Depolymerization of plastics by means of electrified spatiotemporal heating.

Depolymerization is a promising strategy for recycling waste plastic into constituent monomers for subsequent repolymerization1. However, many commodity plastics cannot be selectively depolymerized using conventional thermochemical approaches, as it is difficult to control the reaction progress and pathway. Although catalysts can improve the selectivity, they are susceptible to performance degradation2. Here we present a catalyst-free, far-from-equilibrium thermochemical depolymerization method that can generate monomers from commodity plastics (polypropylene (PP) and poly(ethylene terephthalate) (PET)) by means of pyrolysis. This selective depolymerization process is realized by two features: (1) a spatial temperature gradient and (2) a temporal heating profile. The spatial temperature gradient is achieved using a bilayer structure of porous carbon felt, in which the top electrically heated layer generates and conducts heat down to the underlying reactor layer and plastic. The resulting temperature gradient promotes continuous melting, wicking, vaporization and reaction of the plastic as it encounters the increasing temperature traversing the bilayer, enabling a high degree of depolymerization. Meanwhile, pulsing the electrical current through the top heater layer generates a temporal heating profile that features periodic high peak temperatures (for example, about 600 °C) to enable depolymerization, yet the transient heating duration (for example, 0.11 s) can suppress unwanted side reactions. Using this approach, we depolymerized PP and PET to their monomers with yields of about 36% and about 43%, respectively. Overall, this electrified spatiotemporal heating (STH) approach potentially offers a solution to the global plastic waste problem.

Programmable heating and quenching for efficient thermochemical synthesis.

Conventional thermochemical syntheses by continuous heating under near-equilibrium conditions face critical challenges in improving the synthesis rate, selectivity, catalyst stability and energy efficiency, owing to the lack of temporal control over the reaction temperature and time, and thus the reaction pathways1-3. As an alternative, we present a non-equilibrium, continuous synthesis technique that uses pulsed heating and quenching (for example, 0.02 s on, 1.08 s off) using a programmable electric current to rapidly switch the reaction between high (for example, up to 2,400 K) and low temperatures. The rapid quenching ensures high selectivity and good catalyst stability, as well as lowers the average temperature to reduce the energy cost. Using CH4 pyrolysis as a model reaction, our programmable heating and quenching technique leads to high selectivity to value-added C2 products (>75% versus <35% by the conventional non-catalytic method and versus <60% by most conventional methods using optimized catalysts). Our technique can be extended to a range of thermochemical reactions, such as NH3 synthesis, for which we achieve a stable and high synthesis rate of about 6,000 µmol gFe-1 h-1 at ambient pressure for >100 h using a non-optimized catalyst. This study establishes a new model towards highly efficient non-equilibrium thermochemical synthesis.

Data-driven discovery of chemotactic migration of bacteria via coordinate-invariant machine learning.

BACKGROUND: E. coli chemotactic motion in the presence of a chemonutrient field can be studied using wet laboratory experiments or macroscale-level partial differential equations (PDEs) (among others). Bridging experimental measurements and chemotactic Partial Differential Equations requires knowledge of the evolution of all underlying fields, initial and boundary conditions, and often necessitates strong assumptions. In this work, we propose machine learning approaches, along with ideas from the Whitney and Takens embedding theorems, to circumvent these challenges. RESULTS: Machine learning approaches for identifying underlying PDEs were (a) validated through the use of simulation data from established continuum models and (b) used to infer chemotactic PDEs from experimental data. Such data-driven models were surrogates either for the entire chemotactic PDE right-hand-side (black box models), or, in a more targeted fashion, just for the chemotactic term (gray box models). Furthermore, it was demonstrated that a short history of bacterial density may compensate for the missing measurements of the field of chemonutrient concentration. In fact, given reasonable conditions, such a short history of bacterial density measurements could even be used to infer chemonutrient concentration. CONCLUSION: Data-driven PDEs are an important modeling tool when studying Chemotaxis at the macroscale, as they can learn bacterial motility from various data sources, fidelities (here, computational models, experiments) or coordinate systems. The resulting data-driven PDEs can then be simulated to reproduce/predict computational or experimental bacterial density profile data independent of the coordinate system, approximate meaningful parameters or functional terms, and even possibly estimate the underlying (unmeasured) chemonutrient field evolution.

Transformations establishing equivalence across neural networks: When have two networks learned the same task?

