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Dima Grigoriev

Publications and source records attributed to Dima Grigoriev.

At least 55 records · Page 3Linked to original sources
arXiv2015

Model reduction of biochemical reactions networks by tropical analysis methods

We discuss a method of approximate model reduction for networks of biochemical reactions. This method can be applied to networks with polynomial or rational reaction rates and whose parameters are given by their orders of magnitude. In order to obtain reduced models we solve the problem of tropical equilibration that is a system of equations in max-plus algebra. In the case of networks with nonlinear fast cycles we have to solve the problem of tropical equilibration at least twice, once for the initial system and a second time for an extended system obtained by adding to the initial system the differential equations satisfied by the conservation laws of the fast subsystem. The two steps can be reiterated until the fast subsystem has no conservation laws different from the ones of the full model. Our method can be used for formal model reduction in computational systems biology.

q-bio.MN↗
arXiv2015

Tropical differential equations

Tropical differential equations are introduced and an algorithm is designed which tests solvability of a system of tropical linear differential equations within the complexity polynomial in the size of the system and in its coefficients. Moreover, we show that there exists a minimal solution, and the algorithm constructs it (in case of solvability). This extends a similar complexity bound established for tropical linear systems. In case of tropical linear differential systems in one variable a polynomial complexity algorithm for testing its solvability is designed. We prove also that the problem of solvability of a system of tropical non-linear differential equations in one variable is $NP$-hard, and this problem for arbitrary number of variables belongs to $NP$. Similar to tropical algebraic equations, a tropical differential equation expresses the (necessary) condition on the dominant term in the issue of solvability of a differential equation in power series.

cs.SC↗
arXiv2014

Subtraction-free complexity, cluster transformations, and spanning trees

Subtraction-free computational complexity is the version of arithmetic circuit complexity that allows only three operations: addition, multiplication, and division. We use cluster transformations to design efficient subtraction-free algorithms for computing Schur functions and their skew, double, and supersymmetric analogues, thereby generalizing earlier results by P. Koev. We develop such algorithms for computing generating functions of spanning trees, both directed and undirected. A comparison to the lower bound due to M. Jerrum and M. Snir shows that in subtraction-free computations, "division can be exponentially powerful." Finally, we give a simple example where the gap between ordinary and subtraction-free complexity is exponential.

math.CO↗
arXiv2013

Yao's millionaires' problem and decoy-based public key encryption by classical physics

We use various laws of classical physics to offer several solutions of Yao's millionaires' problem without using any one-way functions. We also describe several informationally secure public key encryption protocols, i.e., protocols secure against passive computationally unbounded adversary. This introduces a new paradigm of decoy-based cryptography, as opposed to "traditional" complexity-based cryptography. In particular, our protocols do not employ any one-way functions.

cs.CR↗
arXiv2013

Tropicalization and tropical equilibration of chemical reactions

Systems biology uses large networks of biochemical reactions to model the functioning of biological cells from the molecular to the cellular scale. The dynamics of dissipative reaction networks with many well separated time scales can be described as a sequence of successive equilibrations of different subsets of variables of the system. Polynomial systems with separation are equilibrated when at least two monomials, of opposite signs, have the same order of magnitude and dominate the others. These equilibrations and the corresponding truncated dynamics, obtained by eliminating the dominated terms, find a natural formulation in tropical analysis and can be used for model reduction.

