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Josh Bongard

Publications and source records attributed to Josh Bongard.

At least 19 recordsLinked to original sources
arXiv2026

Environmental resilience via morphological diversity within machines

Organisms contain diverse, sensorimotor parts across size scales and rapidly adapt to new environments, while machines contain only inert materials at smaller scales and struggle with surprise. We hypothesize that this agents-within-agents quality of organisms may aid their resilience: increasing experiences with internal physical adversity may pre-train organisms and machines to handle external adversity, such as encounters with new environments. Not only has this hypothesis not yet been articulated, mechanisms enabling this phenomenon have yet to be proposed. Here we show a mechanism by which this can occur: we found that physical connectors, in learning to restore behavior to previously independent, morphologically diverse agents they disrupted by tethering them together, trigger and tame sufficiently diverse disruptions that later encounters with new environments trigger disruptions that fall within this manageable range, enabling the collective to continue behaving properly without any additional learning or adaptation. Further, we found that building collectives from more agents, or more diverse agents, further increases the collective's resilience to new environments. This suggests that not just taming but intentionally creating internal physical adversity may indeed prepare organisms for external adversity, and could do so for machines, if they were built from smaller machines.

cs.RO↗
arXiv2026

From description to design: Automated engineering of complex systems with desirable emergent properties

The study of complex systems has produced a huge library of different descriptive statistics that scientists can use to describe the various emergent patterns that characterize complex systems. The problem of engineering systems to display those patterns from first principles is a much harder one, however, as a hallmark of complexity is that macro-scale emergent properties are often difficult to predict from micro-scale features. Here, we propose a general optimization-based pipeline to automate the difficult problem of engineering emergent features by re-purposing descriptive statistics as loss functions, and letting a gradient descent optimizer do the hard work of designing the relevant micro-scale features and interactions. Using Kuramoto systems of coupled oscillators as a test bed, we show that our approach can reliably produce systems with non-trivial global properties, including higher-order synergistic information, multi-attractor metastability, and meso-scale structures such as modules and integrated information. We further show that this pipeline can also account for and accommodate constraints on the system properties, such as the costs of connections, or topological restrictions. This work is a step forward on the path moving complex systems science from a field predicated largely on description and post-hoc storytelling towards one capable of engineering real-world systems with desirable emergent meso-scale and macro-scale properties.

physics.soc-ph↗
arXiv2025

Optimized Architectures for Kolmogorov-Arnold Networks

Efforts to improve Kolmogorov--Arnold networks (KANs) with architectural enhancements have been stymied by the complexity those enhancements bring, undermining the interpretability that makes KANs attractive in the first place. Here we study overprovisioned architectures combined with sparsification, deep supervision, and depth selection, to learn compact, interpretable KANs without sacrificing accuracy. Crucially, we focus on differentiable mechanisms under a principled minimum description length objective, jointly optimizing activations, structure, and depth end-to-end. Experiments across function approximation benchmarks, dynamical systems forecasting, and real-world prediction tasks demonstrate that sparsification alone is insufficient, but the combination with depth selection achieves competitive or superior accuracy while discovering substantially smaller models. The result is a principled path toward models that are both more expressive and more interpretable, addressing a key tension in scientific machine learning.

cs.LG↗
arXiv2025

Softly Symbolifying Kolmogorov-Arnold Networks

Kolmogorov-Arnold Networks (KANs) offer a promising path toward interpretable machine learning: their learnable activations can be studied individually, while collectively fitting complex data accurately. In practice, however, trained activations often lack symbolic fidelity, learning pathological decompositions with no meaningful correspondence to interpretable forms. We propose Softly Symbolified Kolmogorov-Arnold Networks (S2KAN), which integrate symbolic primitives directly into training. Each activation draws from a dictionary of symbolic and dense terms, with learnable gates that sparsify the representation. Crucially, this sparsification is differentiable, enabling end-to-end optimization, and is guided by a principled Minimum Description Length objective. When symbolic terms suffice, S2KAN discovers interpretable forms; when they do not, it gracefully degrades to dense splines. We demonstrate competitive or superior accuracy with substantially smaller models across symbolic benchmarks, dynamical systems forecasting, and real-world prediction tasks, and observe evidence of emergent self-sparsification even without regularization pressure.