Transformations are a key tool in the qualitative study of dynamical systems: transformations to a normal form, for example, underpin the study of instabilities and bifurcations. In this work, we test, and when possible establish, an equivalence between two different artificial neural networks by attempting to construct a data-driven transformation between them, using diffusion maps with a Mahalanobis-like metric. If the construction succeeds, the two networks can be thought of as belonging to the same equivalence class. We first discuss transformation functions between only the outputs of the two networks; we then also consider transformations that take into account outputs (activations) of a number of internal neurons from each network. Whitney's theorem dictates the number of (generic) measurements from one of the networks required to reconstruct each and every feature of the second network. The construction of the transformation function relies on a consistent, intrinsic representation of the network input space. We illustrate our algorithm by matching neural network pairs trained to learn (a) observations of scalar functions, (b) observations of two-dimensional vector fields, and (c) representations of images of a moving three-dimensional object (a rotating horse). We also demonstrate reconstruction of a network's input (and output) from minimal partial observations of intermediate neuron activations. The construction of equivalences across different network instantiations clearly relates to transfer learning and will also be valuable in establishing equivalence between different machine learning-based tools.

Tipping points of evolving epidemiological networks: Machine learning-assisted, data-driven effective modeling.

We study the tipping point collective dynamics of an adaptive susceptible-infected-susceptible (SIS) epidemiological network in a data-driven, machine learning-assisted manner. We identify a parameter-dependent effective stochastic differential equation (eSDE) in terms of physically meaningful coarse mean-field variables through a deep-learning ResNet architecture inspired by numerical stochastic integrators. We construct an approximate effective bifurcation diagram based on the identified drift term of the eSDE and contrast it with the mean-field SIS model bifurcation diagram. We observe a subcritical Hopf bifurcation in the evolving network's effective SIS dynamics that causes the tipping point behavior; this takes the form of large amplitude collective oscillations that spontaneously-yet rarely-arise from the neighborhood of a (noisy) stationary state. We study the statistics of these rare events both through repeated brute force simulations and by using established mathematical/computational tools exploiting the right-hand side of the identified SDE. We demonstrate that such a collective SDE can also be identified (and the rare event computations also performed) in terms of data-driven coarse observables, obtained here via manifold learning techniques, in particular, Diffusion Maps. The workflow of our study is straightforwardly applicable to other complex dynamic problems exhibiting tipping point dynamics.

Learning black- and gray-box chemotactic PDEs/closures from agent based Monte Carlo simulation data.

We propose a machine learning framework for the data-driven discovery of macroscopic chemotactic Partial Differential Equations (PDEs)-and the closures that lead to them- from high-fidelity, individual-based stochastic simulations of Escherichia coli bacterial motility. The fine scale, chemomechanical, hybrid (continuum-Monte Carlo) simulation model embodies the underlying biophysics, and its parameters are informed from experimental observations of individual cells. Using a parsimonious set of collective observables, we learn effective, coarse-grained "Keller-Segel class" chemotactic PDEs using machine learning regressors: (a) (shallow) feedforward neural networks and (b) Gaussian Processes. The learned laws can be black-box (when no prior knowledge about the PDE law structure is assumed) or gray-box when parts of the equation (e.g. the pure diffusion part) is known and "hardwired" in the regression process. More importantly, we discuss data-driven corrections (both additive and functional), to analytically known, approximate closures.

Local conformal autoencoder for standardized data coordinates.

We propose a local conformal autoencoder (LOCA) for standardized data coordinates. LOCA is a deep learning-based method for obtaining standardized data coordinates from scientific measurements. Data observations are modeled as samples from an unknown, nonlinear deformation of an underlying Riemannian manifold, which is parametrized by a few normalized, latent variables. We assume a repeated measurement sampling strategy, common in scientific measurements, and present a method for learning an embedding in [Formula: see text] that is isometric to the latent variables of the manifold. The coordinates recovered by our method are invariant to diffeomorphisms of the manifold, making it possible to match between different instrumental observations of the same phenomenon. Our embedding is obtained using LOCA, which is an algorithm that learns to rectify deformations by using a local z-scoring procedure, while preserving relevant geometric information. We demonstrate the isometric embedding properties of LOCA in various model settings and observe that it exhibits promising interpolation and extrapolation capabilities, superior to the current state of the art. Finally, we demonstrate LOCA's efficacy in single-site Wi-Fi localization data and for the reconstruction of three-dimensional curved surfaces from two-dimensional projections.

Limits of entrainment of circadian neuronal networks.

