Memorial for Dr. Erik Bollt
In this paper, we give a memorial tribute to Prof. Erik M. Bollt (1967--2025).
math.HO↗
arXiv subjects
Jeremie Fish
Publications and source records attributed to Jeremie Fish.
Deep-Koopman-KANDy: Dictionary Discovery for Deep-Koopman Operators with Kolmogorov-Arnold Networks for Dynamics
Symbolic library -- or Koopman dictionary -- selection is a fundamental challenge in data-driven dynamical systems. Extended Dynamic Mode Decomposition (EDMD), Sparse Identification of Nonlinear Dynamics (SINDy), and Kolmogorov--Arnold Networks for Dynamics (KANDy) all require the practitioner to commit to a function library at training time; Deep-Koopman Operators avoid this commitment but produce uninterpretable latent observables. We propose Deep-Koopman-KANDy, a structured approach to post-hoc symbolic dictionary readout that combines Deep-Koopman modeling with Kolmogorov-Arnold Networks for Dynamics (KANDy). The encoder and decoder of a Deep-Koopman Operator are replaced with two-layer Kolmogorov--Arnold Networks (KANs), and a level-set construction together with a chain-rule gradient identity exposes the compositional structure of the learned observables in a basis chosen \emph{after} training. We evaluate the method on the Lorenz system, the Chirikov standard map, the Ikeda map, and the Arnold cat map. On Lorenz it recovers the target dictionary $\{x,y,z,xy,xz\}$ with perfect recall and Jaccard score $0.79\pm0.06$; on the standard map it recovers a low-order Fourier basis matching the analytical structure; on Ikeda -- which has no sparse polynomial representation -- a misspecified polynomial readout still recovers the correct foliation coordinate $g\approx x^2+y^2$ together with a nontrivial outer function; and on the Arnold cat map -- used as a negative control because finite-dimensional Koopman closure is provably impossible -- the method fails to find a sparse closure, as expected.
math.DS↗
KANDy: Kolmogorov-Arnold Networks and Dynamical System Discovery
We introduce the Kolmogorov-Arnold Network for Dynamics (KANDy) as a zero-depth, wide neural architecture capable of discovering governing equations in chaotic and complex dynamical systems. Building on the foundation of Kolmogorov-Arnold Networks (KANs), KANDy explicitly learns governing equations by replacing sparse regression with a KAN. The synthesis of KANs and sparse regression addresses the limitations of equation discovery for KANs applied to dynamical systems and overcomes cases where sparse regression is hindered by sparsity constraints. Additionally, we show that our model, applied to the Hopf Fibration, recovers topological structure, thereby improving coherence with attractor properties. We apply our model to discrete and continuous dynamical systems, as well as to chaotic partial differential equations (PDEs). These results position KANDy as an interpretable and effective alternative for data-driven modeling of nonlinear dynamical systems.
math.DS↗
CausationEntropy: Pythonic Optimal Causation Entropy
Optimal Causation Entropy (oCSE) is a robust causal network modeling technique that reveals causal networks from dynamical systems and coupled oscillators, distinguishing direct from indirect paths. CausationEntropy is a Python package that implements oCSE and several of its significant optimizations and methodological extensions. In this paper, we introduce the version 1.1 release of CausationEntropy, which includes new synthetic data generators, plotting tools, and several advanced information-theoretical causal network discovery algorithms with criteria for estimating Gaussian, k-nearest neighbors (kNN), geometric k-nearest neighbors (geometric-kNN), kernel density (KDE) and Poisson entropic estimators. The package is easy to install from the PyPi software repository, is thoroughly documented, supplemented with extensive code examples, and is modularly structured to support future additions. The entire codebase is released under the MIT license and is available on GitHub and through PyPi Repository. We expect this package to serve as a benchmark tool for causal discovery in complex dynamical systems.
cs.LG↗
Fractal Basins as a Mechanism for the Nimble Brain
An interesting feature of the brain is its ability to respond to disparate sensory signals from the environment in unique ways depending on the environmental context or current brain state. In dynamical systems, this is an example of multi-stability, the ability to switch between multiple stable states corresponding to specific patterns of brain activity/connectivity. In this article, we describe chimera states, which are patterns consisting of mixed synchrony and incoherence, in a brain-inspired dynamical systems model composed of a network with weak individual interactions and chaotic/periodic local dynamics. We illustrate the mechanism using synthetic time series interacting on a realistic anatomical brain network derived from human diffusion tensor imaging (DTI). We introduce the so-called Vector Pattern State (VPS) as an efficient way of identifying chimera states and mapping basin structures. Clustering similar VPSs for different initial conditions, we show that coexisting attractors of such states reveal intricately "mingled" fractal basin boundaries that are immediately reachable. This could explain the nimble brain's ability to rapidly switch patterns between coexisting attractors.
