Efficient Identification of Equivalences in Dynamic Graphs and Pedigree Structures

We propose a new framework for designing test and query functions for complex structures that vary across a given parameter such as genetic marker position. The operations we are interested in include equality testing, set operations, isolating unique states, duplication counting, or finding equivalence classes under identifiability constraints. A motivating application is locating equivalence classes in identity-by-descent (IBD) graphs, graph structures in pedigree analysis that change over genetic marker location. The nodes of these graphs are unlabeled and identified only by their connecting edges, a constraint easily handled by our approach. The general framework introduced is powerful enough to build a range of testing functions for IBD graphs, dynamic populations, and other structures using a minimal set of operations. The theoretical and algorithmic properties of our approach are analyzed and proved. Computational results on several simulations demonstrate the effectiveness of our approach.Comment: Code for paper available at http://www.stat.washington.edu/~hoytak/code/hashreduc

Submodular Minimization Under Congruency Constraints

Submodular function minimization (SFM) is a fundamental and efficiently solvable problem class in combinatorial optimization with a multitude of applications in various fields. Surprisingly, there is only very little known about constraint types under which SFM remains efficiently solvable. The arguably most relevant non-trivial constraint class for which polynomial SFM algorithms are known are parity constraints, i.e., optimizing only over sets of odd (or even) cardinality. Parity constraints capture classical combinatorial optimization problems like the odd-cut problem, and they are a key tool in a recent technique to efficiently solve integer programs with a constraint matrix whose subdeterminants are bounded by two in absolute value. We show that efficient SFM is possible even for a significantly larger class than parity constraints, by introducing a new approach that combines techniques from Combinatorial Optimization, Combinatorics, and Number Theory. In particular, we can show that efficient SFM is possible over all sets (of any given lattice) of cardinality r mod m, as long as m is a constant prime power. This covers generalizations of the odd-cut problem with open complexity status, and with relevance in the context of integer programming with higher subdeterminants. To obtain our results, we establish a connection between the correctness of a natural algorithm, and the inexistence of set systems with specific combinatorial properties. We introduce a general technique to disprove the existence of such set systems, which allows for obtaining extensions of our results beyond the above-mentioned setting. These extensions settle two open questions raised by Geelen and Kapadia [Combinatorica, 2017] in the context of computing the girth and cogirth of certain types of binary matroids

Polynomials that Sign Represent Parity and Descartes' Rule of Signs

A real polynomial $P(X_1,..., X_n)$ sign represents $f: A^n \to \{0,1\}$ if for every $(a_1, ..., a_n) \in A^n$, the sign of $P(a_1,...,a_n)$ equals $(-1)^{f(a_1,...,a_n)}$. Such sign representations are well-studied in computer science and have applications to computational complexity and computational learning theory. In this work, we present a systematic study of tradeoffs between degree and sparsity of sign representations through the lens of the parity function. We attempt to prove bounds that hold for any choice of set $A$. We show that sign representing parity over $\{0,...,m-1\}^n$ with the degree in each variable at most $m-1$ requires sparsity at least $m^n$. We show that a tradeoff exists between sparsity and degree, by exhibiting a sign representation that has higher degree but lower sparsity. We show a lower bound of $n(m -2) + 1$ on the sparsity of polynomials of any degree representing parity over $\{0,..., m-1\}^n$. We prove exact bounds on the sparsity of such polynomials for any two element subset $A$. The main tool used is Descartes' Rule of Signs, a classical result in algebra, relating the sparsity of a polynomial to its number of real roots. As an application, we use bounds on sparsity to derive circuit lower bounds for depth-two AND-OR-NOT circuits with a Threshold Gate at the top. We use this to give a simple proof that such circuits need size $1.5^n$ to compute parity, which improves the previous bound of ${4/3}^{n/2}$ due to Goldmann (1997). We show a tight lower bound of $2^n$ for the inner product function over $\{0,1\}^n \times \{0, 1\}^n$.Comment: To appear in Computational Complexit