arXiv subjects
Publications and source records attributed to Alexey Ovchinnikov.
We develop new tools for constructing redactable authenticated data structures with post-quantum security. In our construction, inverting the proposed one-way function means solving a polynomial equation (or a system of polynomial equations) in more than one variable. This is presently considered quantum-safe, i.e., there is no known quantum algorithm that could solve this problem efficiently if parameters are chosen wisely.
Global parameter identifiability is a property of a parametric ODE model to recover the parameter values uniquely from the input-output data. Not all parametric ODE models have this property, and checking for parameter identifiability is a prerequisite to perform numerical parameter estimation. There are many algorithms and software packages for global parameter identifiability, and frequently the runtime is large. However, the computational complexity for this problem has not been analyzed yet, though there are complexity results for local (finitely many values fit the data) parameter identifiability. In this paper, we estimate the complexity of checking global parameter identifiability over real fields for ODE models that depend linearly on the state variables and rationally on the parameters. In particular, we prove that it is equivalent to the injectivity problem.
Recent investigations suggest that the discrete linear unitary group $U(N)$ can be represented by interlacing a finite sequence of diagonal phase operations with an intervening unitary operator. However, despite rigorous numerical justifications, no formal proof has been provided. Here, we show that elements of $U(N)$ can be decomposed into a sequence of $N$-parameter phases alternating with $1$-parameter propagators of a lattice Hamiltonian. The proof is based on building a Lie group by alternating these two operators and showing its completeness to represent $U(N)$ for a finite number of layers, which is numerically found to be exactly $N$. This architecture can be implemented using elementary optical components and can successfully reconstruct arbitrary unitary matrices. We propose example devices such as optical logic gates, which perform logic gate operations using a single-layer lossless and passive optical circuit design.
The parameter identifiability problem for a dynamical system is to determine whether the parameters of the system can be found from data for the outputs of the system. Verifying whether the parameters are identifiable is a necessary first step before a meaningful parameter estimation can take place. Non-identifiability occurs in practical models. To reparametrize a model to achieve identifiability is a challenge. The existing approaches have been shown to be useful for many important examples. However, these approaches are either limited to linear models and scaling parametrizations or are not guaranteed to find a reparametrization even if it exists. In the present paper, we prove that there always exists a locally identifiable model with the same input-output behaviour as the original one obtained from a given one by a partial specialization of the parameters. As an extra feature of our approach, the resulting (at least) locally identifiable reparameterization has the same shape: the monomials in the new state variables in the new model are formed in the same way as in the original model. Furthermore, we give a sufficient observability condition for the existence of a state space transformation from the original model to the new one. Our proof is constructive and can be translated to an algorithm, which we illustrate by several examples.
Structural identifiability concerns the question of which unknown parameters of a model can be recovered from (perfect) input-output data. If all of the parameters of a model can be recovered from data, the model is said to be identifiable. However, in many models, there are parameters that can take on an infinite number of values but yield the same input-output data. In this case, those parameters and the model are called unidentifiable. The question is then what to do with an unidentifiable model. One can try to add more input-output data or decrease the number of unknown parameters, if experimentally feasible, or try to find a reparametrization to make the model identifiable. In this paper, we take the latter approach. While existing approaches to find identifiable reparametrizations were limited to scaling reparametrizations or were not guaranteed to find a globally identifiable reparametrization even if it exists, we significantly broaden the class of models for which we can find a globally identifiable model with the same input-output behavior as the original one. We also prove that, for linear models, a globally identifiable reparametrization always exists and show that, for a certain class of linear compartmental models, with and without inputs, an explicit reparametrization formula exists. We illustrate our method on several examples and provide detailed analysis in supplementary material on github.
We consider dynamical models given by rational ODE systems. Parameter estimation is an important and challenging task of recovering parameter values from observed data. Recently, a method based on differential algebra and rational interpolation was proposed to express parameter estimation in terms of polynomial system solving. Typically, polynomial system solving is a bottleneck, hence the choice of the polynomial solver is crucial. In this contribution, we compare two polynomial system solvers applied to parameter estimation: homotopy continuation solver from HomotopyContinuation.jl and our new implementation of a certified solver based on rational univariate representation (RUR) and real root isolation. We show how the new RUR solver can tackle examples that are out of reach for the homotopy methods and vice versa.
