arXiv subjects

Bryan C. Daniels

Publications and source records attributed to Bryan C. Daniels.

At least 19 recordsLinked to original sources

arXiv2024

Difficult control is related to instability in biologically inspired Boolean networks

Previous work in Boolean dynamical networks has suggested that the number of components that must be controlled to select an existing attractor is typically set by the number of attractors admitted by the dynamics, with no dependence on the size of the network. Here we study the rare cases of networks that defy this expectation, with attractors that require controlling most nodes. We find empirically that unstable fixed points are the primary recurring characteristic of networks that prove more difficult to control. We describe an efficient way to identify unstable fixed points and show that, in both existing biological models and ensembles of random dynamics, we can better explain the variance of control kernel sizes by incorporating the prevalence of unstable fixed points. In the end, the association of these outliers with dynamics that are unstable to small perturbations reveals them as artifacts of deterministic models, making them less biologically relevant and reinforcing the generality of easy controllability in biological networks.

q-bio.MN↗

arXiv2024

Continuous Attractor Networks for Laplace Neural Manifolds

Many cognitive models, including those for predicting the time of future events, can be mapped onto a particular form of neural representation in which activity across a population of neurons is restricted to manifolds that specify the Laplace transform of functions of continuous variables. These populations coding Laplace transform are associated with another population that inverts the transform, approximating the original function. This paper presents a neural circuit that uses continuous attractor dynamics to represent the Laplace transform of a delta function evolving in time. One population places an edge at any location along a 1-D array of neurons; another population places a bump at a location corresponding to the edge. Together these two populations can estimate a Laplace transform of delta functions in time along with an approximate inverse transform. Building the circuit so the edge moves at an appropriate speed enables the network to represent events as a function of log time. Choosing the connections appropriately within the edge network make the network states map onto Laplace transform with exponential change as a function of time. In this paper we model a learned temporal association in which one stimulus predicts another at some fixed delay $T$. Shortly after $t=0$ the first stimulus recedes into the past. The Laplace Neural Manifold representing the past maintains the Laplace transform $\exp(-st)$. Another Laplace Neural Manifold represents the predicted future. At $t=0$, the second stimulus is represented a time $T$ in the future. At each moment between 0 and $T$, firing over the Laplace transform predicting the future changes as $\exp[-s(T-t)]$. Despite exponential growth in firing, the circuit is robust to noise, making it a practical means to implement Laplace Neural Manifolds in populations of neurons for a variety of cognitive models.

q-bio.NC↗

arXiv2022

Phase Transitions and Criticality in the Collective Behavior of Animals -- Self-organization and biological function

Collective behaviors exhibited by animal groups, such as fish schools, bird flocks, or insect swarms are fascinating examples of self-organization in biology. Concepts and methods from statistical physics have been used to argue theoretically about the potential consequences of collective effects in such living systems. In particular, it has been proposed that such collective systems should operate close to a phase transition, specifically a (pseudo-)critical point, in order to optimize their capability for collective computation. In this chapter, we will first review relevant phase transitions exhibited by animal collectives, pointing out the difficulties of applying concepts from statistical physics to biological systems. Then we will discuss the current state of research on the "criticality hypothesis", including methods for how to measure distance from criticality and specific functional consequences for animal groups operating near a phase transition. We will highlight the emerging view that de-emphasizes the optimality of being exactly at a critical point and instead explores the potential benefits of living systems being able to tune to an optimal distance from criticality. We will close by laying out future challenges for studying collective behavior at the interface of physics and biology.

physics.bio-ph↗

arXiv2021

The basis of easy controllability in Boolean networks

Effective control of biological systems can often be achieved through the control of a surprisingly small number of distinct variables. We bring clarity to such results using the formalism of Boolean dynamical networks, analyzing the effectiveness of external control in selecting a desired final state when that state is among the original attractors of the dynamics. Analyzing 49 existing biological network models, we find strong numerical evidence that the average number of nodes that must be forced scales logarithmically with the number of original attractors. This suggests that biological networks may be typically easy to control even when the number of interacting components is large. We provide a theoretical explanation of the scaling by separating controlling nodes into three types: those that act as inputs, those that distinguish among attractors, and any remaining nodes. We further identify characteristics of dynamics that can invalidate this scaling, and speculate about how this relates more broadly to non-biological systems.