Circadian rhythmicity lies at the center of various important physiological and behavioral processes in mammals, such as sleep, metabolism, homeostasis, mood changes, and more. Misalignment of intrinsic neuronal oscillations with the external day-night cycle can disrupt such processes and lead to numerous disorders. In this work, we computationally determine the limits of circadian synchronization to external light signals of different frequency, duty cycle, and simulated amplitude. Instead of modeling circadian dynamics with generic oscillator models (e.g., Kuramoto-type), we use a detailed computational neuroscience model, which integrates biomolecular dynamics, neuronal electrophysiology, and network effects. This allows us to investigate the effect of small drug molecules, such as Longdaysin, and connect our results with experimental findings. To combat the high dimensionality of such a detailed model, we employ a matrix-free approach, while our entire algorithmic pipeline enables numerical continuation and construction of bifurcation diagrams using only direct simulation. We, thus, computationally explore the effect of heterogeneity in the circadian neuronal network, as well as the effect of the corrective therapeutic intervention of Longdaysin. Last, we employ unsupervised learning to construct a data-driven embedding space for representing neuronal heterogeneity.

Learning effective stochastic differential equations from microscopic simulations: Linking stochastic numerics to deep learning.

We identify effective stochastic differential equations (SDEs) for coarse observables of fine-grained particle- or agent-based simulations; these SDEs then provide useful coarse surrogate models of the fine scale dynamics. We approximate the drift and diffusivity functions in these effective SDEs through neural networks, which can be thought of as effective stochastic ResNets. The loss function is inspired by, and embodies, the structure of established stochastic numerical integrators (here, Euler-Maruyama and Milstein); our approximations can thus benefit from backward error analysis of these underlying numerical schemes. They also lend themselves naturally to "physics-informed" gray-box identification when approximate coarse models, such as mean field equations, are available. Existing numerical integration schemes for Langevin-type equations and for stochastic partial differential equations can also be used for training; we demonstrate this on a stochastically forced oscillator and the stochastic wave equation. Our approach does not require long trajectories, works on scattered snapshot data, and is designed to naturally handle different time steps per snapshot. We consider both the case where the coarse collective observables are known in advance, as well as the case where they must be found in a data-driven manner.

Time-series forecasting using manifold learning, radial basis function interpolation, and geometric harmonics.

We address a three-tier numerical framework based on nonlinear manifold learning for the forecasting of high-dimensional time series, relaxing the "curse of dimensionality" related to the training phase of surrogate/machine learning models. At the first step, we embed the high-dimensional time series into a reduced low-dimensional space using nonlinear manifold learning (local linear embedding and parsimonious diffusion maps). Then, we construct reduced-order surrogate models on the manifold (here, for our illustrations, we used multivariate autoregressive and Gaussian process regression models) to forecast the embedded dynamics. Finally, we solve the pre-image problem, thus lifting the embedded time series back to the original high-dimensional space using radial basis function interpolation and geometric harmonics. The proposed numerical data-driven scheme can also be applied as a reduced-order model procedure for the numerical solution/propagation of the (transient) dynamics of partial differential equations (PDEs). We assess the performance of the proposed scheme via three different families of problems: (a) the forecasting of synthetic time series generated by three simplistic linear and weakly nonlinear stochastic models resembling electroencephalography signals, (b) the prediction/propagation of the solution profiles of a linear parabolic PDE and the Brusselator model (a set of two nonlinear parabolic PDEs), and (c) the forecasting of a real-world data set containing daily time series of ten key foreign exchange rates spanning the time period 3 September 2001-29 October 2020.

Learning the temporal evolution of multivariate densities via normalizing flows.

In this work, we propose a method to learn multivariate probability distributions using sample path data from stochastic differential equations. Specifically, we consider temporally evolving probability distributions (e.g., those produced by integrating local or nonlocal Fokker-Planck equations). We analyze this evolution through machine learning assisted construction of a time-dependent mapping that takes a reference distribution (say, a Gaussian) to each and every instance of our evolving distribution. If the reference distribution is the initial condition of a Fokker-Planck equation, what we learn is the time-T map of the corresponding solution. Specifically, the learned map is a multivariate normalizing flow that deforms the support of the reference density to the support of each and every density snapshot in time. We demonstrate that this approach can approximate probability density function evolutions in time from observed sampled data for systems driven by both Brownian and Lévy noise. We present examples with two- and three-dimensional, uni- and multimodal distributions to validate the method.

Particles to partial differential equations parsimoniously.