cs.LG↗
arXiv2025

ZapGPT: Free-form Language Prompting for Simulated Cellular Control

Human language is one of the most expressive tools for conveying intent, yet most artificial or biological systems lack mechanisms to interpret or respond meaningfully to it. Bridging this gap could enable more natural forms of control over complex, decentralized systems. In AI and artificial life, recent work explores how language can specify high-level goals, but most systems still depend on engineered rewards, task-specific supervision, or rigid command sets, limiting generalization to novel instructions. Similar constraints apply in synthetic biology and bioengineering, where the locus of control is often genomic rather than environmental perturbation. A key open question is whether artificial or biological collectives can be guided by free-form natural language alone, without task-specific tuning or carefully designed evaluation metrics. We provide one possible answer here by showing, for the first time, that simple agents' collective behavior can be guided by free-form language prompts: one AI model transforms an imperative prompt into an intervention that is applied to simulated cells; a second AI model scores how well the prompt describes the resulting cellular dynamics; and the former AI model is evolved to improve the scores generated by the latter. Unlike previous work, our method does not require engineered fitness functions or domain-specific prompt design. We show that the evolved system generalizes to unseen prompts without retraining. By treating natural language as a control layer, the system suggests a future in which spoken or written prompts could direct computational, robotic, or biological systems to desired behaviors. This work provides a concrete step toward this vision of AI-biology partnerships, in which language replaces mathematical objective functions, fixed rules, and domain-specific programming.

cs.AI↗
arXiv2025

Multi-Exit Kolmogorov-Arnold Networks: enhancing accuracy and parsimony

Kolmogorov-Arnold Networks (KANs) uniquely combine high accuracy with interpretability, making them valuable for scientific modeling. However, it is unclear a priori how deep a network needs to be for any given task, and deeper KANs can be difficult to optimize and interpret. Here we introduce multi-exit KANs, where each layer includes its own prediction branch, enabling the network to make accurate predictions at multiple depths simultaneously. This architecture provides deep supervision that improves training while discovering the right level of model complexity for each task. Multi-exit KANs consistently outperform standard, single-exit versions on synthetic functions, dynamical systems, and real-world datasets. Remarkably, the best predictions often come from earlier, simpler exits, revealing that these networks naturally identify smaller, more parsimonious and interpretable models without sacrificing accuracy. To automate this discovery, we develop a differentiable "learning-to-exit" algorithm that balances contributions from exits during training. Our approach offers scientists a practical way to achieve both high performance and interpretability, addressing a fundamental challenge in machine learning for scientific discovery.

cs.LG↗
arXiv2025

Decoupling Representation and Learning in Genetic Programming: the LaSER Approach

Genetic Programming (GP) has traditionally entangled the evolution of symbolic representations with their performance-based evaluation, often relying solely on raw fitness scores. This tight coupling makes GP solutions more fragile and prone to overfitting, reducing their ability to generalize. In this work, we propose LaSER (Latent Semantic Representation Regression)} -- a general framework that decouples representation evolution from lifetime learning. At each generation, candidate programs produce features which are passed to an external learner to model the target task. This approach enables any function approximator, from linear models to neural networks, to serve as a lifetime learner, allowing expressive modeling beyond conventional symbolic forms. Here we show for the first time that LaSER can outcompete standard GP and GP followed by linear regression when it employs non-linear methods to fit coefficients to GP-generated equations against complex data sets. Further, we explore how LaSER enables the emergence of innate representations, supporting long-standing hypotheses in evolutionary learning such as the Baldwin Effect. By separating the roles of representation and adaptation, LaSER offers a principled and extensible framework for symbolic regression and classification.

cs.NE↗
arXiv2025

Giving Simulated Cells a Voice: Evolving Prompt-to-Intervention Models for Cellular Control

