OpenWorm Annual Meeting 2024 (DevoWorm update)

 Here are the slides for the DevoWorm group's report to the OpenWorm Annual Meeting (2024). You can watch Bradly Alicea present the talk on YouTube.

Aside from all the great stuff going on in DevoWorm, there are two new tools being developed by Padraig Gleeson's team at University College London. First up is the Connectome Toolbox, which brings together multiple key datasets and visualization tools for C. elegans connectome analysis. The other is OpenWorm.ai, which uses a large language model (LLM) hosted on Huggingface to query information about C. elegans biology.

Here are some slides from the presentation. Click to enlarge. Thanks to Mehul Arora and Pakhi Banchalia for their Google Summer of Code efforts.

New Paper on Developmental Braitenberg Vehicles now live!

 

The special issue of Artificial Life on Embodied Intelligence is now live! Inside you will find our paper "Braitenberg Vehicles as Developmental Neurosimulation", which has lived on the arXiv since 2020. This paper lays out an approach to Developmental Neurosimulation, involving three adversarial approaches to the agent-based development of embodied brains and embodied cognition. Here is the abstract:

Connecting brain and behavior is a longstanding issue in the areas of behavioral science, artificial intelligence, and neurobiology. As is standard among models of artificial and biological neural networks, an analogue of the fully mature brain is presented as a blank slate. However, this does not consider the realities of biological development and developmental learning. Our purpose is to model the development of an artificial organism that exhibits complex behaviors. We introduce three alternate approaches to demonstrate how developmental embodied agents can be implemented. The resulting developmental Braitenberg vehicles (dBVs) will generate behaviors ranging from stimulus responses to group behavior that resembles collective motion. We will situate this work in the domain of artificial brain networks along with broader themes such as embodied cognition, feedback, and emergence. Our perspective is exemplified by three software instantiations that demonstrate how a BV-genetic algorithm hybrid model, a multisensory Hebbian learning model, and multi-agent approaches can be used to approach BV development. We introduce use cases such as optimized spatial cognition (vehicle-genetic algorithm hybrid model), hinges connecting behavioral and neural models (multisensory Hebbian learning model), and cumulative classification (multi-agent approaches). In conclusion, we consider future applications of the developmental neurosimulation approach.

There are many themes to follow up on in this paper. Just of few examples include:

* brain/body scaling in an embodied agent.

* the role of multisensory integration in the development of cognition.

* ways to classify shapes and motifs in the emergence of multi-agent collectives. 

* spatial cognition and transfer learning in developmental embodied systems.

Congratulations to Stefan Dvoretskii, Ziyi Gong, Ankit Gupta, Jesse Parent, and Bradly Alicea for their hard work.

MAIN and Neuromatch Conference Presentations

The Orthogonal Research and Education Lab is on the virtual move! We have been featured at two conferences this week. The first conference is MAIN (Montreal Artificial Intelligence-Neuroscience) conference, a hybrid conference that focused on cutting-edge research in Neuro-AI. Our submission (Developmental Embodied NeuroSimulation) is a group effort and summarizes our work in this area over the past few years. The graphical abstract can be found below.

Graphical Abstract for Developmental Embodied NeuroSimulation.

We also had a presence at Neuromatch 4, with four flash talk presentations on four different topics. Neuromatch 4 was a great time, with two days of keynote talks, short talks, flash talks, and debate panels. 

Each flash talk was 7.5 minutes long, which requires an efficiency of words and ideas not typical of a longer format. The first talk is "The Universal Theory of Switching", which focuses on transitory "switching" phenomena. Switching behavior is ubiquitous across biological, physical, and algorithmic systems, and is controlled by sudden, first-order phase transition-like behavior we characterize as zeroth-order cybernetic regulation. 

Another talk is on "Allostatic Kinds". Allostatic Kinds are a way to regulate the boundaries of meaning and regulation of internal emotional and conscious states. This talk is presented by Jesse Parent, and features a mix of complex systems regulation, philosophy of mind, and consciousness studies. This talk was in conjunction with CEEALAR (Center for Enabling EA Learning and Research), an academic hostel located in Blackpool, UK.

Daniela Cialfi has built upon the lab's work on Meta-brain Models to develop "Economic Meta-brains", which are bio-economic agents that behave according to the free energy principle. Meta-brains are layered computational models that enable different levels of representation in the same agent. These model layers can be configured in geometrically specific ways, which in turn affects their function. The free energy principle enriches the meta-brains approach by adding a mathematically rigorous energetic component to a meta-brain agent. 

Finally, our presentation on "Gibsonian Information" comes with a preprint. Gibsonian Information is the information content of direct perceptual processing (sensu J.J. Gibson). We draw parallels between Shannon and Gibsonian Information, in addition to the role of such information in the dynamic interactions between agents and their environments. See our graphical abstract below, which simplifies the mathematics in the preprint. The talk also features a number of naturalistic settings in which Gibsonian Information can be demonstrated.

