On unrooted and root-uncertain variants of several well-known phylogenetic network problems

The hybridization number problem requires us to embed a set of binary rooted phylogenetic trees into a binary rooted phylogenetic network such that the number of nodes with indegree two is minimized. However, from a biological point of view accurately inferring the root location in a phylogenetic tree is notoriously difficult and poor root placement can artificially inflate the hybridization number. To this end we study a number of relaxed variants of this problem. We start by showing that the fundamental problem of determining whether an \emph{unrooted} phylogenetic network displays (i.e. embeds) an \emph{unrooted} phylogenetic tree, is NP-hard. On the positive side we show that this problem is FPT in reticulation number. In the rooted case the corresponding FPT result is trivial, but here we require more subtle argumentation. Next we show that the hybridization number problem for unrooted networks (when given two unrooted trees) is equivalent to the problem of computing the Tree Bisection and Reconnect (TBR) distance of the two unrooted trees. In the third part of the paper we consider the "root uncertain" variant of hybridization number. Here we are free to choose the root location in each of a set of unrooted input trees such that the hybridization number of the resulting rooted trees is minimized. On the negative side we show that this problem is APX-hard. On the positive side, we show that the problem is FPT in the hybridization number, via kernelization, for any number of input trees.Comment: 28 pages, 8 Figure

On the hardness of learning sparse parities

This work investigates the hardness of computing sparse solutions to systems of linear equations over F_2. Consider the k-EvenSet problem: given a homogeneous system of linear equations over F_2 on n variables, decide if there exists a nonzero solution of Hamming weight at most k (i.e. a k-sparse solution). While there is a simple O(n^{k/2})-time algorithm for it, establishing fixed parameter intractability for k-EvenSet has been a notorious open problem. Towards this goal, we show that unless k-Clique can be solved in n^{o(k)} time, k-EvenSet has no poly(n)2^{o(sqrt{k})} time algorithm and no polynomial time algorithm when k = (log n)^{2+eta} for any eta > 0. Our work also shows that the non-homogeneous generalization of the problem -- which we call k-VectorSum -- is W[1]-hard on instances where the number of equations is O(k log n), improving on previous reductions which produced Omega(n) equations. We also show that for any constant eps > 0, given a system of O(exp(O(k))log n) linear equations, it is W[1]-hard to decide if there is a k-sparse linear form satisfying all the equations or if every function on at most k-variables (k-junta) satisfies at most (1/2 + eps)-fraction of the equations. In the setting of computational learning, this shows hardness of approximate non-proper learning of k-parities. In a similar vein, we use the hardness of k-EvenSet to show that that for any constant d, unless k-Clique can be solved in n^{o(k)} time there is no poly(m, n)2^{o(sqrt{k}) time algorithm to decide whether a given set of m points in F_2^n satisfies: (i) there exists a non-trivial k-sparse homogeneous linear form evaluating to 0 on all the points, or (ii) any non-trivial degree d polynomial P supported on at most k variables evaluates to zero on approx. Pr_{F_2^n}[P(z) = 0] fraction of the points i.e., P is fooled by the set of points

Maximum-likelihood decoding of Reed-Solomon Codes is NP-hard

Maximum-likelihood decoding is one of the central algorithmic problems in coding theory. It has been known for over 25 years that maximum-likelihood decoding of general linear codes is NP-hard. Nevertheless, it was so far unknown whether maximum- likelihood decoding remains hard for any specific family of codes with nontrivial algebraic structure. In this paper, we prove that maximum-likelihood decoding is NP-hard for the family of Reed-Solomon codes. We moreover show that maximum-likelihood decoding of Reed-Solomon codes remains hard even with unlimited preprocessing, thereby strengthening a result of Bruck and Naor.Comment: 16 pages, no figure

The Complexity of Relating Quantum Channels to Master Equations

Completely positive, trace preserving (CPT) maps and Lindblad master equations are both widely used to describe the dynamics of open quantum systems. The connection between these two descriptions is a classic topic in mathematical physics. One direction was solved by the now famous result due to Lindblad, Kossakowski Gorini and Sudarshan, who gave a complete characterisation of the master equations that generate completely positive semi-groups. However, the other direction has remained open: given a CPT map, is there a Lindblad master equation that generates it (and if so, can we find it's form)? This is sometimes known as the Markovianity problem. Physically, it is asking how one can deduce underlying physical processes from experimental observations. We give a complexity theoretic answer to this problem: it is NP-hard. We also give an explicit algorithm that reduces the problem to integer semi-definite programming, a well-known NP problem. Together, these results imply that resolving the question of which CPT maps can be generated by master equations is tantamount to solving P=NP: any efficiently computable criterion for Markovianity would imply P=NP; whereas a proof that P=NP would imply that our algorithm already gives an efficiently computable criterion. Thus, unless P does equal NP, there cannot exist any simple criterion for determining when a CPT map has a master equation description. However, we also show that if the system dimension is fixed (relevant for current quantum process tomography experiments), then our algorithm scales efficiently in the required precision, allowing an underlying Lindblad master equation to be determined efficiently from even a single snapshot in this case. Our work also leads to similar complexity-theoretic answers to a related long-standing open problem in probability theory.Comment: V1: 43 pages, single column, 8 figures. V2: titled changed; added proof-overview and accompanying figure; 50 pages, single column, 9 figure