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We have developed efficient parameterized algorithms for the enumeration problems of graphs arising in chemistry. In particular, we have focused on the following problems: enumeration of Kekul\'e structures, computation of Hosoya index, computation of Merrifield-Simmons index, and computation of graph entropy based on matchings and independent sets. All these problems are known to be $\# P$-complete. We have developed FPT algorithms for bounded treewidth and bounded pathwidth for these problems with a better time complexity than the known state-of-the-art in the literature. We have also conducted experiments on the entire PubChem database of chemical compounds and tested our algorithms. We also provide a comparison with naive baseline algorithms for these problems, along with a distribution of treewidth for the chemical compounds available in the PubChem database.

Template-based synthesis, also known as sketching, is a localized approach to program synthesis in which the programmer provides not only a specification, but also a high-level ``sketch'' of the program. The sketch is basically a partial program that models the general intuition of the programmer, while leaving the low-level details as unimplemented ``holes''. The role of the synthesis engine is then to fill in these holes such that the completed program satisfies the desired specification. In this work, we focus on template-based synthesis of polynomial imperative programs with real variables, i.e.~imperative programs in which all expressions appearing in assignments, conditions and guards are polynomials over program variables. While this problem can be solved in a sound and complete manner by a reduction to the first-order theory of the reals, the resulting formulas will contain a quantifier alternation and are extremely hard for modern SMT solvers, even when considering toy programs with a handful of lines. Moreover, the classical algorithms for quantifier elimination are notoriously unscalable and not at all applicable to this use-case. In contrast, our main contribution is an algorithm, based on several well-known theorems in polyhedral and real algebraic geometry, namely Putinar's Positivstellensatz, the Real Nullstellensatz, Handelman's Theorem and Farkas' Lemma, which sidesteps the quantifier elimination difficulty and reduces the problem directly to Quadratic Programming (QP). Alternatively, one can view our algorithm as an efficient way of eliminating quantifiers in the particular formulas that appear in the synthesis problem. The resulting QP instances can then be handled quite easily by SMT solvers. Notably, our reduction to QP is sound and semi-complete, i.e.~it is complete if polynomials of a sufficiently high degree are used in the templates...

We consider the global rigidity problem for bar-joint frameworks where each vertex is constrained to lie on a particular line in $\mathbb R^d$. In our setting we allow multiple vertices to be constrained to the same line. Under a mild assumption on the given set of lines we give a complete combinatorial characterisation of graphs that are generically globally rigid in this setting. This gives a $d$-dimensional extension of the well-known combinatorial characterisation of 1-dimensional global rigidity., Comment: 24 pages, 5 figures

The variety of uniform matrix product states arises both in algebraic geometry as a natural generalization of the Veronese variety, and in quantum many-body physics as a model for a translation-invariant system of sites placed on a ring. Using methods from linear algebra, representation theory, and invariant theory of matrices, we study the linear span of this variety.

Lascoux polynomials have been recently introduced to prove polynomiality of the maximum-likelihood degree of linear concentration models. We find the leading coefficient of the Lascoux polynomials (type C) and their generalizations to the case of general matrices (type A) and skew symmetric matrices (type D). In particular, we determine the degrees of such polynomials. As an application, we find the degree of the polynomial $\delta(m,n,n-s)$ of the algebraic degree of semidefinite programming, and when $s=1$ we find its leading coefficient for types C, A and D.

We study varieties associated to hypergraphs from the point of view of projective geometry and matroid theory. We describe their decompositions into matroid varieties, which may be reducible and can have arbitrary singularities by the Mn\"ev--Sturmfels universality theorem. We focus on various families of hypergraph varieties for which we explicitly compute an irredundant irreducible decomposition. Our main findings in this direction are threefold: (1) we describe minimal matroids of such hypergraphs; (2) we prove that the varieties of these matroids are irreducible and their union is the hypergraph variety; and (3) we show that every such matroid is realizable over real numbers. As corollaries, we give conceptual decompositions of various, previously-studied, varieties associated with graphs, hypergraphs, and adjacent minors of generic matrices. In particular, our decomposition strategy gives immediate matroid interpretations of the irreducible components of multiple families of varieties associated to conditional independence (CI) models in statistical theory and unravels their symmetric structures which hugely simplifies the computations., Comment: Final version to appear in International Mathematics Research Notices (IMRN)

We introduce the package "GraphicalModelsMLE" for computing the maximum likelihood estimates (MLEs) of a Gaussian graphical model in the computer algebra system Macaulay2. This package allows the computation of MLEs for the class of loopless mixed graphs. Additional functionality allows the user to explore the underlying algebraic structure of the model, such as its maximum likelihood degree and the ideal of score equations., Comment: 9 pages, 5 figures

We study the connection between probability distributions satisfying certain conditional independence (CI) constraints, and point and line arrangements in incidence geometry. To a family of CI statements, we associate a polynomial ideal whose algebraic invariants are encoded in a hypergraph. The primary decompositions of these ideals give a characterisation of the distributions satisfying the original CI statements. Classically, these ideals are generated by 2-minors of a matrix of variables, however, in the presence of hidden variables, they contain higher degree minors. This leads to the study of the structure of determinantal hypergraph ideals whose decompositions can be understood in terms of point and line configurations in the projective space., Comment: 24 pages, 5 figures