Bradly Alicea

Orthogonal Research and Education Laboratory

The differentiation of neurons and formation of connections between cells is the basis of both the adult phenotype and behaviors tied to cognition, perception, reproduction, and survival. Such behaviors are associated with local (circuits) and global (connectome) brain networks. A solid understanding of how these networks emerge is critical. This o...

Biological development is often described as a dynamic, emergent process. This is evident across a variety of phenomena, from the temporal organization of cell types in the embryo to compounding trends that affect large-scale differentiation. To better understand this, we propose combining quantitative investigations of biological development with...

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 an...

The embryological view of development is that coordinated gene expression, cellular physics and migration provides the basis for phenotypic complexity. This stands in contrast with the prevailing view of embodied cognition, which claims that informational feedback between organisms and their environment is key to the emergence of intelligent behavi...

A classic idea from the cybernetics literature is the good regulator approach first formulated by Conant and Ashby in 1970, who proposed a formalism for good regulation. The Every Good Regulator Theorem (EGRT) provides a unique perspective on intelligent autonomous learning systems reliant on a type of compressed global representation (world model)...

As development varies greatly across the tree of life, it may seem difficult to suggest a model that proposes a single mechanism for understanding collective cell behaviors and the coordination of tissue formation. Here we propose a mechanism called differentiation waves, which unify many disparate results involving developmental systems from acros...

Naturalistic cognition in human performance is defined by dynamical responses to stimuli. Allostasis Machines (AMs) are characterized by an internal model and corresponding output trajectory characterizing a generalized response to stresses and sudden changes. The effects of the environment on the internal model are collectively known as perturbati...

Cellular Automata (CA) have been extensively explored to visualize pattern formation. Parallels between CAs and biological pattern formation have been observed, particularly with respect to the establishment of animal embryos and the formation of snail shells. However, the interpretability of traditional CAs, in addition to the limitations of Neura...

The connection between active perception and the limit of performance provides a path to understanding naturalistic behavior. We can take a comparative cognitive modeling perspective to understand the limits of this performance and the existence of superperformance. We will discuss two categories that are hypothesized to originate in terms of co-ev...

Across the scientific literature, information measurement in the nervous system is posed as a problem of information processing internal to the brain by constructs such as neuronal populations, sensory surprise, or cognitive models. Application of information theory in the nervous system has focused on measuring phenomena such as capacity and integ...

Complex networks can be used to analyze structures and systems in the embryo. Not only can we characterize growth and the emergence of form, but also differentiation. The process of differentiation from precursor cell populations to distinct functional tissues is of particular interest. These phenomena can be captured using a hypergraph consisting...

There is much to learn through synthesis of Developmental Biology, Cognitive Science and Computational Modeling. Our path forward is to present a design for developmentally-inspired learning agents based on Braitenberg Vehicles. Using these agents to exemplify the embodied nature of computational autonomy, we move closer to modeling embodied experi...

Cognitive offloading occurs when environmental affordances expand cognitive capacity while facilitating spatial and social behaviors. Capacity-related constraints are also important, particularly as embodied agents come online during development. Vast differences in brain size and offloading capacity exist across the tree of life. We take from mult...

The connection between active perception and the limits of performance provide a path to understanding naturalistic behavior. We can take a comparative cognitive modeling perspective to understand the limits of this performance and the existence of superperformance. We will discuss two categories that are hypothesized to originate in terms of coevo...

Simulating development has a number of benefits for understanding the acquisition of intelligent behavior. Yet development is not simply a generic form of generativity or emergence. Development is an inherently embodied and interactive process that unfolds in a limited time span. While embodied development provides a basis for grounding intelligent...

One important feature of complex systems is problem domains that have many local minima and substructure. Biological systems manage these local minima by switching between different subsystems depending on their environmental or developmental context. Genetic algorithms (GA) can mimic this switching property as well as provide a means to overcome p...

Collaborative open-source projects require constant maintenance and involvement, but these factors are usually evaluated after the fact, leading to technical debt and project failures. We attempt to resolve this state of affairs by exploring the use of agent-based models to model contributor behavior over long periods of time. Our approach draws fr...

What role does phenotypic complexity play in the systems-level function of an embodied agent? The organismal phenotype is a topologically complex structure that interacts with a genotype, developmental physics, and an informational environment. Using this observation as inspiration, we utilize a type of embodied agent that exhibits layered represen...

The embryological view of development is that coordinated gene expression, cellular physics, and migration provides the basis for phenotypic complexity. This stands in contrast to the prevailing view of embodied cognition, which claims that informational feedback between organisms and their environment is key to the emergence of intelligent behavio...