Equations governing physico-chemical processes are usually known at microscopic spatial scales, yet one suspects that there exist equations, e.g., in the form of partial differential equations (PDEs), that can explain the system evolution at much coarser, meso-, or macroscopic length scales. Discovering those coarse-grained effective PDEs can lead to considerable savings in computation-intensive tasks like prediction or control. We propose a framework combining artificial neural networks with multiscale computation, in the form of equation-free numerics, for the efficient discovery of such macro-scale PDEs directly from microscopic simulations. Gathering sufficient microscopic data for training neural networks can be computationally prohibitive; equation-free numerics enable a more parsimonious collection of training data by only operating in a sparse subset of the space-time domain. We also propose using a data-driven approach, based on manifold learning (including one using the notion of unnormalized optimal transport of distributions and one based on moment-based description of the distributions), to identify macro-scale dependent variable(s) suitable for the data-driven discovery of said PDEs. This approach can corroborate physically motivated candidate variables or introduce new data-driven variables, in terms of which the coarse-grained effective PDE can be formulated. We illustrate our approach by extracting coarse-grained evolution equations from particle-based simulations with a priori unknown macro-scale variable(s) while significantly reducing the requisite data collection computational effort.

Global and local reduced models for interacting, heterogeneous agents.

Large collections of coupled, heterogeneous agents can manifest complex dynamical behavior presenting difficulties for simulation and analysis. However, if the collective dynamics lie on a low-dimensional manifold, then the original agent-based model may be approximated with a simplified surrogate model on and near the low-dimensional space where the dynamics live. Analytically identifying such simplified models can be challenging or impossible, but here we present a data-driven coarse-graining methodology for discovering such reduced models. We consider two types of reduced models: globally based models that use global information and predict dynamics using information from the whole ensemble and locally based models that use local information, that is, information from just a subset of agents close (close in heterogeneity space, not physical space) to an agent, to predict the dynamics of an agent. For both approaches, we are able to learn laws governing the behavior of the reduced system on the low-dimensional manifold directly from time series of states from the agent-based system. These laws take the form of either a system of ordinary differential equations (ODEs), for the globally based approach, or a partial differential equation (PDE) in the locally based case. For each technique, we employ a specialized artificial neural network integrator that has been templated on an Euler time stepper (i.e., a ResNet) to learn the laws of the reduced model. As part of our methodology, we utilize the proper orthogonal decomposition (POD) to identify the low-dimensional space of the dynamics. Our globally based technique uses the resulting POD basis to define a set of coordinates for the agent states in this space and then seeks to learn the time evolution of these coordinates as a system of ODEs. For the locally based technique, we propose a methodology for learning a partial differential equation representation of the agents; the PDE law depends on the state variables and partial derivatives of the state variables with respect to model heterogeneities. We require that the state variables are smooth with respect to model heterogeneities, which permit us to cast the discrete agent-based problem as a continuous one in heterogeneity space. The agents in such a representation bear similarity to the discretization points used in typical finite element/volume methods. As an illustration of the efficacy of our techniques, we consider a simplified coupled neuron model for rhythmic oscillations in the pre-Bötzinger complex and demonstrate how our data-driven surrogate models are able to produce dynamics comparable to the dynamics of the full system. A nontrivial conclusion is that the dynamics can be equally well reproduced by an all-to-all coupled and by a locally coupled model of the same agents.

Initializing LSTM internal states via manifold learning.

We present an approach, based on learning an intrinsic data manifold, for the initialization of the internal state values of long short-term memory (LSTM) recurrent neural networks, ensuring consistency with the initial observed input data. Exploiting the generalized synchronization concept, we argue that the converged, "mature" internal states constitute a function on this learned manifold. The dimension of this manifold then dictates the length of observed input time series data required for consistent initialization. We illustrate our approach through a partially observed chemical model system, where initializing the internal LSTM states in this fashion yields visibly improved performance. Finally, we show that learning this data manifold enables the transformation of partially observed dynamics into fully observed ones, facilitating alternative identification paths for nonlinear dynamical systems.

It doesn't always pay to be fit: success landscapes.

Landscapes play an important role in many areas of biology, in which biological lives are deeply entangled. Here we discuss a form of landscape in evolutionary biology which takes into account (1) initial growth rates, (2) mutation rates, (3) resource consumption by organisms, and (4) cyclic changes in the resources with time. The long-term equilibrium number of surviving organisms as a function of these four parameters forms what we call a success landscape, a landscape we would claim is qualitatively different from fitness landscapes which commonly do not include mutations or resource consumption/changes in mapping genomes to the final number of survivors. Although our analysis is purely theoretical, we believe the results have possibly strong connections to how we might treat diseases such as cancer in the future with a deeper understanding of the interplay between resource degradation, mutation, and uncontrolled cell growth.

Reconstruction of normal forms by learning informed observation geometries from data.