q-bio.MN↗

arXiv2021

Subcritical escape waves in schooling fish

Living systems such as neuronal networks and animal groups process information about their environment via the dynamics of interacting units. These can transition between distinct macroscopic behaviors. Near such a transition (or critical point) collective computation is generally thought to be optimized, due to the associated maximal sensitivity to perturbations and fast dissemination of information. For biological systems, however, optimality depends on environmental context, making the flexible, context-dependent adoption of different distances to a critical point potentially more beneficial than its unique properties. Here, studying escape waves in schooling fish at two levels of perceived environmental risk, we investigate a) if and how distance to criticality is regulated in response to environmental changes and b) how the individual level benefits derived from special properties of the critical point compare to those achieved via regulation of the group's distance to it. We find that the observed fish schools are subcritical (not maximally responsive and sensitive to environmental cues), but decrease their distance to criticality with increased perceived risk. Considering an individual's hypothetical costs of two detection error types, we find that optimal distance to criticality depends on the riskiness and noisiness of the environment, which may explain the observed behavior. Our results highlight the benefit of evaluating biological consequences of different distances to criticality for individuals within animal collectives. This provides insights into the adaptive function of a collective system and motivates future questions about the evolutionary forces that brought the system to make this particular trade-off.

physics.bio-ph↗

arXiv2021

Discovering sparse control strategies in C. elegans

Biological circuits such as neural or gene regulation networks use internal states to map sensory input to an adaptive repertoire of behavior. Characterizing this mapping is a major challenge for systems biology, and though experiments that probe internal states are developing rapidly, organismal complexity presents a fundamental obstacle given the many possible ways internal states could map to behavior. Using C. elegans as an example, we propose a protocol for systematic perturbation of neural states that limits experimental complexity but still characterizes collective aspects of the neural-behavioral map. We consider experimentally motivated small perturbations -- ones that are most likely to preserve natural dynamics and are closer to internal control mechanisms -- to neural states and their impact on collective neural behavior. Then, we connect such perturbations to the local information geometry of collective statistics, which can be fully characterized using pairwise perturbations. Applying the protocol to a minimal model of C. elegans neural activity, we find that collective neural statistics are most sensitive to a few principal perturbative modes. Dominant eigenvalues decay initially as a power law, unveiling a hierarchy that arises from variation in individual neural activity and pairwise interactions. Highest-ranking modes tend to be dominated by a few, "pivotal" neurons that account for most of the system's sensitivity, suggesting a sparse mechanism for control of collective behavior.

q-bio.NC↗

arXiv2020

Quantifying dynamical high-order interdependencies from the O-information: an application to neural spiking dynamics

We address the problem of efficiently and informatively quantifying how multiplets of variables carry information about the future of the dynamical system they belong to. In particular we want to identify groups of variables carrying redundant or synergistic information, and track how the size and the composition of these multiplets changes as the collective behavior of the system evolves. In order to afford a parsimonious expansion of shared information, and at the same time control for lagged interactions and common effect, we develop a dynamical, conditioned version of the O-information, a framework recently proposed to quantify high-order interdependencies via multivariate extension of the mutual information. We thus obtain an expansion of the transfer entropy in which synergistic and redundant effects are separated. We apply this framework to a dataset of spiking neurons from a monkey performing a perceptual discrimination task. The method identifies synergistic multiplets that include neurons previously categorized as containing little relevant information individually.

q-bio.NC↗

arXiv2020

Emergent regularities and scaling in armed conflict data

Armed conflict exhibits regularities beyond known power law distributions of fatalities and duration over varying culture and geography. We systematically cluster conflict reports from a database of $10^5$ events from Africa spanning 20 years into conflict avalanches. Conflict profiles collapse over a range of scales. Duration, diameter, extent, fatalities, and report totals satisfy mutually consistent scaling relations captured with a model combining geographic spread and local conflict-site growth. The emergence of such social scaling laws hints at principles guiding conflict evolution.

physics.soc-ph↗

arXiv2020

A scaling theory of armed conflict avalanches

Armed conflict data display scaling and universal dynamics in both social and physical properties like fatalities and geographic extent. We propose a randomly branching, armed-conflict model that relates multiple properties to one another in a way consistent with data. The model incorporates a fractal lattice on which conflict spreads, uniform dynamics driving conflict growth, and regional virulence that modulates local conflict intensity. The quantitative constraints on scaling and universal dynamics we use to develop our minimal model serve more generally as a set of constraints for other models for armed conflict dynamics. We show how this approach akin to thermodynamics imparts mechanistic intuition and unifies multiple conflict properties, giving insight into causation, prediction, and intervention timing.