Guiding biological systems toward desired states, such as morphogenetic outcomes, remains a fundamental challenge with far-reaching implications for medicine and synthetic biology. While large language models (LLMs) have enabled natural language as an interface for interpretable control in AI systems, their use as mediators for steering biological or cellular dynamics remains largely unexplored. In this work, we present a functional pipeline that translates natural language prompts into spatial vector fields capable of directing simulated cellular collectives. Our approach combines a large language model with an evolvable neural controller (Prompt-to-Intervention, or P2I), optimized via evolutionary strategies to generate behaviors such as clustering or scattering in a simulated 2D environment. We demonstrate that even with constrained vocabulary and simplified cell models, evolved P2I networks can successfully align cellular dynamics with user-defined goals expressed in plain language. This work offers a complete loop from language input to simulated bioelectric-like intervention to behavioral output, providing a foundation for future systems capable of natural language-driven cellular control.

cs.AI↗
arXiv2025

The topology of synergy: linking topological and information-theoretic approaches to higher-order interactions in complex systems

The study of irreducible higher-order interactions has become a core topic of study in complex systems. Two of the most well-developed frameworks, topological data analysis and multivariate information theory, aim to provide formal tools for identifying higher-order interactions in empirical data. Despite similar aims, however, these two approaches are built on markedly different mathematical foundations and have been developed largely in parallel. In this study, we present a head-to-head comparison of topological data analysis and information-theoretic approaches to describing higher-order interactions in multivariate data; with the aim of assessing the similarities and differences between how the frameworks define ``higher-order structures." We begin with toy examples with known topologies, before turning to naturalistic data: fMRI signals collected from the human brain. We find that intrinsic, higher-order synergistic information is associated with three-dimensional cavities in a point cloud: shapes such as spheres are synergy-dominated. In fMRI data, we find strong correlations between synergistic information and both the number and size of three-dimensional cavities. Furthermore, we find that dimensionality reduction techniques such as PCA preferentially represent higher-order redundancies, and largely fail to preserve both higher-order information and topological structure, suggesting that common manifold-based approaches to studying high-dimensional data are systematically failing to identify important features of the data. These results point towards the possibility of developing a rich theory of higher-order interactions that spans topological and information-theoretic approaches while simultaneously highlighting the profound limitations of more conventional methods.

cs.IT↗
arXiv2025

Evolution of Adaptive Force Chains in Reconfigurable Granular Metamaterials

Under an externally applied load, granular packings form force chains that depend on the contact network and moduli of the grains. In this work, we investigate packings of variable modulus (VM) particles, where we can direct force chains by changing the Young's modulus of individual particles within the packing on demand. Each VM particle is made of a silicone shell that encapsulates a core made of a low-melting-point metallic alloy (Field's metal). By sending an electric current through a co-located copper heater, the Field's metal internal to each particle can be melted via Joule heating, which softens the particle. As the particle cools to room temperature, the alloy solidifies and the particle recovers its original modulus. To optimize the mechanical response of granular packings containing both soft and stiff particles, we employ an evolutionary algorithm coupled with discrete element method simulations to predict the patterns of particle moduli that will yield specific force outputs on the assembly boundaries. The predicted patterns of particle moduli from the simulations were realized in experiments using 2D assemblies of VM particles and the force outputs on the assembly boundaries were measured using photoelastic techniques. These studies represent a step towards making robotic granular metamaterials that can dynamically adapt their mechanical properties in response to different environmental conditions or perform specific tasks on demand.

cond-mat.soft↗
arXiv2024

Data-driven Modeling of Granular Chains with Modern Koopman Theory

Externally driven dense packings of particles can exhibit nonlinear wave phenomena that are not described by effective medium theory or linearized approximate models. Such nontrivial wave responses can be exploited to design sound-focusing/scrambling devices, acoustic filters, and analog computational units. At high amplitude vibrations or low confinement pressures, the effect of nonlinear particle contacts becomes increasingly noticeable, and the interplay of nonlinearity, disorder, and discreteness in the system gives rise to remarkable properties, particularly useful in designing structures with exotic properties. In this paper, we build upon the data-driven methods in dynamical system analysis and show that the Koopman spectral theory can be applied to granular crystals, enabling their phase space analysis beyond the linearizable regime and without recourse to any approximations considered in the previous works. We show that a deep neural network can map the dynamics to a latent space where the essential nonlinearity of the granular system unfolds into a high-dimensional linear space. As a proof of concept, we use data from numerical simulations of a two-particle system and evaluate the accuracy of the trajectory predictions under various initial conditions. By incorporating data from experimental measurements, our proposed framework can directly capture the underlying dynamics without imposing any assumptions about the physics model. Spectral analysis of the trained surrogate system can help bridge the gap between the simulation results and the physical realization of granular crystals and facilitate the inverse design of materials with desired behaviors.

