Working groups & centers
Cognition Futures
Research group focused on embodied intelligence, affordance perception, spatial cognition, and the future of mind.
View group →Society Ethics Technology (SET)
Joint initiative between JOPRO and OREL exploring the intersections of society, ethics, and technology.
View group →Representational Brains & Phenotypes
Director
Empirical and artificial models of neurobehavioral complexity
View group →DevoWorm
Founder & Director
Developmental and computational biology centered on C. elegans and other model organisms
View group →Programs & initiatives
From Here to There: Strategy and Mentorship for Innovators
Senior Advisor
Exploring emerging narratives, directionality, and the future of human experience
View program →Joint Open Source Summer Cohort
Program Leadership
A collaborative summer cohort across OREL, DevoWorm, and JOPRO — open-source contribution, instruction, and professional development, anchored by Google Summer of Code.
View program →Open-source Sustainability
Senior Advisor
A multi-year initiative investigating the long-term health and sustainability of open-source communities through agent-based modeling, active inference, and cybernetic approaches.
View program →SMN @ OREL
Program Director
Originally "Saturday Morning NeuroSim", Orthogonal Research and Education Lab weekly public session is a unique space for projects from across the lab network.
View program →CFRG
Senior Contributor
The Cognition Futures Reading Group explores concepts, methods, and opportunities in diverse intelligences (natural and artificial), phenomenology, and contemporary discussions on minds
View program →Projects
Reimagining Cybernetics
BraGenBrain
Mentor
Braitenberg Vehicles Genetic Algorithms Simulation of Neural Development
Modeling Neural Development with Braitenberg Vehicles
Mentor
Evolving embodied neural networks in Braitenberg vehicles to study brain development and connectome motifs
Allostatic Kinds
A taxonomy of permutations of subject-object directionality in causation
Sustainability Auditing Tool (SAT)
Senior Advisor
A web-based auditing platform for evaluating the long-term sustainability and community health of open-source projects.
Publications
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A 'good' regulator may provide a world model for intelligent systems
Philosophical Transactions of the Royal Society A
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The Augmentation of Intelligent Agents for Human-Machine Superperformance
OSF Preprints
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Alicea reviews 'The Open Dynamics of Braitenberg Vehicles' by Hotton and Yoshimi
CogNet / MIT Press
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Developmental Neurosimulation as a Route to Embodied Morphogenetic-inspired Intelligence
Embodied Intelligence 2024 (Self-Organized Systems track)
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The Augmentation of Intelligent Agents for Human-Machine Superperformance
Studies in Computational Intelligence, 1243, 44–51
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A Brief History of Cybernetic Imperatives and Behavior
PsyArXiv
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Continual Developmental Neurosimulation Using Embodied Computational Agents
IOP Conference Series: Materials Science and Engineering, 1321, 012013
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An Ensemble Approach to the Origin of Life
Origin of Life via Archaea, Chapter 8
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The Molecular Basis of Differentiation Wave Activity in Embryogenesis
BioSystems, 105272
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A Primer on Gibsonian Information
arXiv:2403.18829
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Key Concepts in Tech Careers and Tech Ethics in 2023
ACM NYCWiC 2023
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Open-source Community Sustainability using Agent-based Models
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Alicea reviews "The Open Dynamics of Braitenberg Vehicles" by Hotton and Yoshimi
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Embodied Cognitive Morphogenesis as a Route to Intelligent Systems
Royal Society Interface Focus, 20220067
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Hypergraphs Demonstrate Anastomoses During Divergent Integration
arXiv:2311.17067
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Updates from the OpenWorm Project: Incorporating NeuroPAL Data and ASH Neuron Electrophysiological Recordings
International C. elegans Conference, Glasgow, Scotland
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Our Virtual Lives and Digital Companionship: Opportunities and Challenges of Shared Experience in an Augmented Century
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The Psychophysical World of the Motile Diatom Bacillaria Paradoxa
Mathematics and Biology of Diatoms, Chapter 9
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Super-performance: sampling, planning, and ecological information
Studies in Computational Intelligence, 1130, 33–40
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Towards Sharing Cognitive Environments: Methodology and Theory
WeRobot 2022
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Our Virtual Lives and Digital Companionship: Opportunities and Challenges of Shared Experience in an Augmented Century
WeRobot 2022
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Braitenberg Vehicles as Developmental Neurosimulation
Artificial Life, 28(3), 1–27
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DevoLearn: Machine Learning Models and Education that Enable Computational Developmental Biology
INCF / DevoLearn
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Flipping the Switch on Local Exploration: Genetic Algorithms with Reversals
Proceedings of the Conference on Intelligence Systems
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Game Theory of Developmental Processes
Dynamics Days 2022, Atlanta, GA
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Game Theory of Developmental Processes
ResearchGate
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Gibsonian Information: A New Approach to Quantitative Information
Studies in Computational Intelligence, 1032, 15–19
