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Dima Grigoriev

Publications and source records attributed to Dima Grigoriev.

At least 37 records · Page 2Linked to original sources
arXiv2019

Complexity of deciding whether a tropical linear prevariety is a tropical variety

We give an algorithm, with a singly exponential complexity, deciding whether a tropical linear prevariety is a tropical linear variety. The algorithm relies on a criterion to be a tropical linear variety in terms of a duality between the tropical orthogonalization $A^\perp$ and the double tropical orthogonalization $A^{\perp \perp}$ of a subset $A$ of the vector space $({\mathbb R} \cup \{ \infty \})^n$. We also give an example of a countable family of tropical hyperplanes such that their intersection is not a tropical prevariety.

math.AG↗
arXiv2019

Key-agreement based on automaton groups

We suggest several automaton groups as key-agreement platforms for Anshl-Anshel-Goldfeld metascheme, they include Grigorchuk and universal Grigorchuk groups, Hanoi 3-Towers group, Basilica group and a subgroup of the affine group with the unsolvable conjugacy problem

cs.CR↗
arXiv2019

Tropical Combinatorial Nullstellensatz and Sparse Polynomials

Tropical algebra emerges in many fields of mathematics such as algebraic geometry, mathematical physics and combinatorial optimization. In part, its importance is related to the fact that it makes various parameters of mathematical objects computationally accessible. Tropical polynomials play a fundamental role in this, especially for the case of algebraic geometry. On the other hand, many algebraic questions behind tropical polynomials remain open. In this paper we address four basic questions on tropical polynomials closely related to their computational properties: 1. Given a polynomial with a certain support (set of monomials) and a (finite) set of inputs, when is it possible for the polynomial to vanish on all these inputs? 2. A more precise question, given a polynomial with a certain support and a (finite) set of inputs, how many roots can this polynomial have on this set of inputs? 3. Given an integer $k$, for which $s$ there is a set of $s$ inputs such that any non-zero polynomial with at most $k$ monomials has a non-root among these inputs? 4. How many integer roots can have a one variable polynomial given by a tropical algebraic circuit? In the classical algebra well-known results in the direction of these questions are Combinatorial Nullstellensatz due to N. Alon, J. Schwartz - R. Zippel Lemma and Universal Testing Set for sparse polynomials respectively. The classical analog of the last question is known as $τ$-conjecture due to M. Shub - S. Smale. In this paper we provide results on these four questions for tropical polynomials.

math.AG↗
arXiv2019

Decomposing tropical rational functions

An algorithm is designed which decomposes a tropical univariate rational function into a composition of tropical binomials and trinomials. When a function is monotone, the composition consists just of binomials. Similar algorithms are designed for decomposing tropical algebraic rational functions being (in the classical language) piece-wise linear functions with rational slopes of their linear pieces. In addition, we provide a criterion when the composition of two tropical polynomials commutes (for classical polynomials a similar question was answered by J.~Ritt).

math.AG↗
arXiv2019

On a tropical version of the Jacobian conjecture

We prove for a tropical rational map that if for any point the convex hull of Jacobian matrices at smooth points in a neighborhood of the point does not contain singular matrices then the map is an isomorphism. We also show that a tropical polynomial map on the plane is an isomorphism if all the Jacobians have the same sign (positive or negative). In addition, for a tropical rational map we prove that if the Jacobians have the same sign and if its preimage is a singleton at least at one regular point then the map is an isomorphism.

math.AG↗
arXiv2018

Tropical Newton-Puiseux polynomials

We introduce tropical Newton-Puiseux polynomials admitting rational exponents. A resolution of a tropical hypersurface is defined by means of a tropical Newton-Puiseux polynomial. A polynomial complexity algorithm for resolubility of a tropical curve is designed. The complexity of resolubility of tropical prevarieties of arbitrary codimensions is studied. Tropical Newton-Puiseux rational functions are introduced, and we prove that any tropical polynomial has a resolution in tropical Newton-Puiseux rational functions (this can be treated as a tropical analog of the algebraic closedness of the field of Newton-Puiseux series).

math.AG↗
arXiv2018

On semiring complexity of Schur polynomials

Semiring complexity is the version of arithmetic circuit complexity that allows only two operations: addition and multiplication. We show that when the number of variables is fixed, the semiring complexity of a Schur polynomial $s_λ$ is $O(log(λ_1))$; here $λ_1$ is the largest part of the partition $λ$.

cs.CC↗
arXiv2018

Upper bounds on Betti numbers of tropical prevarieties

We prove upper bounds on the sum of Betti numbers of tropical prevarieties in dense and sparse settings. In the dense setting the bound is in terms of the volume of Minkowski sum of Newton polytopes of defining tropical polynomials, or, alternatively, via the maximal degree of these polynomials. In sparse setting, the bound involves the number of the monomials.

math.AG↗
arXiv2017

Symbolic Versus Numerical Computation and Visualization of Parameter Regions for Multistationarity of Biological Networks

We investigate models of the mitogenactivated protein kinases (MAPK) network, with the aim of determining where in parameter space there exist multiple positive steady states. We build on recent progress which combines various symbolic computation methods for mixed systems of equalities and inequalities. We demonstrate that those techniques benefit tremendously from a newly implemented graph theoretical symbolic preprocessing method. We compare computation times and quality of results of numerical continuation methods with our symbolic approach before and after the application of our preprocessing.