cond-mat.soft↗
arXiv2024

Gradient-based Design of Computational Granular Crystals

There is growing interest in engineering unconventional computing devices that leverage the intrinsic dynamics of physical substrates to perform fast and energy-efficient computations. Granular metamaterials are one such substrate that has emerged as a promising platform for building wave-based information processing devices with the potential to integrate sensing, actuation, and computation. Their high-dimensional and nonlinear dynamics result in nontrivial and sometimes counter-intuitive wave responses that can be shaped by the material properties, geometry, and configuration of individual grains. Such highly tunable rich dynamics can be utilized for mechanical computing in special-purpose applications. However, there are currently no general frameworks for the inverse design of large-scale granular materials. Here, we build upon the similarity between the spatiotemporal dynamics of wave propagation in material and the computational dynamics of Recurrent Neural Networks to develop a gradient-based optimization framework for harmonically driven granular crystals. We showcase how our framework can be utilized to design basic logic gates where mechanical vibrations carry the information at predetermined frequencies. We compare our design methodology with classic gradient-free methods and find that our approach discovers higher-performing configurations with less computational effort. Our findings show that a gradient-based optimization method can greatly expand the design space of metamaterials and provide the opportunity to systematically traverse the parameter space to find materials with the desired functionalities.

cs.LG↗
arXiv2023

Efficient automatic design of robots

Robots are notoriously difficult to design because of complex interdependencies between their physical structure, sensory and motor layouts, and behavior. Despite this, almost every detail of every robot built to date has been manually determined by a human designer after several months or years of iterative ideation, prototyping, and testing. Inspired by evolutionary design in nature, the automated design of robots using evolutionary algorithms has been attempted for two decades, but it too remains inefficient: days of supercomputing are required to design robots in simulation that, when manufactured, exhibit desired behavior. Here we show for the first time de-novo optimization of a robot's structure to exhibit a desired behavior, within seconds on a single consumer-grade computer, and the manufactured robot's retention of that behavior. Unlike other gradient-based robot design methods, this algorithm does not presuppose any particular anatomical form; starting instead from a randomly-generated apodous body plan, it consistently discovers legged locomotion, the most efficient known form of terrestrial movement. If combined with automated fabrication and scaled up to more challenging tasks, this advance promises near instantaneous design, manufacture, and deployment of unique and useful machines for medical, environmental, vehicular, and space-based tasks.

cs.RO↗
arXiv2023

Universal Mechanical Polycomputation in Granular Matter

Unconventional computing devices are increasingly of interest as they can operate in environments hostile to silicon-based electronics, or compute in ways that traditional electronics cannot. Mechanical computers, wherein information processing is a material property emerging from the interaction of components with the environment, are one such class of devices. This information processing can be manifested in various physical substrates, one of which is granular matter. In a granular assembly, vibration can be treated as the information-bearing mode. This can be exploited to realize "polycomputing": materials can be evolved such that a single grain within them can report the result of multiple logical operations simultaneously at different frequencies, without recourse to quantum effects. Here, we demonstrate the evolution of a material in which one grain acts simultaneously as two different NAND gates at two different frequencies. NAND gates are of interest as any logical operations can be built from them. Moreover, they are nonlinear thus demonstrating a step toward general-purpose, computationally dense mechanical computers. Polycomputation was found to be distributed across each evolved material, suggesting the material's robustness. With recent advances in material sciences, hardware realization of these materials may eventually provide devices that challenge the computational density of traditional computers.