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Intelligence Offloading and the Neurosimulation of Developmental Agents
IOP Conference Series: Materials Science and Engineering, 1292, 012019 (International Workshop on Embodied Intelligence)
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Layers, Folds, and Semi-Neuronal Information Processing
Procedia Computer Science, 213, 443–452
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Mathematics of DevoWorm
Find Your Inner Modeler V, University of Illinois–Chicago
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Meta-brain Models: Biologically-inspired Cognitive Agents
Proceedings of the Embodied Intelligence Workshop, 20
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Research Methods in Cognition Studies & Phenomenology: Challenges and Opportunities
Neuromatch 5
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Allostasis Machines: a model for understanding internal states and technological environments
PsyArXiv
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Allostatic Kinds: Towards a Taxonomy of Permutations of Subject-Object Directionality in Causation
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Data-theoretical Synthesis of the Early Developmental Process
Neuroinformatics
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Neuromorphogenetic Patterns and the Theory of Deep Learning
NetNeuro Satellite, Networks Conference
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The OpenWorm Project: Progress Update, Available Resources and Future Plans
International C. elegans Conference (Virtual)
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Periodicity in the Embryo: Emergence of Order in Space, Diffusion of Order in Time
BioSystems, 204, 104405
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Towards a Digital Diatom: Image Processing and Deep Learning Analysis of Bacillaria paradoxa Dynamic Morphology
Diatom Gliding Motility
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Cultural, Emotional, and Associative Traits to Determine Literary Inclination
PsyArXiv
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Elementary Morphogenetic Cellular Automata for Modeling Developmental Phenotypes
ResearchGate
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Raising the Connectome: The Emergence of Neuronal Activity and Behavior in C. elegans
Frontiers in Cellular Neuroscience
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Cultural Affinity through Associative Machine Learning and Behavioral Computation
International Conference on Computing, Communication, Control and Automation (ICCUBEA)
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Meta-brain Computational Models for Representing Cultural Diversity
Brain.tc (Twitter conference)
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A New Kind of Developmental Biology
Find Your Inner Modeler III, University of Alabama–Birmingham
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Cell Differentiation Processes as Spatial Networks: Identifying Four-dimensional Structure in Embryogenesis
BioSystems, 173, 235–246
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Data Repository for "Morphogenetic Processes as Data: Quantitative Structure in the Drosophila Eye Imaginal Disc"
Open Science Framework
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Embryo Networks and Connectomes in Caenorhabditis elegans
Open Science Framework
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Morphogenetic Processes as Data: Quantitative Structure in the Drosophila Eye Imaginal Disc
BioSystems, 173, 256–265
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OpenWorm: Overview and Recent Advances in Integrative Biological Simulation of Caenorhabditis elegans
Philosophical Transactions of the Royal Society B, 373, 20170382
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Origins of the Embryo: Self-organization through Cybernetic Regulation
BioSystems, 173, 73–82
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The Emergent Connectome in Caenorhabditis elegans Embryogenesis
BioSystems, 173, 247–255
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Data from: Evolution in Eggs and Phases
Dryad
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Evolution in Eggs and Phases: Experimental Evolution of Fecundity and Reproductive Timing in Caenorhabditis elegans
Royal Society Open Science, 3, 160496
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Genotype-specific Developmental Plasticity Shapes the Timing and Robustness of Reproductive Capacity in Caenorhabditis elegans
bioRxiv
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Information Isometry Technique Reveals Organizational Features in Developmental Cell Lineages
bioRxiv
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Morphozoic: Cellular Automata with Nested Neighborhoods as a Metamorphic Representation of Morphogenesis
Multi-Agent Based Simulations Applied to Biological and Environmental Systems, Chapter 3
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Playing Games with Ideas: When Epistemology Pays Off
Journal of Brief Ideas
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Quantifying Mosaic Development: Towards an Evo-Devo Postmodern Synthesis of the Evolution of Development via Differentiation Trees of Embryos
Biology, 5(3), 33
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DevoWorm: Raising the Worm on Datapoints, Trees, and Matrices
20th International C. elegans Conference, Los Angeles, CA
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The Foundations of Control and Cognition: The Every Good Regulator Theorem
Figshare
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Network Architecture of Embryo Developmental Regulation
Network Frontiers Workshop, Northwestern University
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Contextual and Structural Representations of Market-mediated Economic Value
arXiv:1403.7021
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DevoWorm: Differentiation Waves and Computation in C. elegans Embryogenesis
bioRxiv
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Contextual Geometric Structures: Modeling the Fundamental Components of Cultural Behavior
Proceedings of Artificial Life, 13, 147–154
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Lagrangian Coherent Structures (LCS) May Describe Evolvable Frontiers in Natural Populations
arXiv:1101.6071