physics.soc-ph↗

arXiv2019

Quantifying the impact of network structure on speed and accuracy in collective decision-making

Found in varied contexts from neurons to ants to fish, binary decision-making is one of the simplest forms of collective computation. In this process, information collected by individuals about an uncertain environment is accumulated to guide behavior at the aggregate scale. We study binary decision-making dynamics in networks responding to inputs with small signal-to-noise ratios, looking for quantitative measures of collectivity that control decision-making performance. We find that decision accuracy is controlled largely by three factors: the leading eigenvalue of the network adjacency matrix, the corresponding eigenvector's participation ratio, and distance from the corresponding symmetry-breaking bifurcation. This allows us to predict how decision-making performance scales in large networks based on their spectral properties. Specifically, we explore the effects of localization caused by the hierarchical assortative structure of a "rich club" topology. This gives insight into the tradeoffs involved in the higher-order structure found in living networks performing collective computations.

q-bio.NC↗

arXiv2018

Automated, predictive, and interpretable inference of C. elegans escape dynamics

The roundworm C. elegans exhibits robust escape behavior in response to rapidly rising temperature. The behavior lasts for a few seconds, shows history dependence, involves both sensory and motor systems, and is too complicated to model mechanistically using currently available knowledge. Instead we model the process phenomenologically, and we use the Sir Isaac dynamical inference platform to infer the model in a fully automated fashion directly from experimental data. The inferred model requires incorporation of an unobserved dynamical variable, and is biologically interpretable. The model makes accurate predictions about the dynamics of the worm behavior, and it can be used to characterize the functional logic of the dynamical system underlying the escape response. This work illustrates the power of modern artificial intelligence to aid in discovery of accurate and interpretable models of complex natural systems.

q-bio.NC↗

arXiv2018

Logic and connectivity jointly determine criticality in biological gene regulatory networks

The complex dynamics of gene expression in living cells can be well-approximated using Boolean networks. The average sensitivity is a natural measure of stability in these systems: values below one indicate typically stable dynamics associated with an ordered phase, whereas values above one indicate chaotic dynamics. This yields a theoretically motivated adaptive advantage to being near the critical value of one, at the boundary between order and chaos. Here, we measure average sensitivity for 66 publicly available Boolean network models describing the function of gene regulatory circuits across diverse living processes. We find the average sensitivity values for these networks are clustered around unity, indicating they are near critical. In many types of random networks, mean connectivity and the average activity bias of the logic functions have been found to be the most important network properties in determining average sensitivity, and by extension a network's criticality. Surprisingly, many of these gene regulatory networks achieve the near-critical state with and far from that predicted for critical systems: randomized networks sharing the local causal structure and local logic of biological networks better reproduce their critical behavior than controlling for macroscale properties such as and alone. This suggests the local properties of genes interacting within regulatory networks are selected to collectively be near-critical, and this non-local property of gene regulatory network dynamics cannot be predicted using the density of interactions alone.

q-bio.MN↗

arXiv2016

Control of critical behavior in a small-scale social system

Over the last decade new technologies for making large numbers of fine-grained measurements have led to the surprising discovery that many biological systems sit near a critical point. These systems are potentially more adaptive in that small changes to component behavior can induce large-scale changes in aggregate structure and function. Accounting for criticality remains a challenge as sensitivity to perturbation suggests a lack of robustness. Furthermore, change induced by perturbation may not be adaptive. Complicating matters further critical phenomena can result from history-dependent stochastic processes. A question central to distinguishing among these conflicting views of criticality is to what degree criticality can be controlled by the components of the system. We address the control of criticality using data on conflict dynamics and fight sizes from an animal society model system (Macaca nemestrina, n=48). The system is fundamentally finite so we operationalize criticality in information theoretic terms using Fisher information and a measure of instability. We analyze criticality using empirically-grounded equilibrium (maximum entropy) and dynamic (branching process) models of the monkeys' fight-joining behavior. We find that (1) this heterogeneous, socially organized system, like homogeneous, spatial systems (flocks and schools), sits near a critical point, (2) the contributions individuals make to how critical the system is can be quantified and vary, and (3) the distance from the critical point (DFC) can be controlled through biologically plausible mechanisms operating on this heterogeneity. These mechanisms include third-party policing, which dampens fight participation of the individuals with the largest effect on DFC. Control of DFC allows biological systems to balance the tradeoff between robustness and need for rapid change.

