Reliability of energy landscape analysis of resting-state functional MRI data.

Energy landscape analysis is a data-driven method to analyse multidimensional time series, including functional magnetic resonance imaging (fMRI) data. It has been shown to be a useful characterization of fMRI data in health and disease. It fits an Ising model to the data and captures the dynamics of the data as movement of a noisy ball constrained on the energy landscape derived from the estimated Ising model. In the present study, we examine test-retest reliability of the energy landscape analysis. To this end, we construct a permutation test that assesses whether or not indices characterizing the energy landscape are more consistent across different sets of scanning sessions from the same participant (i.e. within-participant reliability) than across different sets of sessions from different participants (i.e. between-participant reliability). We show that the energy landscape analysis has significantly higher within-participant than between-participant test-retest reliability with respect to four commonly used indices. We also show that a variational Bayesian method, which enables us to estimate energy landscapes tailored to each participant, displays comparable test-retest reliability to that using the conventional likelihood maximization method. The proposed methodology paves the way to perform individual-level energy landscape analysis for given data sets with a statistically controlled reliability.

Spatial biology of Ising-like synthetic genetic networks.

BACKGROUND: Understanding how spatial patterns of gene expression emerge from the interaction of individual gene networks is a fundamental challenge in biology. Developing a synthetic experimental system with a common theoretical framework that captures the emergence of short- and long-range spatial correlations (and anti-correlations) from interacting gene networks could serve to uncover generic scaling properties of these ubiquitous phenomena. RESULTS: Here, we combine synthetic biology, statistical mechanics models, and computational simulations to study the spatial behavior of synthetic gene networks (SGNs) in Escherichia coli quasi-2D colonies growing on hard agar surfaces. Guided by the combined mechanisms of the contact process lattice simulation and two-dimensional Ising model (CPIM), we describe the spatial behavior of bi-stable and chemically coupled SGNs that self-organize into patterns of long-range correlations with power-law scaling or short-range anti-correlations. These patterns, resembling ferromagnetic and anti-ferromagnetic configurations of the Ising model near critical points, maintain their scaling properties upon changes in growth rate and cell shape. CONCLUSIONS: Our findings shed light on the spatial biology of coupled and bistable gene networks in growing cell populations. This emergent spatial behavior could provide insights into the study and engineering of self-organizing gene patterns in eukaryotic tissues and bacterial consortia.

Ising's Roots and the Transfer-Matrix Eigenvalues.

Today, the Ising model is an archetype describing collective ordering processes. As such, it is widely known in physics and far beyond. Less known is the fact that the thesis defended by Ernst Ising 100 years ago (in 1924) contained not only the solution of what we call now the 'classical 1D Ising model' but also other problems. Some of these problems, as well as the method of their solution, are the subject of this note. In particular, we discuss the combinatorial method Ernst Ising used to calculate the partition function for a chain of elementary magnets. In the thermodynamic limit, this method leads to the result that the partition function is given by the roots of a certain polynomial. We explicitly show that 'Ising's roots' that arise within the combinatorial treatment are also recovered by the eigenvalues of the transfer matrix, a concept that was introduced much later. Moreover, we discuss the generalization of the two-state model to a three-state one presented in Ising's thesis, which is not included in his famous paper of 1925 (E. Ising, Z. Physik 31 (1925) 253). The latter model can be considered as a forerunner of the now-abundant models with many-component order parameters.

Kramers-Wannier Duality and Random-Bond Ising Model.

We present a new combinatorial approach to the Ising model incorporating arbitrary bond weights on planar graphs. In contrast to existing methodologies, the exact free energy is expressed as the determinant of a set of ordered and disordered operators defined on a planar graph and the corresponding dual graph, respectively, thereby explicitly demonstrating the Kramers-Wannier duality. The implications of our derived formula for the Random-Bond Ising Model are further elucidated.

Small and Simple Systems That Favor the Arrow of Time.

The 2nd law of thermodynamics yields an irreversible increase in entropy until thermal equilibrium is achieved. This irreversible increase is often assumed to require large and complex systems to emerge from the reversible microscopic laws of physics. We test this assumption using simulations and theory of a 1D ring of N Ising spins coupled to an explicit heat bath of N Einstein oscillators. The simplicity of this system allows the exact entropy to be calculated for the spins and the heat bath for any N, with dynamics that is readily altered from reversible to irreversible. We find thermal-equilibrium behavior in the thermodynamic limit, and in systems as small as N=2, but both results require microscopic dynamics that is intrinsically irreversible.

Bayesian sparse heritability analysis with high-dimensional neuroimaging phenotypes.