cs.ET↗
arXiv2023

Selection for short-term empowerment accelerates the evolution of homeostatic neural cellular automata

Empowerment -- a domain independent, information-theoretic metric -- has previously been shown to assist in the evolutionary search for neural cellular automata (NCA) capable of homeostasis when employed as a fitness function. In our previous study, we successfully extended empowerment, defined as maximum time-lagged mutual information between agents' actions and future sensations, to a distributed sensorimotor system embodied as an NCA. However, the time-delay between actions and their corresponding sensations was arbitrarily chosen. Here, we expand upon previous work by exploring how the time scale at which empowerment operates impacts its efficacy as an auxiliary objective to accelerate the discovery of homeostatic NCAs. We show that shorter time delays result in marked improvements over empowerment with longer delays, when compared to evolutionary selection only for homeostasis. Moreover, we evaluate stability and adaptability of evolved NCAs, both hallmarks of living systems that are of interest to replicate in artificial ones. We find that short-term empowered NCA are more stable and are capable of generalizing better to unseen homeostatic challenges. Taken together, these findings motivate the use of empowerment during the evolution of other artifacts, and suggest how it should be incorporated to accelerate evolution of desired behaviors for them. Source code for the experiments in this paper can be found at: https://github.com/caitlingrasso/empowered-nca-II.

cs.NE↗
arXiv2023

A soft robot that adapts to environments through shape change

Many organisms, including various species of spiders and caterpillars, change their shape to switch gaits and adapt to different environments. Recent technological advances, ranging from stretchable circuits to highly deformable soft robots, have begun to make shape-changing robots a possibility. However, it is currently unclear how and when shape change should occur, and what capabilities could be gained, leading to a wide range of unsolved design and control problems. To begin addressing these questions, here we simulate, design, and build a soft robot that utilizes shape change to achieve locomotion over both a flat and inclined surface. Modeling this robot in simulation, we explore its capabilities in two environments and demonstrate the existence of environment-specific shapes and gaits that successfully transfer to the physical hardware. We found that the shape-changing robot traverses these environments better than an equivalent but non-morphing robot, in simulation and reality.

cs.RO↗
arXiv2022

Evolving Programmable Computational Metamaterials

Granular metamaterials are a promising choice for the realization of mechanical computing devices. As preliminary evidence of this, we demonstrate here how to embed Boolean logic gates (AND and XOR) into a granular metamaterial by evolving where particular grains are placed in the material. Our results confirm the existence of gradients of increasing "AND-ness" and "XOR-ness" within the space of possible materials that can be followed by evolutionary search. We measure the computational functionality of a material by probing how it transforms bits encoded as vibrations with zero or non-zero amplitude. We compared the evolution of materials built from mass-contrasting particles and materials built from stiffness-contrasting particles, and found that the latter were more evolvable. We believe this work may pave the way toward evolutionary design of increasingly sophisticated, programmable, and computationally dense metamaterials with certain advantages over more traditional computational substrates.

cs.ET↗
arXiv2022

Selecting Continuous Life-Like Cellular Automata for Halting Unpredictability: Evolving for Abiogenesis

Substantial efforts have been applied to engineer CA with desired emergent properties, such as supporting gliders. Recent work in continuous CA has generated a wide variety of compelling bioreminiscent patterns, and the expansion of CA research into continuously-valued domains, multiple channels, and higher dimensions complicates their study. In this work we devise a strategy for evolving CA and CA patterns in two steps, based on the simple idea that CA are likely to be complex and computationally capable if they support patterns that grow indefinitely as well as patterns that vanish completely, and are difficult to predict the difference in advance. The second part of our strategy evolves patterns by selecting for mobility and conservation of mean cell value. We validate our pattern evolution method by re-discovering gliders in 17 of 17 Lenia CA, and also report 4 new evolved CA and 1 randomly evolved CA that support novel evolved glider patterns. The CA reported here share neighborhood kernels with previously described Lenia CA, but exhibit a wider range of typical dynamics than their Lenia counterparts. Code for evolving continuous CA is made available under an MIT License (https://github.com/rivesunder/yuca).

cs.NE↗