Artificial Intelligence (AI) systems based solely on neural networks or symbolic computation present a representational complexity challenge. While minimal representations can produce behavioral outputs like locomotion or simple decision-making, more elaborate internal representations might offer a richer variety of behaviors. We propose that these...

Cognitive offloading occurs when environmental affordances expand cognitive capacity as well as facilitate spatial and social behaviors. Yet capacity-related constraints are also important, particularly as an embodied agent comes online during development. Vast differences in brain size and offloading capacity exist across the tree of life. Taking...

What role does phenotypic complexity play in the systems-level function of an embodied agent? The organismal phenotype is a topologically complex structure that interacts with a genotype, developmental physics, and an informational environment. Using this observation as inspiration, we utilize a type of embodied agent that exhibits layered represen...

What role does phenotypic complexity play in the systems-level function of an embodied agent? The organismal phenotype is a topologically complex structure that interacts with a genotype, developmental physics, and an informational environment. Using this observation as inspiration, we utilize a type of embodied agent that exhibits layered represen...

Neuromatch Academy (https://academy.neuromatch.io; (van Viegen et al., 2021)) was designed as an online summer school to cover the basics of computational neuroscience in three weeks. The materials cover dominant and emerging computational neuroscience tools, how they complement one another, and specifically focus on how they can help us to better...

One important feature of complex systems are problem domains that have many local minima and substructure. Biological systems manage these local minima by switching between different subsystems depending on their environmental or developmental context. Genetic Algorithms (GA) can mimic this switching property as well as provide a means to overcome...

We introduce the DevoLearn open-source software, a pre-trained model customized for the analysis of C. elegans developmental processes. The model description, training data, and applications of the model are discussed. We also introduce the DevoLearn platform, an educational resource and software suite for analyzing a wider variety of model organis...

Developmental processes are dynamic and complex, and can be viewed from the perspective of interacting agents. We will provide a means to understand developmental agency at multiple organizational scales through the notion of ontogenetic agency, which will in turn enable an approach called developmental game theory. We will begin by reviewing the n...

We propose a new way to quantitatively characterize information: Gibsonian Information (GI). GI provides a means to characterize how agents extract information from direct perceptual signals. In this paper, we characterize GI quantitatively, and contrast this with rival approaches to quantitative information. Our formulation differs from existing a...

Artificial Intelligence (AI) systems based solely on neural networks or symbolic computation present a representational complexity challenge. While minimal representations can produce behavioral outputs like locomotion or simple decision-making, more elaborate internal representations might offer a richer variety of behaviors. We propose that these...

Recent years have witnessed a convergence of data and methods that allow us to approximate the shape, size, and functional attributes of biological organisms. This is not only limited to traditional model species: given the ability to culture and visualize a specific organism, we can capture both its structural and functional attributes. We present...

Readers many times look for similar books, similar movies or creative artefacts with reference to a particular creative artefact of their interest. This similarity is not simply about the subject but also about overall presentation and the way overall plot in a creative artefact evolves. Most of the systems generally consider meta-data, authors, ti...

Synopsis Two hallmarks of biological processes are complexity and time. While complexity can have many meanings, in this paper we propose an explicit link to the flow of time and how it is experienced by the organism. While the flow of time is rooted in constraints of fundamental physics, understanding the operation of biological systems in terms o...

The evolutionary transition to multicellular life in the form of cellular aggregates and embryos is marked by a need to form internal networks for oxygen and nutrient transfer between cells. This can occur through vascular networks, but even this relies on the configuration of cells in morphologies of a particular shape. How does this requirement c...

Literary artefacts are generally indexed and searched based on titles, meta data and keywords over the years. This searching and indexing works well when user/reader already knows about that particular creative textual artefact or document. This indexing and search hardly takes into account interest and emotional makeup of readers and its mapping t...

Literary artefacts are generally indexed and searched based on titles, meta data and keywords over the years. This searching and indexing works well when user/reader already knows about that particular creative textual artefact or document. This indexing and search hardly takes into account interest and emotional makeup of readers and its mapping t...

Requested Slides from NYCWiC.

In this talk, we will introduce participants to the Orthogonal Research and Education Laboratory (OREL). OREL is a distributed research organization that enables computational education and research virtually and enables collaborations across vast geographic distances. This entirely virtual entity is managed using an open-source ethos. Academic con...

In the present paper we will approach enactivism from the perspective of internal regulation: while the environment shapes the organism, it is also true that organisms have complex internal states with regulatory machinery with a set of continuous phenotype-environment interactions. The aim of the present paper is to provide a visual means to analy...

