More Like this

1. Breaking reflection symmetry: evolving long dynamical cycles in Boolean systems

   https://doi.org/10.1088/1367-2630/ad1bdd  

   Ouellet, Mathieu; Kim, Jason Z.; Guillaume, Harmange; Shaffer, Sydney M.; Bassett, Lee C.; Bassett, Dani S. (February 2024, New Journal of Physics)

   Abstract In interacting dynamical systems, specific local interaction rules for system components give rise to diverse and complex global dynamics. Long dynamical cycles are a key feature of many natural interacting systems, especially in biology. Examples of dynamical cycles range from circadian rhythms regulating sleep to cell cycles regulating reproductive behavior. Despite the crucial role of cycles in nature, the properties of network structure that give rise to cycles still need to be better understood. Here, we use a Boolean interaction network model to study the relationships between network structure and cyclic dynamics. We identify particular structural motifs that support cycles, and other motifs that suppress them. More generally, we show that the presence ofdynamical reflection symmetryin the interaction network enhances cyclic behavior. In simulating an artificial evolutionary process, we find that motifs that break reflection symmetry are discarded. We further show that dynamical reflection symmetries are over-represented in Boolean models of natural biological systems. Altogether, our results demonstrate a link between symmetry and functionality for interacting dynamical systems, and they provide evidence for symmetry’s causal role in evolving dynamical functionality. 

   more » « less
2. Adjoint dynamics of stable limit cycle neural networks

   Sokol, P.; Jordan, I.; Kadile, E.; Park, I. M. (October 2019, Asilomar Conference on Signals, Systems and Computers)

   Exploding and vanishing gradient are both major problems often faced when an artificial neural network is trained with gradient descent. Inspired by the ubiquity and robustness of nonlinear oscillations in biological neural systems, we investigate the properties of their artificial counterpart, the stable limit cycle neural networks. Using a continuous time dynamical system interpretation of neural networks and backpropagation, we show that stable limit cycle neural networks have non-exploding gradients, and at least one effective non-vanishing gradient dimension. We conjecture that limit cycles can support the learning of long temporal dependence in both biological and artificial neural networks. 

   more » « less
3. Characterizing Distances of Networks on the Tensor Manifold

   https://doi.org/10.1007/978-3-030-36687-2_79  

   Islam, Bipul; Liu, Ji; Sandhu, Romeil (November 2019, International Conference on Complex Networks and Their Applications)

   At the core of understanding dynamical systems is the ability to maintain and control the systems behavior that includes notions of robustness, heterogeneity, and/or regime-shift detection. Recently, to explore such functional properties, a convenient representation has been to model such dynamical systems as a weighted graph consisting of a finite, but very large number of interacting agents. This said, there exists very limited relevant statistical theory that is able cope with real-life data, i.e., how does perform analysis and/or statistics over a “family” of networks as opposed to a specific network or network-to-network variation. Here, we are interested in the analysis of network families whereby each network represents a “point” on an underlying statistical manifold. To do so, we explore the Riemannian structure of the tensor manifold developed by Pennec previously applied to Diffusion Tensor Imaging (DTI) towards the problem of network analysis. In particular, while this note focuses on Pennec definition of “geodesics” amongst a family of networks, we show how it lays the foundation for future work for developing measures of network robustness for regime-shift detection. We conclude with experiments highlighting the proposed distance on synthetic networks and an application towards biological (stem-cell) systems. 

   more » « less
4. Merging dynamical and structural indicators to measure resilience in multispecies systems

   https://doi.org/10.1111/1365-2656.13421  

   Medeiros, Lucas P.; Song, Chuliang; Saavedra, Serguei (February 2021, Journal of Animal Ecology)

   Abstract Resilience is broadly understood as the ability of an ecological system to resist and recover from perturbations acting on species abundances and on the system's structure. However, one of the main problems in assessing resilience is to understand the extent to which measures of recovery and resistance provide complementary information about a system. While recovery from abundance perturbations has a strong tradition under the analysis of dynamical stability, it is unclear whether this same formalism can be used to measure resistance to structural perturbations (e.g. perturbations to model parameters).Here, we provide a framework grounded on dynamical and structural stability in Lotka–Volterra systems to link recovery from small perturbations on species abundances (i.e. dynamical indicators) with resistance to parameter perturbations of any magnitude (i.e. structural indicators). We use theoretical and experimental multispecies systems to show that the faster the recovery from abundance perturbations, the higher the resistance to parameter perturbations.We first use theoretical systems to show that the return rate along the slowest direction after a small random abundance perturbation (what we call full recovery) is negatively correlated with the largest random parameter perturbation that a system can withstand before losing any species (what we call full resistance). We also show that the return rate along the second fastest direction after a small random abundance perturbation (what we call partial recovery) is negatively correlated with the largest random parameter perturbation that a system can withstand before at most one species survives (what we call partial resistance). Then, we use a dataset of experimental microbial systems to confirm our theoretical expectations and to demonstrate that full and partial components of resilience are complementary.Our findings reveal that we can obtain the same level of information about resilience by measuring either a dynamical (i.e. recovery) or a structural (i.e. resistance) indicator. Irrespective of the chosen indicator (dynamical or structural), our results show that we can obtain additional information by separating the indicator into its full and partial components. We believe these results can motivate new theoretical approaches and empirical analyses to increase our understanding about risk in ecological systems. 

   more » « less
5. Neurodynamical Computing at the Information Boundaries of Intelligent Systems

   https://doi.org/10.1007/s12559-022-10081-9  

   Monaco, Joseph_D; Hwang, Grace_M (December 2022, Cognitive Computation)

   Abstract Artificial intelligence has not achieved defining features of biological intelligence despite models boasting more parameters than neurons in the human brain. In this perspective article, we synthesize historical approaches to understanding intelligent systems and argue that methodological and epistemic biases in these fields can be resolved by shifting away from cognitivist brain-as-computer theories and recognizing that brains exist within large, interdependent living systems. Integrating the dynamical systems view of cognition with the massive distributed feedback of perceptual control theory highlights a theoretical gap in our understanding of nonreductive neural mechanisms. Cell assemblies—properly conceived as reentrant dynamical flows and not merely as identified groups of neurons—may fill that gap by providing a minimal supraneuronal level of organization that establishes a neurodynamical base layer for computation. By considering information streams from physical embodiment and situational embedding, we discuss this computational base layer in terms of conserved oscillatory and structural properties of cortical-hippocampal networks. Our synthesis of embodied cognition, based in dynamical systems and perceptual control, aims to bypass the neurosymbolic stalemates that have arisen in artificial intelligence, cognitive science, and computational neuroscience. 

   more » « less