Heritability analysis plays a central role in quantitative genetics to describe genetic contribution to human complex traits and prioritize downstream analyses under large-scale phenotypes. Existing works largely focus on modeling single phenotype and currently available multivariate phenotypic methods often suffer from scaling and interpretation. In this article, motivated by understanding how genetic underpinning impacts human brain variation, we develop an integrative Bayesian heritability analysis to jointly estimate heritabilities for high-dimensional neuroimaging traits. To induce sparsity and incorporate brain anatomical configuration, we impose hierarchical selection among both regional and local measurements based on brain structural network and voxel dependence. We also use a nonparametric Dirichlet process mixture model to realize grouping among single nucleotide polymorphism-associated phenotypic variations, providing biological plausibility. Through extensive simulations, we show the proposed method outperforms existing ones in heritability estimation and heritable traits selection under various scenarios. We finally apply the method to two large-scale imaging genetics datasets: the Alzheimer's Disease Neuroimaging Initiative and United Kingdom Biobank and show biologically meaningful results.

The vertebrate muscle superlattice: discovery, consequences, and link to geometric frustration.

Early x-ray diffraction studies of muscle revealed spacings larger than the basic thick filament lattice spacing and led to a number of speculations on the mutual rotations of the filaments in the myosin lattice. The nature of the arrangements of the filaments was resolved by John Squire and Pradeep Luther using careful electron microscopy and image analysis. The intriguing disorder in the rotations, that they termed the myosin superlattice, remained a curiosity, until work with Rick Millane and colleagues showed a connection to "geometric frustration," a well-known phenomenon in statistical and condensed matter physics. In this review, we describe how this connection gives a satisfying physical basis for the myosin superlattice, and how recent work has shown relationships to muscle mechanical behaviour.

A stochastic block Ising model for multi-layer networks with inter-layer dependence.

Community detection has attracted tremendous interests in network analysis, which aims at finding group of nodes with similar characteristics. Various detection methods have been developed to detect homogeneous communities in multi-layer networks, where inter-layer dependence is a widely acknowledged but severely under-investigated issue. In this paper, we propose a novel stochastic block Ising model (SBIM) to incorporate the inter-layer dependence to help with community detection in multi-layer networks. The community structure is modeled by the stochastic block model (SBM) and the inter-layer dependence is incorporated via the popular Ising model. Furthermore, we develop an efficient variational EM algorithm to tackle the resultant optimization task and establish the asymptotic consistency of the proposed method. Extensive simulated examples and a real example on gene co-expression multi-layer network data are also provided to demonstrate the advantage of the proposed method.

Loop expansion around the Bethe solution for the random magnetic field Ising ferromagnets at zero temperature.

We apply to the random-field Ising model at zero temperature ([Formula: see text]) the perturbative loop expansion around the Bethe solution. A comparison with the standard ϵ expansion is made, highlighting the key differences that make the expansion around the Bethe solution much more appropriate to correctly describe strongly disordered systems, especially those controlled by a [Formula: see text] renormalization group (RG) fixed point. The latter loop expansion produces an effective theory with cubic vertices. We compute the one-loop corrections due to cubic vertices, finding additional terms that are absent in the ϵ expansion. However, these additional terms are subdominant with respect to the standard, supersymmetric ones; therefore, dimensional reduction is still valid at this order of the loop expansion.

Generation of thermofield double states and critical ground states with a quantum computer.

Finite-temperature phases of many-body quantum systems are fundamental to phenomena ranging from condensed-matter physics to cosmology, yet they are generally difficult to simulate. Using an ion trap quantum computer and protocols motivated by the quantum approximate optimization algorithm (QAOA), we generate nontrivial thermal quantum states of the transverse-field Ising model (TFIM) by preparing thermofield double states at a variety of temperatures. We also prepare the critical state of the TFIM at zero temperature using quantum-classical hybrid optimization. The entanglement structure of thermofield double and critical states plays a key role in the study of black holes, and our work simulates such nontrivial structures on a quantum computer. Moreover, we find that the variational quantum circuits exhibit noise thresholds above which the lowest-depth QAOA circuits provide the best results.

Idiographic Ising and Divide and Color Models: Encompassing Networks for Heterogeneous Binary Data.

The Ising model is a graphical model that has played an essential role in network psychometrics. It has been used as a theoretical model to conceptualize psychological concepts and as a statistical model to analyze psychological data. Using graphical models such as the Ising model to analyze psychological data has been heavily critiqued since these data often come from cross-sectional applications. An often voiced concern is the inability of the Ising model to express heterogeneity in the population. The idiographic approach has been posed as an alternative and aims to infer individual network structures. While idiographic networks overcome population heterogeneity, it is unclear how they aggregate into established cross-sectional phenomena. This paper establishes a formal bridge between idiographic and cross-sectional network approaches of the Ising model. We ascertain unique topological structures that characterize individuals and aggregate into an Ising model cross-sectionally. This new formulation supports population heterogeneity while being consistent with cross-sectional phenomena. The proposed theory also establishes a new statistical framework for analyzing populations of idiographic networks for binary variables. The Ising model and the divide and color model are special cases of this new framework. We introduce a Gibbs sampling algorithm to estimate models from this new framework.