physics.soc-ph↗

arXiv2015

Sloppiness and Emergent Theories in Physics, Biology, and Beyond

Large scale models of physical phenomena demand the development of new statistical and computational tools in order to be effective. Many such models are `sloppy', i.e., exhibit behavior controlled by a relatively small number of parameter combinations. We review an information theoretic framework for analyzing sloppy models. This formalism is based on the Fisher Information Matrix, which we interpret as a Riemannian metric on a parameterized space of models. Distance in this space is a measure of how distinguishable two models are based on their predictions. Sloppy model manifolds are bounded with a hierarchy of widths and extrinsic curvatures. We show how the manifold boundary approximation can extract the simple, hidden theory from complicated sloppy models. We attribute the success of simple effective models in physics as likewise emerging from complicated processes exhibiting a low effective dimensionality. We discuss the ramifications and consequences of sloppy models for biochemistry and science more generally. We suggest that the reason our complex world is understandable is due to the same fundamental reason: simple theories of macroscopic behavior are hidden inside complicated microscopic processes.

cond-mat.stat-mech↗

arXiv2014

Efficient inference of parsimonious phenomenological models of cellular dynamics using S-systems and alternating regression

The nonlinearity of dynamics in systems biology makes it hard to infer them from experimental data. Simple linear models are computationally efficient, but cannot incorporate these important nonlinearities. An adaptive method based on the S-system formalism, which is a sensible representation of nonlinear mass-action kinetics typically found in cellular dynamics, maintains the efficiency of linear regression. We combine this approach with adaptive model selection to obtain efficient and parsimonious representations of cellular dynamics. The approach is tested by inferring the dynamics of yeast glycolysis from simulated data. With little computing time, it produces dynamical models with high predictive power and with structural complexity adapted to the difficulty of the inference problem.

q-bio.QM↗

arXiv2014

Automated adaptive inference of coarse-grained dynamical models in systems biology

Cellular regulatory dynamics is driven by large and intricate networks of interactions at the molecular scale, whose sheer size obfuscates understanding. In light of limited experimental data, many parameters of such dynamics are unknown, and thus models built on the detailed, mechanistic viewpoint overfit and are not predictive. At the other extreme, simple ad hoc models of complex processes often miss defining features of the underlying systems. Here we propose an approach that instead constructs phenomenological, coarse-grained models of network dynamics that automatically adapt their complexity to the amount of available data. Such adaptive models lead to accurate predictions even when microscopic details of the studied systems are unknown due to insufficient data. The approach is computationally tractable, even for a relatively large number of dynamical variables, allowing its software realization, named Sir Isaac, to make successful predictions even when important dynamic variables are unobserved. For example, it matches the known phase space structure for simulated planetary motion data, avoids overfitting in a complex biological signaling system, and produces accurate predictions for a yeast glycolysis model with only tens of data points and over half of the interacting species unobserved.

q-bio.QM↗

arXiv2011

Nucleation at the DNA supercoiling transition

Twisting DNA under a constant applied force reveals a thermally activated transition into a state with a supercoiled structure known as a plectoneme. Using transition state theory, we predict the rate of this plectoneme nucleation to be of order 10^4 Hz. We reconcile this with experiments that have measured hopping rates of order 10 Hz by noting that the viscosity of the bead used to manipulate the DNA limits the measured rate. We find that the intrinsic bending caused by disorder in the base-pair sequence is important for understanding the free energy barrier that governs the transition. Both analytic and numerical methods are used in the calculations. We provide extensive details on the numerical methods for simulating the elastic rod model with and without disorder.

physics.bio-ph↗

arXiv2009

Discontinuities at the DNA supercoiling transition

While slowly turning the ends of a single molecule of DNA at constant applied force, a discontinuity was recently observed at the supercoiling transition, when a small plectoneme is suddenly formed. This can be understood as an abrupt transition into a state in which stretched and plectonemic DNA coexist. We argue that there should be discontinuities in both the extension and the torque at the transition, and provide experimental evidence for both. To predict the sizes of these discontinuities and how they change with the overall length of DNA, we organize a theory for the coexisting plectonemic state in terms of four length-independent parameters. We also test plectoneme theories, including our own elastic rod simulation, finding discrepancies with experiment that can be understood in terms of the four coexisting state parameters.

q-bio.BM↗