Structural global parameter identifiability indicates whether one can determine a parameter's value in an ODE model from given inputs and outputs. If a given model has parameters for which there is exactly one value, such parameters are called globally identifiable. Given an ODE model involving not globally identifiable parameters, first we transform the system into one with locally identifiable parameters. As a main contribution of this paper, then we present a procedure for replacing, if possible, the ODE model with an equivalent one that has globally identifiable parameters. We first derive this as an algorithm for one-dimensional ODE models and then reuse this approach for higher-dimensional models.
Dynamic models describe phenomena across scientific disciplines, yet to make these models useful in application the unknown parameter values of the models must be determined. Discrete-time dynamic models are widely used to model biological processes, but it is often difficult to determine these parameters. In this paper, we propose a symbolic-numeric approach for parameter estimation in discrete-time models that involve univariate non-algebraic (locally) analytic functions such as exp. We illustrate the performance (precision) of our approach by applying our approach to two archetypal discrete-time models in biology (the flour beetle 'LPA' model and discrete Lotka-Volterra competition model). Unlike optimization-based methods, our algorithm guarantees to find all solutions of the parameter values up to a specified precision given time-series data for the measured variables provided that there are finitely many parameter values that fit the data and that the used polynomial system solver can find all roots of the associated polynomial system with interval coefficients.
Symbolic computation for systems of differential equations is often computationally expensive. Many practical differential models have a form of polynomial or rational ODE system with specified outputs. A basic symbolic approach to analyze these models is to compute and then symbolically process the polynomial system obtained by sufficiently many Lie derivatives of the output functions with respect to the vector field given by the ODE system. In this paper, we present a method for speeding up Gröbner basis computation for such a class of polynomial systems by using specific monomial ordering, including weights for the variables, coming from the structure of the ODE model. We provide empirical results that show improvement across different symbolic computing frameworks and apply the method to speed up structural identifiability analysis of ODE models.
Imaging Mueller polarimetry has already proved its potential for metrology, remote sensing and biomedicine. The real-time applications of this modality require both video rate image acquisition and fast data post-processing algorithms. First, one must check the physical realizability of the experimental Mueller matrices in order to filter out non-physical data, i.e. to test the positive semi-definiteness of the 4x4 Hermitian coherency matrix calculated from the elements of the corresponding Mueller matrix pixel-wise. For this purpose, we compared the execution time for the calculations of i) eigenvalues, ii) Cholesky decomposition, iii) Sylvester's criterion, and iv) coefficients of the characteristic polynomial of the Hermitian coherency matrix using two different approaches, all calculated for the experimental Mueller matrix images (600 pixels x 700 pixels) of mouse uterine cervix. The calculations were performed using C++ and Julia programming languages. Our results showed the superiority of the algorithm iv), in particular, the version based on the simplification via Pauli matrices, in terms of execution time for our dataset, over other algorithms. The sequential implementation of the latter algorithm on a single core already satisfies the requirements of real-time polarimetric imaging in various domains. This can be further amplified by the proposed parallelization (for example, we achieve a 5-fold speed up on 6 cores).
Differential equation models are crucial to scientific processes. The values of model parameters are important for analyzing the behaviour of solutions. A parameter is called globally identifiable if its value can be uniquely determined from the input and output functions. To determine if a parameter estimation problem is well-posed for a given model, one must check if the model parameters are globally identifiable. This problem has been intensively studied for ordinary differential equation models, with theory and several efficient algorithms and software packages developed. A comprehensive theory of algebraic identifiability for PDEs has hitherto not been developed due to the complexity of initial and boundary conditions. Here, we provide theory and algorithms, based on differential algebra, for testing identifiability of polynomial PDE models. We showcase this approach on PDE models arising in the sciences.
We present a new approach for estimating parameters in rational ODE models from given (measured) time series data. In typical existing approaches, an initial guess for the parameter values is made from a given search interval. Then, in a loop, the corresponding outputs are computed by solving the ODE numerically, followed by computing the error from the given time series data. If the error is small, the loop terminates and the parameter values are returned. Otherwise, heuristics/theories are used to possibly improve the guess and continue the loop. These approaches tend to be non-robust in the sense that their accuracy depend on the search interval and the true parameter values; furthermore, they cannot handle the case where the parameters are locally identifiable. In this paper, we propose a new approach, which does not suffer from the above non-robustness. In particular, it does not require making good initial guesses for the parameter values or specifying search intervals. Instead, it uses differential algebra, interpolation of the data using rational functions, and multivariate polynomial system solving. We also compare the performance of the resulting software with several other estimation software packages.