A comparison of logistic regression methods for Ising model estimation.

The Ising model has received significant attention in network psychometrics during the past decade. A popular estimation procedure is IsingFit, which uses nodewise l1-regularized logistic regression along with the extended Bayesian information criterion to establish the edge weights for the network. In this paper, we report the results of a simulation study comparing IsingFit to two alternative approaches: (1) a nonregularized nodewise stepwise logistic regression method, and (2) a recently proposed global l1-regularized logistic regression method that estimates all edge weights in a single stage, thus circumventing the need for nodewise estimation. MATLAB scripts for the methods are provided as supplemental material. The global l1-regularized logistic regression method generally provided greater accuracy and sensitivity than IsingFit, at the expense of lower specificity and much greater computation time. The stepwise approach showed considerable promise. Relative to the l1-regularized approaches, the stepwise method provided better average specificity for all experimental conditions, as well as comparable accuracy and sensitivity at the largest sample size.

Relevant Analytic Spontaneous Magnetization Relation for the Face-Centered-Cubic Ising Lattice.

The relevant approximate spontaneous magnetization relations for the simple-cubic and body-centered-cubic Ising lattices have recently been obtained analytically by a novel approach that conflates the Callen-Suzuki identity with a heuristic odd-spin correlation magnetization relation. By exploiting this approach, we study an approximate analytic spontaneous magnetization expression for the face-centered-cubic Ising lattice. We report that the results of the analytic relation obtained in this work are nearly consistent with those derived from the Monte Carlo simulation.

Emergent Criticality in Coupled Boolean Networks.

Early embryonic development involves forming all specialized cells from a fluid-like mass of identical stem cells. The differentiation process consists of a series of symmetry-breaking events, starting from a high-symmetry state (stem cells) to a low-symmetry state (specialized cells). This scenario closely resembles phase transitions in statistical mechanics. To theoretically study this hypothesis, we model embryonic stem cell (ESC) populations through a coupled Boolean network (BN) model. The interaction is applied using a multilayer Ising model that considers paracrine and autocrine signaling, along with external interventions. It is demonstrated that cell-to-cell variability can be interpreted as a mixture of steady-state probability distributions. Simulations have revealed that such models can undergo a series of first- and second-order phase transitions as a function of the system parameters that describe gene expression noise and interaction strengths. These phase transitions result in spontaneous symmetry-breaking events that generate new types of cells characterized by various steady-state distributions. Coupled BNs have also been shown to self-organize in states that allow spontaneous cell differentiation.

Higher-Order Interactions and Their Duals Reveal Synergy and Logical Dependence beyond Shannon-Information.

Information-theoretic quantities reveal dependencies among variables in the structure of joint, marginal, and conditional entropies while leaving certain fundamentally different systems indistinguishable. Furthermore, there is no consensus on the correct higher-order generalisation of mutual information (MI). In this manuscript, we show that a recently proposed model-free definition of higher-order interactions among binary variables (MFIs), such as mutual information, is a Möbius inversion on a Boolean algebra, except of surprisal instead of entropy. This provides an information-theoretic interpretation to the MFIs, and by extension to Ising interactions. We study the objects dual to mutual information and the MFIs on the order-reversed lattices. We find that dual MI is related to the previously studied differential mutual information, while dual interactions are interactions with respect to a different background state. Unlike (dual) mutual information, interactions and their duals uniquely identify all six 2-input logic gates, the dy- and triadic distributions, and different causal dynamics that are identical in terms of their Shannon information content.

Local Phase Transitions in a Model of Multiplex Networks with Heterogeneous Degrees and Inter-Layer Coupling.

Multilayer networks represent multiple types of connections between the same set of nodes. Clearly, a multilayer description of a system adds value only if the multiplex does not merely consist of independent layers. In real-world multiplexes, it is expected that the observed inter-layer overlap may result partly from spurious correlations arising from the heterogeneity of nodes, and partly from true inter-layer dependencies. It is therefore important to consider rigorous ways to disentangle these two effects. In this paper, we introduce an unbiased maximum entropy model of multiplexes with controllable intra-layer node degrees and controllable inter-layer overlap. The model can be mapped to a generalized Ising model, where the combination of node heterogeneity and inter-layer coupling leads to the possibility of local phase transitions. In particular, we find that node heterogeneity favors the splitting of critical points characterizing different pairs of nodes, leading to link-specific phase transitions that may, in turn, increase the overlap. By quantifying how the overlap can be increased by increasing either the intra-layer node heterogeneity (spurious correlation) or the strength of the inter-layer coupling (true correlation), the model allows us to disentangle the two effects. As an application, we show that the empirical overlap observed in the International Trade Multiplex genuinely requires a nonzero inter-layer coupling in its modeling, as it is not merely a spurious result of the correlation between node degrees across different layers.

