Knight, the Active Inference Institute has taken the route of invited livestreams and summary podcasts. These materials introduce collaborators to difficult academic concepts while making them more accessible. While YouTube has options for live streaming, it is not always the best option. I use OBS Studio (free and open source) to compose a desktop recording and edit before making it public. 

Recorded meetings are also good for coding demos, particularly when they do not go as planned. One can either prepare a recording in advance to include in the meeting recording or strip the demo down to a minimal approach using a CoLab notebook. This reduces the friction of failed screenshares and execution errors, while also easing the burden of performing in front of a group.

Coding demos from a recent Saturday Morning NeuroSim meeting.

But completely virtual experiences are not the only option for bringing people together from around the world. OREL has been experimenting with hybrid meetings. This type of meeting brings the ethos of virtual meetings to more traditional in-person meetings. This enables more inclusive participation from distant geographical points. Last Spring, we experimented with our own virtual meeting experience at the New York Celebration of Women in Computing (NYCWiC), hosted live at Fort William Henry, NY. The hybrid session "Frontiers in Data Privacy and Tech Ethics" featured a buffet of topics on AI and technology ethics. Soem of the participants were live, while others were virtual (recorded or located in different parts of the globe). For this type of meeting, experimenting with ways to optimize live/virtual synchronization and media capture quality are essential. We plan to experiment with this more in the near future. 

Virtual (top) and in-person (bottom) components of the session.

Opening Access, Virtual, Distributed Lab Edition

Welcome to Open Access Week 2021! This year's theme is building structural equity. In the Orthogonal Research and Education Lab and the DevoWorm group, this has been an ongoing priority: from the recruitment of scholars to the production and engagement with research. This week we will highlight some of the ways we open up the research process, and how this is the only way the principles of open access (Figure 1) can be fully realized.

Figure 1. From the short film "What is Open Access" (PhD Comics, 2012).

One thing that enables Open Access is an open collaboration structure. Both Orthogonal Lab and DevoWorm are based on a virtual, distributed framework. People can join in and collaborate as long as they have an internet connection and the initiative to work on a related problem. The communication structure is likewise flexible: you can join in our weekly meetings, participate in our Slack channels or Github teams, or join in on a collaborative doc. We also sponsor or participate in various open educational initiatives. Two of these are Google Summer of Code and Neuromatch Academy.

Figure 2. The global reach (physical and virtual) of the Orthogonal Lab.

This brings together participants from multiple continents and research specialties, while also enabling students, professional academics, and lifelong learners to collaborate in ways large and small. We participate in the academic community through virtual and hybrid conferences, peer-reviewed publication venues, book chapters, and preprints. Self-publication platforms (blogging platforms) and social media are also good for advancing fledgling ideas and chronicling progress. Along with an emphasis on open code and data, these venues are utilized to maximize access and reusability.

More recently, we have been focusing on the role of professional development in enabling the virtual, distributed research process. As many of our contributors aspire to further their research careers through participation, we have become more active in cultivating an individual's research agenda. Between active recruitment of participants and enabling them to take ownership of a research topic, we can contribute to greater equity and diversity in the research enterprise.

            

Finally, our Open Access agenda includes an interdisciplinary focus, as both Orthogonal Lab and DevoWorm engage individuals from a variety of different backgrounds. There is an intentionality towards enabling interdisciplinary skillsets, as well as a focus on providing individuals space to pursue these connections between traditional disciplines. For more information on how these components work to form a virtual, distributed lab, see our preprint "Building a Distributed Virtual Laboratory Adjacent to Academia". 

While there are still many administrative and functional barriers to pursuing this as a full-fledged research organization on par with a large corporation or University, this is a unique and emergent way of opening access. If you would like to participate, please contact us. Additionally, be sure to check out the #OAWeek hashtag for this blog (Synthetic Daisies), as we have content going back to 2016 on a variety of topics. 

OREL and DevoWorm Review of 2020

As part of our preparations for the New Year, I prepared a set of presentations for my two research groups: Representational Brains and Phenotypes and DevoWorm. I have posted the slides below, and if you see something interesting that you would like to participate in, please contact me. If you are interested in learning more, please join the Orthogonal Research and Education Lab or OpenWorm Slack. You can also attend our weekly meetings: 3pm UTC Saturdays for Saturday Morning NeuroSim (more info), or 3pm UTC Mondays for DevoWorm (more info).

Saturday Morning NeuroSim presentation, with a focus on the Representational Brains and Phenotypes group (click slides to enlarge).

 

DevoWorm weekly meeting presentation, with a focus on the DevoWorm group  (click slides to enlarge).

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.

Contrast Between Biological and Artificial Neural Networks (BNNs vs ANNs). Download slides from Figshare. Video on YouTube. Click to enlarge.

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.

Approaching Artificial Intelligence as an Embodied Developmental Process. Download slides from Figshare. Video on YouTube. Click to enlarge.