q-bio.MN↗
arXiv2013

Secrecy without one-way functions

We show that some problems in information security can be solved without using one-way functions. The latter are usually regarded as a central concept of cryptography, but the very existence of one-way functions depends on difficult conjectures in complexity theory, most notably on the notorious "$P \ne NP$" conjecture. In this paper, we suggest protocols for secure computation of the sum, product, and some other functions, without using any one-way functions. A new input that we offer here is that, in contrast with other proposals, we conceal "intermediate results" of a computation. For example, when we compute the sum of $k$ numbers, only the final result is known to the parties; partial sums are not known to anybody. Other applications of our method include voting/rating over insecure channels and a rather elegant and efficient solution of Yao's "millionaires' problem". Then, while it is fairly obvious that a secure (bit) commitment between two parties is impossible without a one-way function, we show that it is possible if the number of parties is at least 3. We also show how our (bit) commitment scheme for 3 parties can be used to arrange an unconditionally secure (bit) commitment between just two parties if they use a "dummy" (e.g., a computer) as the third party. We explain how our concept of a "dummy" is different from a well-known concept of a "trusted third party". We also suggest a protocol, without using a one-way function, for "mental poker", i.e., a fair card dealing (and playing) over distance. We also propose a secret sharing scheme where an advantage over Shamir's and other known secret sharing schemes is that nobody, including the dealer, ends up knowing the shares owned by any particular player. It should be mentioned that computational cost of our protocols is negligible to the point that all of them can be executed without a computer.

cs.CR↗
arXiv2013

Tropical cryptography

We employ tropical algebras as platforms for several cryptographic schemes that would be vulnerable to linear algebra attacks were they based on "usual" algebras as platforms.

cs.CR↗
arXiv2012

Hybrid models of the cell cycle molecular machinery

Piecewise smooth hybrid systems, involving continuous and discrete variables, are suitable models for describing the multiscale regulatory machinery of the biological cells. In hybrid models, the discrete variables can switch on and off some molecular interactions, simulating cell progression through a series of functioning modes. The advancement through the cell cycle is the archetype of such an organized sequence of events. We present an approach, inspired from tropical geometry ideas, allowing to reduce, hybridize and analyse cell cycle models consisting of polynomial or rational ordinary differential equations.

cs.CE↗
arXiv2012

Effective Hironaka resolution and its Complexity (with appendix on applications in positive characteristic)

Building upon works of Hironaka, Bierstone-Milman, Villamayor and Wlodarczyk, we give an a priori estimate for the complexity of the simplified Hironaka algorithm. As a consequence of this result, we show that there exists canonical Hironaka embedded desingularization and principalization over fields of large characteristic (relative to the degrees of generating polynomials).

math.AG↗
arXiv2012

Complexity of tropical and min-plus linear prevarieties

A tropical (or min-plus) semiring is a set $\mathbb{Z}$ (or $\mathbb{Z \cup \{\infty\}}$) endowed with two operations: $\oplus$, which is just usual minimum, and $\odot$, which is usual addition. In tropical algebra the vector $x$ is a solution to a polynomial $g_1(x) \oplus g_2(x) \oplus...\oplus g_k(x)$, where $g_i(x)$'s are tropical monomials, if the minimum in $\min_i(g_{i}(x))$ is attained at least twice. In min-plus algebra solutions of systems of equations of the form $g_1(x)\oplus...\oplus g_k(x) = h_1(x)\oplus...\oplus h_l(x)$ are studied. In this paper we consider computational problems related to tropical linear system. We show that the solvability problem (both over $\mathbb{Z}$ and $\mathbb{Z} \cup \{\infty\}$) and the problem of deciding the equivalence of two linear systems (both over $\mathbb{Z}$ and $\mathbb{Z} \cup \{\infty\}$) are equivalent under polynomial-time reduction to mean payoff games and are also equivalent to analogous problems in min-plus algebra. In particular, all these problems belong to $\mathsf{NP} \cap \mathsf{coNP}$. Thus we provide a tight connection of computational aspects of tropical linear algebra with mean payoff games and min-plus linear algebra. On the other hand we show that computing the dimension of the solution space of a tropical linear system and of a min-plus linear system are $\mathsf{NP}$-complete. We also extend some of our results to the systems of min-plus linear inequalities.

cs.CC↗
arXiv2011

Tropical geometries and dynamics of biochemical networks. Application to hybrid cell cycle models

