Rate-induced tipping in complex high-dimensional ecological networks.

In an ecosystem, environmental changes as a result of natural and human processes can cause some key parameters of the system to change with time. Depending on how fast such a parameter changes, a tipping point can occur. Existing works on rate-induced tipping, or R-tipping, offered a theoretical way to study this phenomenon but from a local dynamical point of view, revealing, e.g., the existence of a critical rate for some specific initial condition above which a tipping point will occur. As ecosystems are subject to constant disturbances and can drift away from their equilibrium point, it is necessary to study R-tipping from a global perspective in terms of the initial conditions in the entire relevant phase space region. In particular, we introduce the notion of the probability of R-tipping defined for initial conditions taken from the whole relevant phase space. Using a number of real-world, complex mutualistic networks as a paradigm, we find a scaling law between this probability and the rate of parameter change and provide a geometric theory to explain the law. The real-world implication is that even a slow parameter change can lead to a system collapse with catastrophic consequences. In fact, to mitigate the environmental changes by merely slowing down the parameter drift may not always be effective: Only when the rate of parameter change is reduced to practically zero would the tipping be avoided. Our global dynamics approach offers a more complete and physically meaningful way to understand the important phenomenon of R-tipping.

Folding State within a Hysteresis Loop: Hidden Multistability in Nonlinear Physical Systems.

Identifying hidden states in nonlinear physical systems that evade direct experimental detection is important as disturbances and noises can place the system in a hidden state with detrimental consequences. We study a cavity magnonic system whose main physics is photon and magnon Kerr effects. Sweeping a bifurcation parameter in numerical experiments (as would be done in actual experiments) leads to a hysteresis loop with two distinct stable steady states, but analytic calculation gives a third folded steady state "hidden" in the loop, which gives rise to the phenomenon of hidden multistability. We propose an experimentally feasible control method to drive the system into the folded hidden state. We demonstrate, through a ternary cavity magnonic system and a gene regulatory network, that such hidden multistability is in fact quite common. Our findings shed light on hidden dynamical states in nonlinear physical systems which are not directly observable but can present challenges and opportunities in applications.

Adaptable reservoir computing: A paradigm for model-free data-driven prediction of critical transitions in nonlinear dynamical systems.

A problem in nonlinear and complex dynamical systems with broad applications is forecasting the occurrence of a critical transition based solely on data without knowledge about the system equations. When such a transition leads to system collapse, as often is the case, all the available data are from the pre-critical regime where the system still functions normally, making the prediction problem challenging. In recent years, a machine-learning based approach tailored to solving this difficult prediction problem, adaptable reservoir computing, has been articulated. This Perspective introduces the basics of this machine-learning scheme and describes representative results. The general setting is that the system dynamics live on a normal attractor with oscillatory dynamics at the present time and, as a bifurcation parameter changes into the future, a critical transition can occur after which the system switches to a completely different attractor, signifying system collapse. To predict a critical transition, it is essential that the reservoir computer not only learns the dynamical "climate" of the system of interest at some specific parameter value but, more importantly, discovers how the system dynamics changes with the bifurcation parameter. It is demonstrated that this capability can be endowed into the machine through a training process with time series from a small number of distinct, pre-critical parameter values, thereby enabling accurate and reliable prediction of the catastrophic critical transition. Three applications are presented: predicting crisis, forecasting amplitude death, and creating digital twins of nonlinear dynamical systems. Limitations and future perspectives are discussed.

Deep-learning reconstruction of complex dynamical networks from incomplete data.

Reconstructing complex networks and predicting the dynamics are particularly challenging in real-world applications because the available information and data are incomplete. We develop a unified collaborative deep-learning framework consisting of three modules: network inference, state estimation, and dynamical learning. The complete network structure is first inferred and the states of the unobserved nodes are estimated, based on which the dynamical learning module is activated to determine the dynamical evolution rules. An alternating parameter updating strategy is deployed to improve the inference and prediction accuracy. Our framework outperforms baseline methods for synthetic and empirical networks hosting a variety of dynamical processes. A reciprocity emerges between network inference and dynamical prediction: better inference of network structure improves the accuracy of dynamical prediction, and vice versa. We demonstrate the superior performance of our framework on an influenza dataset consisting of 37 US States and a PM2.5 dataset covering 184 cities in China.

Short-lived chimera states.