Graphical abstract for the Gibsonian Information paper/presentation (direct perception as information content).

Hybrid Models and Representations, latest developments

Our research group Representational Brains and Phenotypes has recently been doing a lot of work in the area of embodied nervous systems simulation. Our go-to model over the past year and a half [1] has been the Braitenberg Vehicle (BV), which makes explicit the relationships between interactions with the environment, a neuronal network, and behavior. In the recently open-sourced Meta-Brain Models initiative, we are looking beyond the highly-limited representational framework of the BV by creating hybrid models that combine Vehicles with a representation-rich model (one that specifies symbolic and semantic properties).  

Representational Brains and Phenotypes website. Click to enlarge.

A few weeks ago, members of our research group presented on this topic at the DevoNN (virtual) workshop. Our paper and presentation "Developmental Embodied Agents as Meta-brain Models" introduced the Meta-brain concept to a wider audience, which in this case coupled a developmental Braitenberg Vehicles (dBV) and Contextual Geometric Sturctures (CGS) [2,3]. dBV and CGS are coupled as layers that interact in ways that resemble central nervous systems [4]. Other model combinations are possible, but must conform to the representation-free/representation-rich layering.

 

DevoNN logo and the layered representations approach. Click to enlarge.

This has the potential to leverage not only embodied aspects of intelligent behavior, but its symbolic aspects of as well. There are also opportunities to expand our layered representations in the direction of growth, form, and analogues of biological plasticity [5]. DevoNN was part of Artificial Life 2020, which was in itself a great virtual conference experience. Everything from digital evolution to robotics, and from computational social science to adaptive systems. 

Artificial Life 2020 (proceedings here). Click to enlarge.

While our extended abstract is not in the Proceedings, I was also able to given a lightning talk on the OpenWorm approach to virtual organisms. 

OpenWorm lightning talk. Click to enlarge.

NOTES:

[1] Check out our Saturday Morning NeuroSim research meetings on YouTube. Contact the Orthogonal Research and Education Lab if you would like to join in!

[2] Dvoretskii, S., Gong, Z., Gupta, A., Parent, J., and Alicea, B. Braitenberg Vehicles as Developmental Neurosimulation. arXiv, 2003.07689. doi:10.13140/RG.2.2.31149.23526.

[3] Alicea, B. Contextual Geometric Structures: modeling the fundamental components of cultural behavior. Proceedings of Artificial Life, 13, 147-154.

[4] examples include the relationship between the Thalamus and Neocortex of Mammals. For functional and evolutionary context, see: Karten H.J. (2015). Vertebrate brains and evolutionary connectomics: on the origins of the mammalian "neocortex". Philosophical Transactions of the Royal Society B, 370, 20150060

[5] this recent paper is the subject of a presentation at the Dynamics Days Digital conference, but is providing some inspiration for further development towards AI innateness: Alicea, B. (2020). Developmental Incongruity as a Dynamical Representation of Heterochrony. ResearchGate, doi:10. 13140/RG.2.2.17401.08807/1

Virtuality: a new view on virtual experience

The first images when you Google "virtuality". Products from the Virtuality Group. LEFT: Virtual Reality Society, RIGHT: Wikimedia (Dr.  Jonathan D. Waldern/Virtuality Group).

At Neuromatch 2.0, I gave a talk on the concept of virtuality titled "Computational Virtuality as a Form of Artificial Intelligence" (slides available on Figshare). Virtuality is a means to summarize all brain and body systems involved in a virtual experience. This talk features two big ideas, the second of which the Saturday Morning NeuroSim group will be building on in the coming months.  

1) "Being Virtual" as Human Performance (click to enlarge).

2) Differentiating Allostasis machine (click to enlarge). Allostatic load is induced collectively by stimulus [1], leads to dysregulation of system and ultimately to a new homeostatic setpoint.

Overall, virtuality can be characterized as a constructive sensory experience (h/t to Anson Lim). The first big idea stems from the observation that current theories are too limiting to properly characterize virtual experiences at the systems-level. Indeed, the very notion of objective reality is based in part on the synchronization of perception and action. When this synchronization is disrupted or perturbed in any way, we observe virtuality. This does not even require a virtual environment -- virtuality can be experienced in our interaction with the physical world [for an example from fly-human interaction, see 2]. But virtual environments are the most common way to elicit the allostatic load required to observe virtuality.

There are two aspects of embodied performance essential to understanding the virtuality effect. The first is the idea of cognitive gaps, or disruptions to spatiotemporal representations caused by the perturbation of reality. The second involves inducing allostatic load in the internal model the represents perception-action coupling. The latter has wide-ranging effects in the homeostat (nervous system), and can lead to many different effects of varying length scales.