math.DS↗
Learning Transfer Operators by Kernel Density Estimation
Inference of transfer operators from data is often formulated as a classical problem that hinges on the Ulam method. The conventional description, known as the Ulam-Galerkin method, involves projecting onto basis functions represented as characteristic functions supported over a fine grid of rectangles. From this perspective, the Ulam-Galerkin approach can be interpreted as density estimation using the histogram method. In this study, we recast the problem within the framework of statistical density estimation. This alternative perspective allows for an explicit and rigorous analysis of bias and variance, thereby facilitating a discussion on the mean square error. Through comprehensive examples utilizing the logistic map and a Markov map, we demonstrate the validity and effectiveness of this approach in estimating the eigenvectors of the Frobenius-Perron operator. We compare the performance of Histogram Density Estimation(HDE) and Kernel Density Estimation(KDE) methods and find that KDE generally outperforms HDE in terms of accuracy. However, it is important to note that KDE exhibits limitations around boundary points and jumps. Based on our research findings, we suggest the possibility of incorporating other density estimation methods into this field and propose future investigations into the application of KDE-based estimation for high-dimensional maps. These findings provide valuable insights for researchers and practitioners working on estimating the Frobenius-Perron operator and highlight the potential of density estimation techniques in this area of study. Keywords: Transfer Operators; Frobenius-Perron operator; probability density estimation; Ulam-Galerkin method; Kernel Density Estimation; Histogram Density Estimation.
cs.LG↗
How fragile is your network? More than you think
Graphs are pervasive in our everyday lives, with relevance to biology, the internet, and infrastructure, as well as numerous other applications. It is thus necessary to have an understanding as to how quickly a graph disintegrates, whether by random failure or by targeted attack. While much of the interest in this subject has been focused on targeted removal of nodes, there has been some recent interest in targeted edge removal. Here, we focus on how robust a graph is against edge removal. We define a measure of network fragility that relates the fraction of edges removed to the largest connected component. We construct a class of graphs that is robust to edge removal. Furthermore, it is demonstrated that graphs generally disintegrate faster than would be anticipated by greedy targeted attack. Finally it is shown that our fragility measure as demonstrated real and natural networks.
cs.SI↗
Non-normality, optimality and synchronization
It has been recognized for quite some time that for some matrices the spectra are not enough to tell the complete story of the dynamics of the system, even for linear ODEs. While it is true that the eigenvalues control the asymptotic behavior of the system, if the matrix representing the system is non-normal, short term transients may appear in the linear system. Recently it has been recognized that since the matrices representing directed networks are non-normal, analysis based on spectra alone may be misleading. Both a normal and a non-normal system may be stable according to the master stability paradigm, but the non-normal system may have an arbitrarily small attraction basin to the synchronous state whereas an equivalent normal system may have a significantly larger sync basin. This points to the need to study synchronization in non-normal networks more closely. In this work, various tools will be utilized to examine synchronization in directed networks, including pseudospectra, an adaption of pseudospectra that we will call Laplacian pseudospectra. We define a resulting concept that we call Laplacian pseudospectral resilience (LPR). It will be shown that LPR outperforms other scalar measures for estimating the stability of the synchronous state to finite perturbations in a class of networks known as optimal networks. Finally we find that the ideal choice of optimal network, with an eye toward synchronization, is the one which minimizes LPR
nlin.CD↗
The Essential Synchronization Backbone Problem
Network optimization strategies for the process of synchronization have generally focused on the re-wiring or re-weighting of links in order to: (1) expand the range of coupling strengths that achieve synchronization, (2) expand the basin of attraction for the synchronization manifold, or (3) lower the average time to synchronization. A new optimization goal is proposed in seeking the minimum subset of the edge set of the original network that enables the same essential ability to synchronize in that the synchronization manifolds have conjugate stability. We call this type of minimal spanning subgraph an Essential Synchronization Backbone (ESB) of the original system, and we present two algorithms: one is a strategy for an exhaustive search for a true solution, while the other is a method of approximation for this combinatorial problem. The solution spaces that result from different choices of dynamical systems and coupling schemes vary with the level of hierarchical structure present and also the number of interwoven central cycles. Applications can include the important problem in civil engineering of power grid hardening, where new link creation may be costly, and the defense of certain key links to the functional process may be prioritized.