In the classic Kuramoto system of coupled two-dimensional rotators, chimera states characterized by the coexistence of synchronous and asynchronous groups of oscillators are long-lived because the average lifetime of these states increases exponentially with the system size. Recently, it was discovered that, when the rotators in the Kuramoto model are three-dimensional, the chimera states become short-lived in the sense that their lifetime scales with only the logarithm of the dimension-augmenting perturbation. We introduce transverse-stability analysis to understand the short-lived chimera states. In particular, on the unit sphere representing three-dimensional (3D) rotations, the long-lived chimera states in the classic Kuramoto system occur on the equator, to which latitudinal perturbations that make the rotations 3D are transverse. We demonstrate that the largest transverse Lyapunov exponent calculated with respect to these long-lived chimera states is typically positive, making them short-lived. The transverse-stability analysis turns the previous numerical scaling law of the transient lifetime into an exact formula: the "free" proportional constant in the original scaling law can now be precisely determined in terms of the largest transverse Lyapunov exponent. Our analysis reinforces the speculation that in physical systems, chimera states can be short-lived as they are vulnerable to any perturbations that have a component transverse to the invariant subspace in which they live.

Reservoir computing as digital twins for nonlinear dynamical systems.

We articulate the design imperatives for machine learning based digital twins for nonlinear dynamical systems, which can be used to monitor the "health" of the system and anticipate future collapse. The fundamental requirement for digital twins of nonlinear dynamical systems is dynamical evolution: the digital twin must be able to evolve its dynamical state at the present time to the next time step without further state input-a requirement that reservoir computing naturally meets. We conduct extensive tests using prototypical systems from optics, ecology, and climate, where the respective specific examples are a chaotic CO2 laser system, a model of phytoplankton subject to seasonality, and the Lorenz-96 climate network. We demonstrate that, with a single or parallel reservoir computer, the digital twins are capable of a variety of challenging forecasting and monitoring tasks. Our digital twin has the following capabilities: (1) extrapolating the dynamics of the target system to predict how it may respond to a changing dynamical environment, e.g., a driving signal that it has never experienced before, (2) making continual forecasting and monitoring with sparse real-time updates under non-stationary external driving, (3) inferring hidden variables in the target system and accurately reproducing/predicting their dynamical evolution, (4) adapting to external driving of different waveform, and (5) extrapolating the global bifurcation behaviors to network systems of different sizes. These features make our digital twins appealing in applications, such as monitoring the health of critical systems and forecasting their potential collapse induced by environmental changes or perturbations. Such systems can be an infrastructure, an ecosystem, or a regional climate system.

Metamorphoses and explosively remote synchronization in dynamical networks.

We uncover a phenomenon in coupled nonlinear networks with a symmetry: as a bifurcation parameter changes through a critical value, synchronization among a subset of nodes can deteriorate abruptly, and, simultaneously, perfect synchronization emerges suddenly among a different subset of nodes that are not directly connected. This is a synchronization metamorphosis leading to an explosive transition to remote synchronization. The finding demonstrates that an explosive onset of synchrony and remote synchronization, two phenomena that have been studied separately, can arise in the same system due to symmetry, providing another proof that the interplay between nonlinear dynamics and symmetry can lead to a surprising phenomenon in physical systems.

Structural position vectors and symmetries in complex networks.

Symmetries, due to their fundamental importance to dynamical processes on networks, have attracted a great deal of current research. Finding all symmetric nodes in large complex networks typically relies on automorphism groups from algebraic-group theory, which are solvable in quasipolynomial time. We articulate a conceptually appealing and computationally extremely efficient approach to finding and characterizing all symmetric nodes by introducing a structural position vector (SPV) for each node in networks. We establish the mathematical result that symmetric nodes must have the same SPV value and demonstrate, using six representative complex networks from the real world, that all symmetric nodes in these networks can be found in linear time. Furthermore, the SPVs not only characterize the similarity of nodes but also quantify the nodal influences in propagation dynamics. A caveat is that the proved mathematical result relating the SPV values to nodal symmetries is not sufficient; i.e., nodes having the same SPV values may not be symmetric, which arises in regular networks or networks with a dominant regular component. We point out with an analysis that this caveat is, in fact, shared by the known existing approaches to finding symmetric nodes in the literature. We further argue, with the aid of a mathematical analysis, that our SPV method is generally effective for finding the symmetric nodes in real-world networks that typically do not have a dominant regular component. Our SPV-based framework, therefore, provides a physically intuitive and computationally efficient way to uncover, understand, and exploit symmetric structures in complex networks arising from real-world applications.