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.

The Psychophysics of Non-neuronal Cognition. Download slides from Figshare. Video on YouTube. Click to enlarge.

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.

Trajectories in Cognition Studies - a focus on embodiment and future frontiers. Click to enlarge.

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.

Overcompensation of lens-accommodation in case of Convergence Insufficiency- A theoretical model. Click to enlarge.

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!

Welcome, Summer of Coders (2020)!

The Google Summer of Code selections for 2020 have been made! Congratulations to Ujjwal Singh and Mayukh Deb, who will be joining the OpenWorm Foundation and the DevoWorm group for a summer of community engagement and code. Ujjwal's project is called OpenDevoCell Integration, and here is the description:

This project will focus on improving the data science and machine learning infrastructure of the DevoWorm group. The work will focus on an extension of the Summer of Code projects completed in 2017 and 2019. The first two aims are to improve upon the OpenDevoCell web interface and to improve segmentation techniques overall. While the OpenDevoCell interface has been implemented as a Heroku app, we would like to develop a dashboard for interpretation as well as tighter integration with DevoZoo's collection of open-source microscopy data. The third aim is to deploy the code package as a unified Python library, which would be done in concert with the improvement of segmentation techniques.The priority for this Summer is to improve the web interface both in terms of interactivity and functionality. Ideally, we would like to provide users with multiple options for analysis. This includes the ability to incorporate new forms of analysis as well as algorithms for new types of data. Currently, our web app is optimized for microscopy images acquired using the SPIM technique. However, we would also like to segment microscopy images acquired using a wide range of technologies. Feeding into this is the ability to segment and obtain features for the data in our DevoZoo. The ability to extract quantitative data from these movie images is key to conducting the comparative and time-series analysis. The development of a dashboard would ideally enable users to employ various machine learning and simulation techniques in one place.These improvements are meant to increase participation in our open science initiative and make sophisticated analytical techniques more accessible to students and potential collaborators alike. 

Mayukh's project is called Pre-trained Models for Developmental Neuroscience, and is based on previous work done in the group during the DevoWormML course [1]. This project is described thusly:

This project will center around building a pre-trained model for shapes and processes related to Developmental Biology and Neurobiology and extracted from image data. Our organization's Machine Learning interest group (DevoWormML) has published a blog post [1] on the advantages and need for pre-trained models in this area. In short, biological development is characterized by characteristic shapes, movements, changes in shape, and temporal processes that define important features. Pre-trained models are used in NLP and Deep Learning for the domains of sequence discovery in language processing (GPT-2) and bounding box methods for segmenting complex images (DeepLabv3). Models specialized for biology, however, do not exist. A suitable pre-trained model would greatly reduce the need for input data without sacrificing the ability to generalize to different contexts.Our main interest is in extracting spatiotemporal features from image data. We will focus on microscopy data such as that found in the DevoZoo or from more specialized sources [2]. For a typical pre-trained model, the network is pre-trained with non-random weights that approximate the generalized versions of the features we would like to discover. However, we are also interested in a semantic component, particularly the ability to incorporate elements such as meaning assigned to static knowledge (semantics) and multiple meanings for a single feature (polysemy). This will enable relational modeling and the mapping of segmented image data to lineage trees and taxonomies. This will enable relational modeling and the mapping of segmented image data to lineage trees and taxonomies. Our model, tentatively called DevLearningv1, should be applicable to a wide range of neural network and deep learning techniques.

Thanks to INCF for sponsoring our activities once again this year. Thanks also go to Vinay Varma, who will be providing support on all things mentorship this summer. Vinay was a GSoC student last summer, and will be sharing his wisdom with this year's students. I would also like to invite all those who applied for these projects to contribute to the Organization in some other way. Often, interaction with the community now can lead to additional opportunities down the road. 

As for the Orthogonal Research and Education Lab project (Contextual Neurodevelopmental Dynamics), we unfortunately did not get any slots this year. Thanks to Ankit Gupta and Jesse Parent for their excellent proposals. But I would like to continue pursuing the initiative as an open-source effort, hopefully leading to other avenues for development and funding. The same community interaction advice given for OpenWorm applies to Orthogonal Lab as well. 

We are going to be developing in the Meta-Brain repository on Github. Be sure to check out our Saturday Morning NeuroSim meetings for more information on this project (join our mailing list!). And register for the Neuromatch Summer School if you have not already, as it will be quite relevant to what we will be doing.

A sample of Saturday Morning NeuroSim (with a recap of the ICLR conference). Click to enlarge.

UPDATE (5/5): One of our regular meeting attendees (Devansh Batra) has also received a Google Summer of Code position with the OpenCV organization. Congrats!

NOTES:

[1] Alicea, B., Gordon, R., Kohrmann, A., Parent, J., and Varma, V. (2019). Pre-trained Machine Learning Models for Developmental Biology. The Node blog, October 29.