Scientists routinely use images to display data. Readers often examine figures first; therefore, it is important that figures are accessible to a broad audience. Many resources discuss fraudulent image manipulation and technical specifications for image acquisition; however, data on the legibility and interpretability of images are scarce. We syste...

While Artificial Neural Networks (ANNs) have yielded impressive results in the realm of simulated intelligent behavior, it is important to remember that they are but sparse approximations of Biological Neural Networks (BNNs). We go beyond comparison of ANNs and BNNs to introduce principles from BNNs that might guide the further development of ANNs...

Does embryonic development exhibit characteristic temporal features? This is apparent in evolution, where evolutionary change has been shown to occur in bursts of activity. Using two animal models (Nematode, Caenorhabditis elegans and Zebrafish, Danio rerio) and simulated data, we demonstrate that temporal heterogeneity exists in embryogenesis at t...

As a biochemical process, direct cellular reprogramming is slow and complex. The early stages of this process is the most critical determinant of successful phenotypic conversion. This study provides insight into the statistical signatures that describe temporal structure in the reprogramming process. We examine two sources of variation in reprogra...

Does embryonic development exhibit characteristic temporal features? This is quite apparent in evolution, where evolutionary change has been shown to occur in bursts of activity. Using two animal models (Nematode, Caenorhabditis elegans and Zebrafish, Danio rerio) and simulated data, we demonstrate that temporal heterogeneity exists in embryogenesi...

In many areas of science and philosophy, observers are seen as an integral part of understanding the natural world. Aside from a pedagogical role, observers are seen as less important in computational forms of inquiry. In this talk, I will reconsider a role for the observer in computational models as fully integrated with the agent. perhaps more fu...

Reproducibility is a cornerstone of the scientific method and sets apart science from pseudoscience. Unfortunately, a majority of scientists have experienced difficulties in reproducing their own or someone else’s results. This inability to confirm scientific findings negatively impacts individual scientists, funding bodies, academic journals, phar...

Scientists routinely use images to display data. Readers often examine figures first; therefore, it is important that figures are accessible to a broad audience. Many resources discuss fraudulent image manipulation and technical specifications for image acquisition; however, data on the legibility and interpretability of images are scarce. We syste...

The theory of heterochrony provides us with a generalized quantitative perspective on the dynamics of developmental trajectories. While useful, these linear developmental trajectories merely characterize changes in the speed and extent of growth in developmental time. One open problem in the literature involves how to characterize developmental tra...

The theory of heterochrony provides us with a generalized quantitative perspective on the dynamics of developmental trajectories. While useful, these linear developmental trajectories merely characterize changes in the speed and extent of growth in developmental time. One open problem in the literature involves how to characterize developmental tra...

We present a framework for meta-brain models, or hybrid models that capture multiple aspects of developmental neuro-biology and behavior. A developmentally-inspired embodied learning agent architecture is combined with a contextually-explicit representational layer to form a complex artificial nervous system. The architectural description is summar...

We present a framework for meta-brain models, or hybrid models that capture multiple aspects of developmental neurobiology and behavior. A developmentally-inspired embodied learning agent architecture is combined with a contextually-explicit representational layer to form a complex artificial nervous system. The architectural description is summari...

Various cultural and behavioral preferences delineate human creativity. One such set of preferences, literary inclination, impacts not only the books people choose to read but also on the way they perceive the narrative and human relationships contained within. Understanding the overall development of a plot and the evolution of relationships among...

A number of contemporary forces have conspired to drive highly-competent academics away from the academy. The vagaries of departmental hiring, institutional conservatism, and growth in the number of researchers versus available positions have displaced talent and innovation. Enter the alt-academic institution: small-scale institutions engaged in ac...

The ability to formalize problems in a quantitative manner is the key to predictive power. We characterize a lack of formality as unruliness, relate unruliness as a property of un(3) (undecidability, uncomputability, and unpredictability), and define a class of problems which even when well-posed remain highly informal in nature. Despite this lack...

The connection between brain and behavior is a longstanding issue in the areas of behavioral science, artificial intelligence, and neurobiology. Particularly in artificial intelligence research, behavior is generated by a black box approximating the brain. As is standard among models of artificial and biological neural networks, an analogue of the...

The differentiation of neurons and formation of connections between cells is the basis of both the adult phenotype and behaviors tied to cognition, perception, reproduction, and survival. Such behaviors are associated with local (circuits) and global (connectome) brain networks. A solid understanding of how these networks emerge is critical. This o...