Heat-Bath and Metropolis Dynamics in Ising-like Models on Directed Regular Random Graphs.

Using a single-site mean-field approximation (MFA) and Monte Carlo simulations, we examine Ising-like models on directed regular random graphs. The models are directed-network implementations of the Ising model, Ising model with absorbing states, and majority voter models. When these nonequilibrium models are driven by the heat-bath dynamics, their stationary characteristics, such as magnetization, are correctly reproduced by MFA as confirmed by Monte Carlo simulations. It turns out that MFA reproduces the same result as the generating functional analysis that is expected to provide the exact description of such models. We argue that on directed regular random graphs, the neighbors of a given vertex are typically uncorrelated, and that is why MFA for models with heat-bath dynamics provides their exact description. For models with Metropolis dynamics, certain additional correlations become relevant, and MFA, which neglects these correlations, is less accurate. Models with heat-bath dynamics undergo continuous phase transition, and at the critical point, the power-law time decay of the order parameter exhibits the behavior of the Ising mean-field universality class. Analogous phase transitions for models with Metropolis dynamics are discontinuous.

The Capabilities of Boltzmann Machines to Detect and Reconstruct Ising System's Configurations from a Given Temperature.

The restricted Boltzmann machine (RBM) is a generative neural network that can learn in an unsupervised way. This machine has been proven to help understand complex systems, using its ability to generate samples of the system with the same observed distribution. In this work, an Ising system is simulated, creating configurations via Monte Carlo sampling and then using them to train RBMs at different temperatures. Then, 1. the ability of the machine to reconstruct system configurations and 2. its ability to be used as a detector of configurations at specific temperatures are evaluated. The results indicate that the RBM reconstructs configurations following a distribution similar to the original one, but only when the system is in a disordered phase. In an ordered phase, the RBM faces levels of irreproducibility of the configurations in the presence of bimodality, even when the physical observables agree with the theoretical ones. On the other hand, independent of the phase of the system, the information embodied in the neural network weights is sufficient to discriminate whether the configurations come from a given temperature well. The learned representations of the RBM can discriminate system configurations at different temperatures, promising interesting applications in real systems that could help recognize crossover phenomena.

Characteristics of an Ising-like Model with Ferromagnetic and Antiferromagnetic Interactions.

In the framework of mean field approximation, we consider a spin system consisting of two interacting sub-ensembles. The intra-ensemble interactions are ferromagnetic, while the inter-ensemble interactions are antiferromagnetic. We define the effective number of the nearest neighbors and show that if the two sub-ensembles have the same effective number of the nearest neighbors, the classical form of critical exponents (α=0, ß=1/2, γ=γ'=1, δ=3) gives way to the non-classical form (α=0, ß=3/2, γ=γ'=0, δ=1), and the scaling function changes simultaneously. We demonstrate that this system allows for two second-order phase transitions and two first-order phase transitions. We observe that an external magnetic field does not destroy the phase transitions but only shifts their critical points, allowing for control of the system's parameters. We discuss the regime when the magnetization as a function of the magnetic field develops a low-magnetization plateau and show that the height of this plateau abruptly rises to the value of one when the magnetic field reaches a critical value. Our analytical results are supported by a Monte Carlo simulation of a three-dimensional layered model.

Inferring Cultural Landscapes with the Inverse Ising Model.

The space of possible human cultures is vast, but some cultural configurations are more consistent with cognitive and social constraints than others. This leads to a "landscape" of possibilities that our species has explored over millennia of cultural evolution. However, what does this fitness landscape, which constrains and guides cultural evolution, look like? The machine-learning algorithms that can answer these questions are typically developed for large-scale datasets. Applications to the sparse, inconsistent, and incomplete data found in the historical record have received less attention, and standard recommendations can lead to bias against marginalized, under-studied, or minority cultures. We show how to adapt the minimum probability flow algorithm and the Inverse Ising model, a physics-inspired workhorse of machine learning, to the challenge. A series of natural extensions-including dynamical estimation of missing data, and cross-validation with regularization-enables reliable reconstruction of the underlying constraints. We demonstrate our methods on a curated subset of the Database of Religious History: records from 407 religious groups throughout human history, ranging from the Bronze Age to the present day. This reveals a complex, rugged, landscape, with both sharp, well-defined peaks where state-endorsed religions tend to concentrate, and diffuse cultural floodplains where evangelical religions, non-state spiritual practices, and mystery religions can be found.