We offer a digital signature scheme using Boolean automorphisms of a multivariate polynomial algebra over integers. Verification part of this scheme is based on the approximation of the number of zeros of a multivariate Boolean function.
Many real-world processes and phenomena are modeled using systems of ordinary differential equations with parameters. Given such a system, we say that a parameter is globally identifiable if it can be uniquely recovered from input and output data. The main contribution of this paper is to provide theory, an algorithm, and software for deciding global identifiability. First, we rigorously derive an algebraic criterion for global identifiability (this is an analytic property), which yields a deterministic algorithm. Second, we improve the efficiency by randomizing the algorithm while guaranteeing the probability of correctness. With our new algorithm, we can tackle problems that could not be tackled before. A software based on the algorithm (called SIAN) is available at https://github.com/pogudingleb/SIAN.
Structural global parameter identifiability indicates whether one can determine a parameter's value from given inputs and outputs in the absence of noise. If a given model has parameters for which there may be infinitely many values, such parameters are called non-identifiable. We present a procedure for accelerating a global identifiability query by eliminating algebraically independent non-identifiable parameters. Our proposed approach significantly improves performance across different computer algebra frameworks.
Structural identifiability is a property of a differential model with parameters that allows for the parameters to be determined from the model equations in the absence of noise. The method of input-output equations is one method for verifying structural identifiability. This method stands out in its importance because the additional insights it provides can be used to analyze and improve models. However, its complete theoretical grounds and applicability are still to be established. A subtlety and key for this method to work correctly is knowing whether the coefficients of these equations are identifiable. In this paper, to address this, we prove identifiability of the coefficients of input-output equations for types of differential models that often appear in practice, such as linear models with one output and linear compartment models in which, from each compartment, one can reach either a leak or an input. This shows that checking identifiability via input-output equations for these models is legitimate and, as we prove, that the field of identifiable functions is generated by the coefficients of the input-output equations. Finally, we exploit a connection between input-output equations and the transfer function matrix to show that, for a linear compartment model with an input and strongly connected graph, the field of all identifiable functions is generated by the coefficients of the transfer function matrix even if the initial conditions are generic.
Consider an algorithm computing in a differential field with several commuting derivations such that the only operations it performs with the elements of the field are arithmetic operations, differentiation, and zero testing. We show that, if the algorithm is guaranteed to terminate on every input, then there is a computable upper bound for the size of the output of the algorithm in terms of the size of the input. We also generalize this to algorithms working with models of good enough theories (including for example, difference fields). We then apply this to differential algebraic geometry to show that there exists a computable uniform upper bound for the number of components of any variety defined by a system of polynomial PDEs. We then use this bound to show the existence of a computable uniform upper bound for the elimination problem in systems of polynomial PDEs with delays.
Structural identifiability is a property of an ODE model with parameters that allows for the parameters to be determined from continuous noise-free data. This is a natural prerequisite for practical identifiability. Conducting multiple independent experiments could make more parameters or functions of parameters identifiable, which is a desirable property to have. How many experiments are sufficient? In the present paper, we provide an algorithm to determine the exact number of experiments for multi-experiment local identifiability and obtain an upper bound that is off at most by one for the number of experiments for multi-experiment global identifiability. Interestingly, the main theoretical ingredient of the algorithm has been discovered and proved using model theory (in the sense of mathematical logic). We hope that this unexpected connection will stimulate interactions between applied algebra and model theory, and we provide a short introduction to model theory in the context of parameter identifiability. As another related application of model theory in this area, we construct a nonlinear ODE system with one output such that single-experiment and multiple-experiment identifiability are different for the system. This contrasts with recent results about single-output linear systems. We also present a Monte Carlo randomized version of the algorithm with a polynomial arithmetic complexity. Implementation of the algorithm is provided and its performance is demonstrated on several examples. The source code is available at https://github.com/pogudingleb/ExperimentsBound.