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Purushottam D. Dixit

Purushottam D. Dixit contributes to research discovery and scholarly infrastructure.

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Published work

12 published item(s)

preprint2026arXiv

Discovering interpretable low-dimensional dynamics using maximum entropy

Models (i.e., governing equations) are fundamental to science and engineering. Advances in data acquisition now make it possible to extract interpretable, low dimensional descriptions from high dimensional observations. However, existing approaches sacrifice either interpretability for reconstruction accuracy or infer symbolic dynamics without relating latent coordinates to physically meaningful observables. Here we present Edwin (maximum entropy driven compression with interpretable nonlinear model discovery), a unified framework that simultaneously performs dimensionality reduction using the dynamic maximum entropy (DME) principle and discovers sparse symbolic models governing latent dynamics, as well as the coupling between learned features and external metadata. We validate Edwin on diverse simulated systems, including stochastic diffusion, the Ornstein-Uhlenbeck process, self assembling particles, spiking neural populations, and low rank recurrent neural networks, as well as on a noisy experimental time series of aggregating RNA-liposome complexes. Across all systems, Edwin recovers low dimensional symbolic models that are physically interpretable and generalize to unseen conditions. Together, these results establish Edwin as a powerful framework for inferring interpretable, low dimensional dynamics directly from high dimensional data.

preprint2019arXiv

TMI: Thermodynamic inference of data manifolds

The Gibbs-Boltzmann distribution offers a physically interpretable way to massively reduce the dimensionality of high dimensional probability distributions where the extensive variables are `features' and the intensive variables are `descriptors'. However, not all probability distributions can be modeled using the Gibbs-Boltzmann form. Here, we present TMI: TMI, {\bf T}hermodynamic {\bf M}anifold {\bf I}nference; a thermodynamic approach to approximate a collection of arbitrary distributions. TMI simultaneously learns from data intensive and extensive variables and achieves dimensionality reduction through a multiplicative, positive valued, and interpretable decomposition of the data. Importantly, the reduced dimensional space of intensive parameters is not homogeneous. The Gibbs-Boltzmann distribution defines an analytically tractable Riemannian metric on the space of intensive variables allowing us to calculate geodesics and volume elements. We discuss the applications of TMI with multiple real and artificial data sets. Possible extensions are discussed as well.

preprint2015arXiv

A maximum entropy framework for non-exponential distributions

Probability distributions having power-law tails are observed in a broad range of social, economic, and biological systems. We describe here a potentially useful common framework. We derive distribution functions $\{p_k\}$ for situations in which a `joiner particle' $k$ pays some form of price to enter a `community' of size $k-1$, where costs are subject to economies-of-scale (EOS). Maximizing the Boltzmann-Gibbs-Shannon entropy subject to this energy-like constraint predicts a distribution having a power-law tail; it reduces to the Boltzmann distribution in the absence of EOS. We show that the predicted function gives excellent fits to 13 different distribution functions, ranging from friendship links in social networks, to protein-protein interactions, to the severity of terrorist attacks. This approach may give useful insights into when to expect power-law distributions in the natural and social sciences.

preprint2015arXiv

Detecting temperature fluctuations at equilibrium

Gibbs and Boltzmann definitions of temperature agree only in the macroscopic limit. The ambiguity in identifying the equilibrium temperature of a finite sized `small' system exchanging energy with a bath is usually understood as a limitation of conventional statistical mechanics. We interpret this ambiguity as resulting from a stochastically fluctuating temperature coupled with the phase space variables giving rise to a broad temperature distribution. With this ansatz, we develop the equilibrium statistics and dynamics of small systems. Numerical evidence using an analytically tractable model shows that the effects of temperature fluctuations can be detected in equilibrium and dynamical properties of the phase space of the small system. Our theory generalizes statistical mechanics to small systems relevant to biophysics and nanotechnology.

preprint2015arXiv

Inferring transition rates on networks with incomplete knowledge

Across many fields, a problem of interest is to predict the transition rates between nodes of a network, given limited stationary state and dynamical information. We give a solution using the principle of Maximum Caliber. We find the transition rate matrix by maximizing the path entropy of a random walker on the network constrained to reproducing a stationary distribution and a few dynamical averages. A main finding here is that when constrained only by the mean jump rate, the rate matrix is given by a square-root dependence of the rate, $ω_{ab} \propto \sqrt{p_b/p_a}$, on $p_a$ and $p_b$, the stationary state populations at nodes a and b. We give two examples of our approach. First, we show that this method correctly predicts the correlated rates in a biochemical network of two genes, where we know the exact results from prior simulation. Second, we show that it correctly predicts rates of peptide conformational transitions, when compared to molecular dynamics simulations. This method can be used to infer large numbers of rates on known networks where smaller numbers of steady-state node populations are known.

preprint2015arXiv

Maximum caliber is a general variational principle for nonequilibrium statistical mechanics

There has been interest in finding a general variational principle for non-equilibrium statistical mechanics. We give evidence that Maximum Caliber (Max Cal) is such a principle. Max Cal, a variant of Maximum Entropy, predicts dynamical distribution functions by maximizing a path entropy subject to dynamical constraints, such as average fluxes. We first show that Max Cal leads to standard near-equilibrium results -including the Green-Kubo relations, Onsager's reciprocal relations of coupled flows, and Prigogine's principle of minimum entropy production -in a way that is particularly simple. More importantly, because Max Cal does not require any notion of 'local equilibrium', or any notion of entropy dissipation, or even any restriction to material physics, it is more general than many traditional approaches. We develop some generalizations of the Onsager and Prigogine results that apply arbitrarily far from equilibrium. Max Cal is not limited to materials and fluids; it also applies, for example, to flows and trafficking on networks more broadly.