nlin.AO↗
Beach-level 24-hour forecasts of Florida red tide-induced respiratory irritation
An accurate forecast of the red tide respiratory irritation level would improve the lives of many people living in areas affected by algal blooms. Using a decades-long database of daily beach conditions, two conceptually different models to forecast the respiratory irritation risk level one day ahead of time are trained. One model is wind-based, using the current days' respiratory level and the predicted wind direction of the following day. The other model is a probabilistic self-exciting Hawkes process model. Both models are trained on beaches in Florida during 2011-2017 and applied to the red tide bloom during 2018-2019. For beaches where there is enough historical data to develop a model, the model which performs best depends on the beach. The wind-based model is the most accurate at half the beaches, correctly predicting the respiratory risk level on average about 84% of the time. The Hawkes model is the most accurate (81% accuracy) at nearly all of the remaining beaches.
physics.data-an↗
Emergent hierarchy through conductance-based node constraints
The presence of hierarchy in many real-world networks is not yet fully explained. Complex interaction networks are often coarse-grain models of vast modular networks, where tightly connected subgraphs are agglomerated into nodes for simplicity of representation and feasibility of analysis. The emergence of hierarchy in growing complex networks may stem from one particular property of these ignored subgraphs: their graph conductance. Being a quantification of the main bottleneck of flow on the subgraph, all such subgraphs will then have a specific structural limitation associated with this scalar value. This supports the consideration of heterogeneous degree restrictions on a randomly growing network for which a hidden variable model is proposed based on the basic \textit{rich-get-richer} scheme. Such node degree restrictions are drawn from various probability distributions, and it is shown that restriction generally leads to increased measures of hierarchy, while altering the tail of the degree distribution. Thus, a general mechanism is provided whereby inherent limitations lead to hierarchical self-organization.
physics.soc-ph↗
Entropic Causal Inference for Neurological Applications
The ultimate goal of cognitive neuroscience is to understand the mechanistic neural processes underlying the functional organization of the brain. Key to this study is understanding structure of both the structural and functional connectivity between anatomical regions. In this paper we follow previous work in developing a simple dynamical model of the brain by simulating its various regions as Kuramoto oscillators whose coupling structure is described by a complex network. However in our simulations rather than generating synthetic networks, we simulate our synthetic model but coupled by a real network of the anatomical brain regions which has been reconstructed from diffusion tensor imaging (DTI) data. By using an information theoretic approach that defines direct information flow in terms of causation entropy (CSE), we show that we can more accurately recover the true structural network than either of the popular correlation or LASSO regression techniques. We demonstrate the effectiveness of our method when applied to data simulated on the realistic DTI network, as well as on randomly generated small-world and Erd\"os-R\'enyi (ER) networks.
q-bio.NC↗
Interaction Networks from Discrete Event Data by Poisson Multivariate Mutual Information Estimation and Information Flow with Applications from Gene Expression Data
In this work, we introduce a new methodology for inferring the interaction structure of discrete valued time series which are Poisson distributed. While most related methods are premised on continuous state stochastic processes, in fact, discrete and counting event oriented stochastic process are natural and common, so called time-point processes (TPP). An important application that we focus on here is gene expression. Nonparameteric methods such as the popular k-nearest neighbors (KNN) are slow converging for discrete processes, and thus data hungry. Now, with the new multi-variate Poisson estimator developed here as the core computational engine, the causation entropy (CSE) principle, together with the associated greedy search algorithm optimal CSE (oCSE) allows us to efficiently infer the true network structure for this class of stochastic processes that were previously not practical. We illustrate the power of our method, first in benchmarking with synthetic datum, and then by inferring the genetic factors network from a breast cancer micro-RNA (miRNA) sequence count data set. We show the Poisson oCSE gives the best performance among the tested methods anfmatlabd discovers previously known interactions on the breast cancer data set.
stat.ME↗
Construction,sensitivity index, and synchronization speed of optimal networks
The stability (or instability) of synchronization is important in a number of real world systems, including the power grid, the human brain and biological cells. For identical synchronization, the synchronizability of a network, which can be measured by the range of coupling strength that admits stable synchronization, can be optimized for a given number of nodes and links. Depending on the geometric degeneracy of the Laplacian eigenvectors, optimal networks can be classified into different sensitivity levels, which we define as a network's sensitivity index. We introduce an efficient and explicit way to construct optimal networks of arbitrary size over a wide range of sensitivity and link densities. Using coupled chaotic oscillators, we study synchronization dynamics on optimal networks, showing that cospectral optimal networks can have drastically different speed of synchronization. Such difference in dynamical stability is found to be closely related to the different structural sensitivity of these networks: generally, networks with high sensitivity index are slower to synchronize, and, surprisingly, may not synchronize at all, despite being theoretically stable under linear stability analysis.
nlin.CD↗