But where does the artificial intelligence part come in? In the second part of the talk, I conclude that the effect sizes for human experiments are too small and formal experimental design is too limiting to demonstrate virtuality. This is particularly true for observing virtuality over long periods of time. Therefore, we can use computational agents! To propose a general approach, we want to identify two attentional and three sensorimotor features essential for any agent to exhibit virtuality.

Naturally, we want our agents to be embodied in some manner. We propose working with two types of agent: Morphogenetic Agents, a novel agent type that can exhibit both pattern recognition and morphogenesis (percepetion-action), and the well-known Braitenberg Vehicle, in this case experiencing incongruous environmental physics which leads to gaps in the perception-action loop. 

NOTES:

[1] this requires a ecological view of perception. For a short introduction, please see: Lobo, L., Heras-Escribano, M. and Travieso, D. (2018). The History and Philosophy of Ecological Psychology. Frontiers in Psychology, doi:10.3389/fpsyg.2018.02228.

[2] Alicea, B. (2013). Perceptual Time and the Evolution of Informational Investment. Synthetic Daisies blog, September 24.

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.

NOTES:

[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.

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!

OpenWorm: Royal Society B special issue now live!

Worm images courtesy of the OpenWorm browser (Drs. Christian Grove and Padraig Gleeson)

Regular readers of this blog might recall that the OpenWorm Foundation spearheaded a workshop (From Connectome to Behavior) at the Royal Society (London) in January 2018. This workshop generated a lot of social media content and internal (to OpenWorm Slack) discussion of the presented topics.

Since then, the participants have been hard at work putting together a special issue (now live in Royal Society B) that presents in more detail what was discussed at the meeting. Lots of great papers on interesting topics ranging from network theory to movement models, and from foraging behavior to quantitative phenotyping.

Many of these papers feature ongoing work related to the OpenWorm Foundation, including the Geppetto, c302, and Sibernetic projects. There is also an OpenWorm overview paper that provides a current state of the initiative. Enjoy!

An Infographical Survey of the Bitcoin Landscape

Josh Wardini sent me information on a new Bitcoin infographic that serves as a survey of events over the last 10 years in the world of Bitcoin development and legal regulation. Many interesting factoids in this graphic, some of which were unbeknownst to me. In the next few paragraphs, I will discuss my impressions that are brought to bear by each subset of factoids.

The relationship between blockchain and mining is an interesting one, and underscores the power of blockchain as both a data structure and a secure transaction system. Bitcoin is also its own economic system, complete with social interactions. In particular, the competitive and cooperative aspects of cryptocurrency can serve as a model for understanding the social structure of markets.

This is another interesting feature of bitcoin: the network has computational power to both unlock the value of existing blockchain as well as to create new currency. Bitcoin mining has always been a bit of a black box to me [1], but it seems as though it has potentially two roles in the bitcoin economy. In a Synthetic Daisies post from 2014, I mentioned that the supply of bitcoin is fixed (in the manner of a precious metals supply), but it turns out that it is not that simple. Of course, since then blockchain technology has become the latest hot emerging technology in a number of areas unrelated to Bitcoin and even the digital economy [2].

It turns out the computational systems (unlike people) is not all that hard to understand. However, digital currency, which is based on human systems, is much harder to understand (or at least fully appreciate). In 2013, I did a brief Synthetic Daisies mention of a flash crash on one of the main Bitcoin exchanges. There is a lot of opportunity to use blockchain and even perhaps cryptocurrency in the world of research. If ways are found to make these technologies more easily scalable, then they might be applied to many research problems involving human social systems [3].

NOTES:

[1] So I sought out a few introductory materials on Bitcoin mining to clarify what I did not know: 

a) startbitcoin (2016). Beginner's Guide to Mining Bitcoins. 99 Bitcoins blog, July 1.

* mining consists of discovery blocks in the blockchain data structure, the discovery of which is rewarded through a "bounty" of x bitcoins. From there, inequality emerges (or not).

b) Mining page. Bitcoin Wiki.

* the total number of blocks is agreed to by the community, as is the total amount of computational power of the network. This makes the monetary supply nominally fixed, but is not required by the technology.

c) Hashcash Algorithm page. Bitcoin Wiki.

Despite the clear metaphoric overtones, Bitcoin mining is essentially like breaking encryption in that it requires a massive amount of computing power thrown at a computationally hard problem, but is also has elements of an artificial life model (e.g. competition for blockchain elements).

Water-cooled rigs probably maximize your investment margin....

[2] Of course, there has been innovation in the use of blockchain for Bitcoin and more general cryptocurrency transactions. For more, please see:

Portegys, T.E. (2017). Coinspermia: a cryptocurrency unchained. Working Paper, ResearchGate, doi:10.13140/RG.2.2.33317.91360.

Brock, A. (2016). Beyond Blockchain: simple scalable cryptocurrencies. Metacurrency project blog, March 31.

[3] A few potential examples:

a) Data Management. 1  2

b) Alternative forms of social exchange.

c) Smart contracts.

d) Peer-to-peer cloud storage.

e) Electronic health records.