preprint2015arXiv

Stationary properties of maximum entropy random walks

Maximum entropy (maxEnt) inference of state probabilities using state-dependent constraints is popular in the study of complex systems. In stochastic dynamical systems, the effect of state space topology and path-dependent constraints on the inferred state probabilities is unknown. To that end, we derive the transition probabilities and the stationary distribution of a maximum {\it path} entropy Markov process subject to state- and path-dependent constraints. The stationary distribution reflects a competition between path multiplicity and imposed constraints and is significantly different from the Boltzmann distribution. We illustrate our results with a particle diffusing on an energy landscape. Connections with the path integral approach to diffusion are discussed.

preprint2014arXiv

Inferring microscopic kinetics of a Markov process using maximum caliber

We present a principled approach for estimating the matrix of microscopic rates among states of a Markov process, given only its stationary state population distribution and a single average global kinetic observable. We adapt Maximum Caliber, a variational principle in which a path entropy is maximized over the distribution of all the possible trajectories, subject to basic kinetic constraints and some average dynamical observables. We show that this approach leads, under appropriate conditions, to the continuous-time master equation and a Smoluchowski-like equation that is valid for both equilibrium and non-equilibrium stationary states. We illustrate the method by computing the solvation dynamics of water molecules from molecular dynamics trajectories.

preprint2013arXiv

A maximum entropy thermodynamics of small systems

We present a maximum entropy approach to analyze the internal dynamics of a small system in contact with a large bath e.g. a solute-solvent system. For the small solute, the fluctuations around the mean values of observables are not negligible and the probability distribution P(r) of the state space depends on the intricate details of the interaction of the solute with the solvent. Here, we employ a superstatistical approach: P(r) is expressed as a marginal distribution summed over the variation in β, the inverse temperature of the solute. The joint distribution P(β,r) is estimated by maximizing its entropy. We also calculate the first order system-size corrections to the canonical ensemble description of the state space. We test the development on a simple harmonic oscillator interacting with two baths with very different chemical identities viz. a) Lennard-Jones particles and b) water molecules. In both cases, our method captures the state space of the oscillator sufficiently well. Future directions and connections with traditional statistical mechanics are discussed.

preprint2013arXiv

Quantifying extrinsic noise in gene expression using the maximum entropy framework

We present a maximum entropy framework to separate intrinsic and extrinsic contributions to noisy gene expression solely from the profile of expression. We express the experimentally accessible probability distribution of the copy number of the gene product (mRNA or protein) by accounting for possible variations in extrinsic factors. The distribution of extrinsic factors is estimated using the maximum entropy principle. Our results show that extrinsic factors qualitatively and quantitatively affect the probability distribution of the gene product. We work out, in detail, the transcription of mRNA from a constitutively expressed promoter in {\it E. coli}. We suggest that the variation in extrinsic factors may account for the observed {\it wider than Poisson} distribution of mRNA copy numbers. We successfully test our framework on a numerical simulation of a simple gene expression scheme that accounts for the variation in extrinsic factors. We also make falsifiable predictions, some of which are tested on previous experiments in {\it E. coli} while others need verification. Application of the current framework to more complex situations is also discussed.

preprint2011arXiv

Ion-water clusters, bulk medium effects, and ion hydration

Thermochemistry of gas-phase ion-water clusters together with estimates of the hydration free energy of the clusters and the water ligands are used to calculate the hydration free energy of the ion. Often the hydration calculations use a continuum model of the solvent. The primitive quasichemical approximation to the quasichemical theory provides a transparent framework to anchor such efforts. Here we evaluate the approximations inherent in the primitive quasichemical approach and elucidate the different roles of the bulk medium. We find that the bulk medium can stabilize configurations of the cluster that are usually not observed in the gas phase, while also simultaneously lowering the excess chemical potential of the ion. This effect is more pronounced for soft ions. Since the coordination number that minimizes the excess chemical potential of the ion is identified as the optimal or most probable coordination number, for such soft ions, the optimum cluster size and the hydration thermodynamics obtained without account of the bulk medium on the ion-water clustering reaction can be different from those observed in simulations of the aqueous ion. The ideas presented in this work are expected to be relevant to experimental studies that translate thermochemistry of ion-water clusters to the thermodynamics of the hydrated ion and to evolving theoretical approaches that combine high-level calculations on clusters with coarse-grained models of the medium.

preprint2010arXiv

Molecular packing and chemical association in liquid water simulated using ab initio hybrid Monte Carlo and different exchange-correlation functionals

In the free energy of hydration of a solute, the chemical contribution is given by the free energy required to expel water molecules from the coordination sphere and the packing contribution is given by the free energy required to create the solute-free coordination sphere (the observation volume) in bulk water. With the SPC/E water model as a reference, we examine the chemical and packing contributions in the free energy of water simulated using different electron density functionals. The density is fixed at a value corresponding to that for SPC/E water at a pressure of 1 bar. The chemical contribution shows that water simulated at 300 K with BLYP is somewhat more tightly bound than water simulated at 300 K with the revPBE functional or at 350 K with the BLYP and BLYP-D functionals. The packing contribution for various radii of the observation volume is studied. In the size range where the distribution of water molecules in the observation volume is expected to be Gaussian, the packing contribution is expected to scale with the volume of the observation sphere. Water simulated at 300 K with the revPBE and at 350 K with BLYP-D or BLYP conforms to this expectation, but the results suggest an earlier onset of system size effects in the BLYP 350 K and revPBE 300 K systems than that observed for either BLYP-D 350 K or SPC/E. The implication of this observation for constant pressure simulations is indicated. For water simulated at 300 K with BLYP, in the size range where Gaussian distribution of occupation is expected, we instead find non-Gaussian behavior, and the packing contribution scales with surface area of the observation volume, suggesting the presence of heterogeneities in the system.