Beyond Boolean: Ternary networks and dynamics.

Boolean networks introduced by Kauffman, originally intended as a prototypical model for gaining insights into gene regulatory dynamics, have become a paradigm for understanding a variety of complex systems described by binary state variables. However, there are situations, e.g., in biology, where a binary state description of the underlying dynamical system is inadequate. We propose random ternary networks and investigate the general dynamical properties associated with the ternary discretization of the variables. We find that the ternary dynamics can be either ordered or disordered with a positive Lyapunov exponent, and the boundary between them in the parameter space can be determined analytically. A dynamical event that is key to determining the boundary is the emergence of an additional fixed point for which we provide numerical verification. We also find that the nodes playing a pivotal role in shaping the system dynamics have characteristically distinct behaviors in different regions of the parameter space, and, remarkably, the boundary between these regions coincides with that separating the ordered and disordered dynamics. Overall, our framework of ternary networks significantly broadens the classical Boolean paradigm by enabling a quantitative description of richer and more complex dynamical behaviors.

Spin Fano Resonances in Chiral Molecules: An Alternative Mechanism for the CISS Effect and Experimental Implications.

Experiments on spin transport through a chiral molecule demonstrated the attainment of significant spin polarization, demanding a theoretical explanation. We report the emergence of spin Fano resonances as a mechanism in the chiral-induced spin-selectivity (CISS) effect associated with transport through a chiral polyacetylene molecule. Initializing electrons through optical excitation, we derive the Fano resonance formula for the spin polarization. Computations reveal that quasidegeneracy is common in this complex molecular system. A remarkable phenomenon is the generation of pronounced spin Fano resonances due to the contributions of two near-degeneracy states. We also find that the Fano resonance width increases linearly with the coupling strength between the molecule and the lead. Our findings provide another mechanism to explain the experimental observations and lead to new insights into the role of the CISS effect in complex molecules from the perspective of transport and spin polarization resonance, paving the way for chiral molecule-based spintronics applications.

Detecting the causal influence of thermal environments among climate regions in the United States.

The quantification of cross-regional interactions for the atmospheric transport processes is of crucial importance to improve the predictive capacity of climatic and environmental system modeling. The dynamic interactions in these complex systems are often nonlinear and non-separable, making conventional approaches of causal inference, such as statistical correlation or Granger causality, infeasible or ineffective. In this study, we applied an advanced approach, based on the convergent cross mapping algorithm, to detect and quantify the causal influence among different climate regions in the contiguous U.S. in response to temperature perturbations using the long-term (1901-2018) climatology of near surface air temperature record. Our results show that the directed causal network constructed by convergent cross mapping algorithm, enables us to distinguish the causal links from spurious ones rendered by statistical correlation. We also find that the Ohio Valley region, as an atmospheric convergent zone, acts as the regional gateway and mediator to the long-term thermal environments in the U.S. In addition, the temporal evolution of dynamic causality of temperature exhibits superposition of periodicities at various time scales, highlighting the impact of prominent low frequency climate variabilities such as El Niño-Southern Oscillation. The proposed method in this work will help to promote novel system-based and data-driven framework in studying the integrated environmental system dynamics.

Dynamical network analysis reveals key microRNAs in progressive stages of lung cancer.

Non-coding RNAs are fundamental to the competing endogenous RNA (CeRNA) hypothesis in oncology. Previous work focused on static CeRNA networks. We construct and analyze CeRNA networks for four sequential stages of lung adenocarcinoma (LUAD) based on multi-omics data of long non-coding RNAs (lncRNAs), microRNAs and mRNAs. We find that the networks possess a two-level bipartite structure: common competing endogenous network (CCEN) composed of an invariant set of microRNAs over all the stages and stage-dependent, unique competing endogenous networks (UCENs). A systematic enrichment analysis of the pathways of the mRNAs in CCEN reveals that they are strongly associated with cancer development. We also find that the microRNA-linked mRNAs from UCENs have a higher enrichment efficiency. A key finding is six microRNAs from CCEN that impact patient survival at all stages, and four microRNAs that affect the survival from a specific stage. The ten microRNAs can then serve as potential biomarkers and prognostic tools for LUAD.

Predicting tipping points in mutualistic networks through dimension reduction.