The discovery of physical laws consistent with empirical observations is at the heart of (applied) science and engineering. These laws typically take the form of nonlinear differential equations depending on parameters; dynamical systems theory provides, through the appropriate normal forms, an "intrinsic" prototypical characterization of the types of dynamical regimes accessible to a given model. Using an implementation of data-informed geometry learning, we directly reconstruct the relevant "normal forms": a quantitative mapping from empirical observations to prototypical realizations of the underlying dynamics. Interestingly, the state variables and the parameters of these realizations are inferred from the empirical observations; without prior knowledge or understanding, they parametrize the dynamics intrinsically without explicit reference to fundamental physical quantities.

Intrinsic map dynamics exploration for uncharted effective free-energy landscapes.

We describe and implement a computer-assisted approach for accelerating the exploration of uncharted effective free-energy surfaces (FESs). More generally, the aim is the extraction of coarse-grained, macroscopic information from stochastic or atomistic simulations, such as molecular dynamics (MD). The approach functionally links the MD simulator with nonlinear manifold learning techniques. The added value comes from biasing the simulator toward unexplored phase-space regions by exploiting the smoothness of the gradually revealed intrinsic low-dimensional geometry of the FES.

Coarse-scale PDEs from fine-scale observations via machine learning.

Complex spatiotemporal dynamics of physicochemical processes are often modeled at a microscopic level (through, e.g., atomistic, agent-based, or lattice models) based on first principles. Some of these processes can also be successfully modeled at the macroscopic level using, e.g., partial differential equations (PDEs) describing the evolution of the right few macroscopic observables (e.g., concentration and momentum fields). Deriving good macroscopic descriptions (the so-called "closure problem") is often a time-consuming process requiring deep understanding/intuition about the system of interest. Recent developments in data science provide alternative ways to effectively extract/learn accurate macroscopic descriptions approximating the underlying microscopic observations. In this paper, we introduce a data-driven framework for the identification of unavailable coarse-scale PDEs from microscopic observations via machine-learning algorithms. Specifically, using Gaussian processes, artificial neural networks, and/or diffusion maps, the proposed framework uncovers the relation between the relevant macroscopic space fields and their time evolution (the right-hand side of the explicitly unavailable macroscopic PDE). Interestingly, several choices equally representative of the data can be discovered. The framework will be illustrated through the data-driven discovery of macroscopic, concentration-level PDEs resulting from a fine-scale, lattice Boltzmann level model of a reaction/transport process. Once the coarse evolution law is identified, it can be simulated to produce long-term macroscopic predictions. Different features (pros as well as cons) of alternative machine-learning algorithms for performing this task (Gaussian processes and artificial neural networks) are presented and discussed.

Manifold learning for organizing unstructured sets of process observations.

Data mining is routinely used to organize ensembles of short temporal observations so as to reconstruct useful, low-dimensional realizations of an underlying dynamical system. In this paper, we use manifold learning to organize unstructured ensembles of observations ("trials") of a system's response surface. We have no control over where every trial starts, and during each trial, operating conditions are varied by turning "agnostic" knobs, which change system parameters in a systematic, but unknown way. As one (or more) knobs "turn," we record (possibly partial) observations of the system response. We demonstrate how such partial and disorganized observation ensembles can be integrated into coherent response surfaces whose dimension and parametrization can be systematically recovered in a data-driven fashion. The approach can be justified through the Whitney and Takens embedding theorems, allowing reconstruction of manifolds/attractors through different types of observations. We demonstrate our approach by organizing unstructured observations of response surfaces, including the reconstruction of a cusp bifurcation surface for hydrogen combustion in a continuous stirred tank reactor. Finally, we demonstrate how this observation-based reconstruction naturally leads to informative transport maps between the input parameter space and output/state variable spaces.

On learning Hamiltonian systems from data.

Concise, accurate descriptions of physical systems through their conserved quantities abound in the natural sciences. In data science, however, current research often focuses on regression problems, without routinely incorporating additional assumptions about the system that generated the data. Here, we propose to explore a particular type of underlying structure in the data: Hamiltonian systems, where an "energy" is conserved. Given a collection of observations of such a Hamiltonian system over time, we extract phase space coordinates and a Hamiltonian function of them that acts as the generator of the system dynamics. The approach employs an autoencoder neural network component to estimate the transformation from observations to the phase space of a Hamiltonian system. An additional neural network component is used to approximate the Hamiltonian function on this constructed space, and the two components are trained jointly. As an alternative approach, we also demonstrate the use of Gaussian processes for the estimation of such a Hamiltonian. After two illustrative examples, we extract an underlying phase space as well as the generating Hamiltonian from a collection of movies of a pendulum. The approach is fully data-driven and does not assume a particular form of the Hamiltonian function.