Recent years have witnessed a convergence of data and methods that allow us to approximate the shape, size, and functional attributes of biological organisms. This is not only limited to traditional model species: given the ability to culture and visualize a specific organism, we can capture both its structural and functional attributes. We present...

Two hallmarks of biological processes are complexity and time. While complexity can have many meanings, in this paper we propose an explicit link to the flow of time and how it is experienced by the organism. The flow of time is rooted in constraints of fundamental physics. Understanding the experience of time, particularly in terms of flow and tem...

Virtual Reality (VR) and human interaction with virtual worlds can greatly enhance communication neuroscience research. VR provides opportunities for novel approaches to empirical investigation. This chapter will discuss why VR and the varieties of virtual experience is of interest to communication neuroscientists. This leads to a discussion of mul...

Virtual Reality (VR) and human interaction with virtual worlds can greatly enhance communication neuroscience research. VR provides opportunities for novel approaches to empirical investigation. This chapter will discuss why VR and the varieties of virtual experience is of interest to communication neuroscientists. This leads to a discussion of mul...

Participation in open data initiatives require two semi-independent actions: the sharing of data produced by a researcher or group, and a consumer of shared data. Consumers of shared data range from people interested in validating the results of a given study to people who actively transform the available data. These data transformers are of partic...

Culture is core to human civilization, and is essential for human intellectual achievements in social context. Culture also influences how humans work together, perform particular task and overall lifestyle and dealing with other groups of civilization. Thus, culture is concerned with establishing shared ideas, particularly those playing a key role...

Culture is core to human civilization, and is essential for human intellectual achievements in social context. Culture also influences how humans work together, perform particular task and overall lifestyle and dealing with other groups of civilization. Thus, culture is concerned with establishing shared ideas, particularly those playing a key role...

Our objective was to focus on linkages between the process of learning and memory and the placement of objects within an array of targets in a virtual workspace. Participants were instructed to place virtual objects serially within a three-dimensional target array. One phase presented each target sequentially, and required participants to make time...

We can improve our understanding of biological processes through the use of computational and mathematical modeling. One such morphogenetic process (ommatidia formation in the Drosophila eye imaginal disc) provides us with an opportunity to demonstrate the power of this approach. We use a high-resolution image that catches the spatially- and tempor...

One overarching principle of eukaroytic development is the generative spatial emergence and self-organization of cell populations. As cells divide and differentiate, they and their descendants form a spatiotemporally explicit and increasingly compartmentalized complex system. Yet despite this compartmentalization, there is selective functional over...

One overarching principle of eukaroytic development is the generative spatial emergence and self-organization of cell populations. As cells divide and differentiate, they and their descendants form a spatiotemporally explicit and increasingly compartmentalized complex system. Yet despite this compartmentalization, there is selective functional over...

The adoption of powerful software tools and computational methods from the software industry by the scientific research community has resulted in a renewed interest in integrative, large-scale biological simulations. These typically involve the development of computational platforms to combine diverse, process-specific models into a coherent whole....

The relatively new field of connectomics provides us with a unique window into nervous system function. In the model organism Caenorhabditis elegans, this promise is even greater due to the relatively small number of cells (302) in its nervous system. While the adult C. elegans connectome has been characterized, the emergence of these networks in d...

One overarching principle of eukaroytic development is the generative spatial emergence and self-organization of cell populations. As cells divide and differentiate, they and their descendents form a spatiotemporal explicit and increasingly compartmentalized complex system. Yet despite this comparmentalization, there is selective functional overlap...

We can improve our understanding of biological processes through the use of computational and mathematical modeling. One such morphogenetic process (ommatidia formation in the Drosophila eye imaginal disc) provides us with an opportunity to demonstrate the power of this approach. We use a high-resolution image that catches the spatially- and tempor...

The construction of an embryo from a single cell precursor is a highly complex process. Evolutionary emergence of the first embryos is even more complex, and involves both a transition to multicellularity along with the establishment of developmental mechanisms. We propose that embryogenesis relies on a community of cells conforming to a regulatory...

This study investigates the dynamics of attention during continuous, naturalistic interactions in a video game. Specifically, the effect of repeated distraction on a continuous primary task is related to a functional model of network connectivity. We introduce the Non-linear Attentional Saturation Hypothesis (NASH), which predicts that effective co...

Supporting Methods. Methodological detail, including mathematical and descriptive details for measures and statistical models (PDF File).

Inspired by Human-Computer Interaction (HCI), Human-Assisted AI can serve to both augment both human performance and artificial systems. This talk will feature a discussion of Human-assisted AI as an instance of Intelligence Augmentation (IA). We will discuss instances of so-called weak and strong IA, in addition to contemporary examples of and pat...