Complex networked systems ranging from ecosystems and the climate to economic, social, and infrastructure systems can exhibit a tipping point (a "point of no return") at which a total collapse of the system occurs. To understand the dynamical mechanism of a tipping point and to predict its occurrence as a system parameter varies are of uttermost importance, tasks that are hindered by the often extremely high dimensionality of the underlying system. Using complex mutualistic networks in ecology as a prototype class of systems, we carry out a dimension reduction process to arrive at an effective 2D system with the two dynamical variables corresponding to the average pollinator and plant abundances. We show, using 59 empirical mutualistic networks extracted from real data, that our 2D model can accurately predict the occurrence of a tipping point, even in the presence of stochastic disturbances. We also find that, because of the lack of sufficient randomness in the structure of the real networks, weighted averaging is necessary in the dimension reduction process. Our reduced model can serve as a paradigm for understanding and predicting the tipping point dynamics in real world mutualistic networks for safeguarding pollinators, and the general principle can be extended to a broad range of disciplines to address the issues of resilience and sustainability.

Finding nonlinear system equations and complex network structures from data: A sparse optimization approach.

In applications of nonlinear and complex dynamical systems, a common situation is that the system can be measured, but its structure and the detailed rules of dynamical evolution are unknown. The inverse problem is to determine the system equations and structure from time series. The principle of exploiting sparse optimization to find the equations of dynamical systems from data was first articulated in 2011 by the ASU group. The basic idea is to expand the system equations into a power series or a Fourier series of a finite number of terms and then to determine the vector of the expansion coefficients based solely on data through sparse optimization. This Tutorial presents a brief review of the recent progress in this area. Issues discussed include discovering the equations of stationary or nonstationary chaotic systems to enable the prediction of critical transition and system collapse, inferring the full topology of complex oscillator networks and social networks hosting evolutionary game dynamics, and identifying partial differential equations for spatiotemporal dynamical systems. Situations where sparse optimization works or fails are pointed out. The relation with the traditional delay-coordinate embedding method is discussed, and the recent development of a model-free, data-driven prediction framework based on machine learning is mentioned.

Controlled generation of self-sustained oscillations in complex artificial neural networks.

Spatially distinct, self-sustained oscillations in artificial neural networks are fundamental to information encoding, storage, and processing in these systems. Here, we develop a method to induce a large variety of self-sustained oscillatory patterns in artificial neural networks and a controlling strategy to switch between different patterns. The basic principle is that, given a complex network, one can find a set of nodes-the minimum feedback vertex set (mFVS), whose removal or inhibition will result in a tree-like network without any loop structure. Reintroducing a few or even a single mFVS node into the tree-like artificial neural network can recover one or a few of the loops and lead to self-sustained oscillation patterns based on these loops. Reactivating various mFVS nodes or their combinations can then generate a large number of distinct neuronal firing patterns with a broad distribution of the oscillation period. When the system is near a critical state, chaos can arise, providing a natural platform for pattern switching with remarkable flexibility. With mFVS guided control, complex networks of artificial neurons can thus be exploited as potential prototypes for local, analog type of processing paradigms.

Predicting phase and sensing phase coherence in chaotic systems with machine learning.

Recent interest in exploiting machine learning for model-free prediction of chaotic systems focused on the time evolution of the dynamical variables of the system as a whole, which include both amplitude and phase. In particular, in the framework based on reservoir computing, the prediction horizon as determined by the largest Lyapunov exponent is often short, typically about five or six Lyapunov times that contain approximately equal number of oscillation cycles of the system. There are situations in the real world where the phase information is important, such as the ups and downs of species populations in ecology, the polarity of a voltage variable in an electronic circuit, and the concentration of certain chemical above or below the average. Using classic chaotic oscillators and a chaotic food-web system from ecology as examples, we demonstrate that reservoir computing can be exploited for long-term prediction of the phase of chaotic oscillators. The typical prediction horizon can be orders of magnitude longer than that with predicting the entire variable, for which we provide a physical understanding. We also demonstrate that a properly designed reservoir computing machine can reliably sense phase synchronization between a pair of coupled chaotic oscillators with implications to the design of the parallel reservoir scheme for predicting large chaotic systems.

A network approach to quantifying radiotherapy effect on cancer: Radiosensitive gene group centrality.