cs.SC↗
arXiv2017

A Case Study on the Parametric Occurrence of Multiple Steady States

We consider the problem of determining multiple steady states for positive real values in models of biological networks. Investigating the potential for these in models of the mitogen-activated protein kinases (MAPK) network has consumed considerable effort using special insights into the structure of corresponding models. Here we apply combinations of symbolic computation methods for mixed equality/inequality systems, specifically virtual substitution, lazy real triangularization and cylindrical algebraic decomposition. We determine multistationarity of an 11-dimensional MAPK network when numeric values are known for all but potentially one parameter. More precisely, our considered model has 11 equations in 11 variables and 19 parameters, 3 of which are of interest for symbolic treatment, and furthermore positivity conditions on all variables and parameters.

cs.SC↗
arXiv2015

Bounds on the number of connected components for tropical prevarieties

For a tropical prevariety in ${R}^n$ given by a system of $k$ tropical polynomials in $n$ variables with degrees at most $d$, we prove that its number of connected components is less than ${k+7n-1 \choose 3n} \cdot \frac{d^{3n}}{k+n+1}$. On a number of $0$-dimensional connected components a better bound ${k+4n \choose 3n} \cdot \frac{d^n}{k+n+1}$ is obtained, which extends the Bezout bound due to B.~Sturmfels from the the case $k=n$ to an arbitrary $k\ge n$. Also we show that the latter bound is close to sharp, in particular, the number of connected components can depend on $k$.

math.AG↗
arXiv2015

Geometric analysis of pathways dynamics: application to versatility of TGF-β receptors

We propose a new geometric approach to describe the qualitative dynamics of chemical reactions networks. By this method we identify metastable regimes, defined as low dimensional regions of the phase space close to which the dynamics is much slower compared to the rest of the phase space. Given the network topology and the orders of magnitude of kinetic parameters, the number of such metastable regimes is finite. The dynamics of the network can be described as a sequence of jumps from one metastable regime to another. We show that a geometrically computed connectivity graph restricts the set of possible jumps. We also provide finite state machine (Markov chain) models for such dynamic changes. Applied to signal transduction models, our approach unravels dynamical and functional capacities of signaling pathways, as well as parameters responsible for specificity of the pathway response. In particular, for a model of TGF$β$ signalling, we find that the ratio of TGFBR1 to TGFBR2 concentrations can be used to discriminate between metastable regimes. Using expression data from the NCI60 panel of human tumor cell lines, we show that aggressive and non-aggressive tumour cell lines function in different metastable regimes and can be distinguished by measuring the relative concentrations of receptors of the two types.

q-bio.MN↗
arXiv2015

A geometric method for model reduction of biochemical networks with polynomial rate functions

Model reduction of biochemical networks relies on the knowledge of slow and fast variables. We provide a geometric method, based on the Newton polytope, to identify slow variables of a biochemical network with polynomial rate functions. The gist of the method is the notion of tropical equilibration that provides approximate descriptions of slow invariant manifolds. Compared to extant numerical algorithms such as the intrinsic low dimensional manifold method, our approach is symbolic and utilizes orders of magnitude instead of precise values of the model parameters. Application of this method to a large collection of biochemical network models supports the idea that the number of dynamical variables in minimal models of cell physiology can be small, in spite of the large number of molecular regulatory actors.

q-bio.MN↗
arXiv2015

Analysis of Reaction Network Systems Using Tropical Geometry

We discuss a novel analysis method for reaction network systems with polynomial or rational rate functions. This method is based on computing tropical equilibrations defined by the equality of at least two dominant monomials of opposite signs in the differential equations of each dynamic variable. In algebraic geometry, the tropical equilibration problem is tantamount to finding tropical prevarieties, that are finite intersections of tropical hypersurfaces. Tropical equilibrations with the same set of dominant monomials define a branch or equivalence class. Minimal branches are particularly interesting as they describe the simplest states of the reaction network. We provide a method to compute the number of minimal branches and to find representative tropical equilibrations for each branch.

q-bio.MN↗
arXiv2015

Symbolic dynamics of biochemical pathways as finite states machines

We discuss the symbolic dynamics of biochemical networks with separate timescales. We show that symbolic dynamics of monomolecular reaction networks with separated rate constants can be described by deterministic, acyclic automata with a number of states that is inferior to the number of biochemical species. For nonlinear pathways, we propose a general approach to approximate their dynamics by finite state machines working on the metastable states of the network (long life states where the system has slow dynamics). For networks with polynomial rate functions we propose to compute metastable states as solutions of the tropical equilibration problem. Tropical equilibrations are defined by the equality of at least two dominant monomials of opposite signs in the differential equations of each dynamic variable. In algebraic geometry, tropical equilibrations are tantamount to tropical prevarieties, that are finite intersections of tropical hypersurfaces.

q-bio.MN↗
arXiv2015

Tropical Effective Primary and Dual Nullstellensätze

Tropical algebra is an emerging field with a number of applications in various areas of mathematics. In many of these applications appeal to tropical polynomials allows to study properties of mathematical objects such as algebraic varieties and algebraic curves from the computational point of view. This makes it important to study both mathematical and computational aspects of tropical polynomials. In this paper we prove a tropical Nullstellensatz and moreover we show an effective formulation of this theorem. Nullstellensatz is a natural step in building algebraic theory of tropical polynomials and its effective version is relevant for computational aspects of this field. On our way we establish a simple formulation of min-plus and tropical linear dualities. We also observe a close connection between tropical and min-plus polynomial systems.

math.AG↗