We use the Litvinov-Maslov correspondence principle to reduce and hybridize networks of biochemical reactions. We apply this method to a cell cycle oscillator model. The reduced and hybridized model can be used as a hybrid model for the cell cycle. We also propose a practical recipe for detecting quasi-equilibrium QE reactions and quasi-steady state QSS species in biochemical models with rational rate functions and use this recipe for model reduction. Interestingly, the QE/QSS invariant manifold of the smooth model and the reduced dynamics along this manifold can be put into correspondence to the tropical variety of the hybridization and to sliding modes along this variety, respectively

q-bio.MN↗
arXiv2011

On a tropical dual Nullstellensatz

Since a tropical Nullstellensatz fails even for tropical univariate polynomials we study a conjecture on a tropical {\it dual} Nullstellensatz for tropical polynomial systems in terms of solvability of a tropical linear system with the Cayley matrix associated to the tropical polynomial system. The conjecture on a tropical effective dual Nullstellensatz is proved for tropical univariate polynomials.

math.AC↗
arXiv2010

Authentication from matrix conjugation

We propose an authentication scheme where forgery (a.k.a. impersonation) seems infeasible without finding the prover's long-term private key. The latter would follow from solving the conjugacy search problem in the platform (noncommutative) semigroup, i.e., to recovering X from X^{-1}AX and A. The platform semigroup that we suggest here is the semigroup of nxn matrices over truncated multivariable polynomials over a ring.

cs.CR↗
arXiv2008

Zero-knowledge authentication schemes from actions on graphs, groups, or rings

We propose a general way of constructing zero-knowledge authentication schemes from actions of a semigroup on a set, without exploiting any specific algebraic properties of the set acted upon. Then we give several concrete realizations of this general idea, and in particular, we describe several zero-knowledge authentication schemes where forgery (a.k.a. impersonation) is NP-hard. Computationally hard problems that can be employed in these realizations include (Sub)graph Isomorphism, Graph Colorability, Diophantine Problem, and many others.

cs.CR↗
arXiv2007

Probabilistic communication complexity over the reals

Deterministic and probabilistic communication protocols are introduced in which parties can exchange the values of polynomials (rather than bits in the usual setting). It is established a sharp lower bound $2n$ on the communication complexity of recognizing the $2n$-dimensional orthant, on the other hand the probabilistic communication complexity of its recognizing does not exceed 4. A polyhedron and a union of hyperplanes are constructed in $\RR^{2n}$ for which a lower bound $n/2$ on the probabilistic communication complexity of recognizing each is proved. As a consequence this bound holds also for the EMPTINESS and the KNAPSACK problems.

cs.CC↗
arXiv2007

Complexity of Janet basis of a D-module

We prove a double-exponential upper bound on the degree and on the complexity of constructing a Janet basis of a $D$-module. This generalizes a well known bound on the complexity of a Gröbner basis of a module over the algebra of polynomials. We would like to emphasize that the obtained bound can not be immediately deduced from the commutative case.

math.AP↗
arXiv2004

Polynomial-time computing over quadratic maps I: sampling in real algebraic sets

Given a quadratic map Q : K^n -> K^k defined over a computable subring D of a real closed field K, and a polynomial p(Y_1,...,Y_k) of degree d, we consider the zero set Z=Z(p(Q(X)),K^n) of the polynomial p(Q(X_1,...,X_n)). We present a procedure that computes, in (dn)^O(k) arithmetic operations in D, a set S of (real univariate representations of) sampling points in K^n that intersects nontrivially each connected component of Z. As soon as k=o(n), this is faster than the standard methods that all have exponential dependence on n in the complexity. In particular, our procedure is polynomial-time for constant k. In contrast, the best previously known procedure (due to A.Barvinok) is only capable of deciding in n^O(k^2) operations the nonemptiness (rather than constructing sampling points) of the set Z in the case of p(Y)=sum_i Y_i^2 and homogeneous Q. A by-product of our procedure is a bound (dn)^O(k) on the number of connected components of Z. The procedure consists of exact symbolic computations in D and outputs vectors of algebraic numbers. It involves extending K by infinitesimals and subsequent limit computation by a novel procedure that utilizes knowledge of an explicit isomorphism between real algebraic sets.

cs.SC↗