Radiotherapy plays a vital role in cancer treatment, for which accurate prognosis is important for guiding sequential treatment and improving the curative effect for patients. An issue of great significance in radiotherapy is to assess tumor radiosensitivity for devising the optimal treatment strategy. Previous studies focused on gene expression in cells closely associated with radiosensitivity, but factors such as the response of a cancer patient to irradiation and the patient survival time are largely ignored. For clinical cancer treatment, a specific pre-treatment indicator taking into account cancer cell type and patient radiosensitivity is of great value but it has been missing. Here, we propose an effective indicator for radiosensitivity: radiosensitive gene group centrality (RSGGC), which characterizes the importance of the group of genes that are radiosensitive in the whole gene correlation network. We demonstrate, using both clinical patient data and experimental cancer cell lines, which RSGGC can provide a quantitative estimate of the effect of radiotherapy, with factors such as the patient survival time and the survived fraction of cancer cell lines under radiotherapy fully taken into account. Our main finding is that, for patients with a higher RSGGC score before radiotherapy, cancer treatment tends to be more effective. The RSGGC can have significant applications in clinical prognosis, serving as a key measure to classifying radiosensitive and radioresistant patients.

A model for meme popularity growth in social networking systems based on biological principle and human interest dynamics.

We analyze five big data sets from a variety of online social networking (OSN) systems and find that the growth dynamics of meme popularity exhibit characteristically different behaviors. For example, there is linear growth associated with online recommendation and sharing platforms, a plateaued (or an "S"-shape) type of growth behavior in a web service devoted to helping users to collect bookmarks, and an exponential increase on the largest and most popular microblogging website in China. Does a universal mechanism with a common set of dynamical rules exist, which can explain these empirically observed, distinct growth behaviors? We provide an affirmative answer in this paper. In particular, inspired by biomimicry to take advantage of cell population growth dynamics in microbial ecology, we construct a base growth model for meme popularity in OSNs. We then take into account human factors by incorporating a general model of human interest dynamics into the base model. The final hybrid model contains a small number of free parameters that can be estimated purely from data. We demonstrate that our model is universal in the sense that, with a few parameters estimated from data, it can successfully predict the distinct meme growth dynamics. Our study represents a successful effort to exploit principles in biology to understand online social behaviors by incorporating the traditional microbial growth model into meme popularity. Our model can be used to gain insights into critical issues such as classification, robustness, optimization, and control of OSN systems.

Quantitative assessment of cerebral connectivity deficiency and cognitive impairment in children with prenatal alcohol exposure.

It is common knowledge that alcohol consumption during pregnancy would cause cognitive impairment in children. However, recent works suggested that the risk of drinking during pregnancy may have been exaggerated. It is critical to determine whether and up to which amount the consumption of alcohol will affect the cognitive development of children. We evaluate time-varying functional connectivity using magnetoencephalogram data from somatosensory evoked response experiments for 19 teenage subjects with prenatal alcohol exposure and 21 healthy control teenage subjects using a new time-varying connectivity approach, combining renormalised partial directed coherence with state space modeling. Children exposed to alcohol prenatally are at risk of developing a Fetal Alcohol Spectrum Disorder (FASD) characterized by cerebral connectivity deficiency and impaired cognitive abilities. Through a comparison study of teenage subjects exposed to alcohol prenatally with healthy control subjects, we establish that the inter-hemispheric connectivity is deficient for the former, which may lead to disruption in the cortical inter-hemispheric connectivity and deficits in higher order cognitive functions as measured by an IQ test, for example. We provide quantitative evidence that the disruption is correlated with cognitive deficits. These findings could lead to a novel, highly sensitive biomarker for FASD and support a recommendation of no safe amount of alcohol consumption during pregnancy.

Chaos in Dirac Electron Optics: Emergence of a Relativistic Quantum Chimera.

We uncover a remarkable quantum scattering phenomenon in two-dimensional Dirac material systems where the manifestations of both classically integrable and chaotic dynamics emerge simultaneously and are electrically controllable. The distinct relativistic quantum fingerprints associated with different electron spin states are due to a physical mechanism analogous to a chiroptical effect in the presence of degeneracy breaking. The phenomenon mimics a chimera state in classical complex dynamical systems but here in a relativistic quantum setting-henceforth the term "Dirac quantum chimera," associated with which are physical phenomena with potentially significant applications such as enhancement of spin polarization, unusual coexisting quasibound states for distinct spin configurations, and spin selective caustics. Experimental observations of these phenomena are possible through, e.g., optical realizations of ballistic Dirac fermion systems.