Searching for interacting QTL in related populations of an outbreeding species

Many important crop species are outbreeding. In outbreeding species the search for genes affecting traits is complicated by the fact that in a single cross up to four alleles may be present at each locus. This paper is concerned with the search for interacting quantitative trait loci (QTL) in populations which have been obtained by crossing a number of parents. It will be assumed that the parents are unrelated, but the methods can be extended easily to allow a pedigree structure. The approach has two goals: (1) finding QTL that are interacting with other loci and also loci which behave additively; (2) finding parents which segregate at two or more interacting QTL. Large populations obtained by crossing these parents can be used to study interactions in detail. QTL analysis is carried out by means of regression on predictions of QTL genotypes

Sunflowers Meet Sparsity: A Linear-Vertex Kernel for Weighted Clique-Packing on Sparse Graphs

We study the kernelization complexity of the Weighted H-Packing problem on sparse graphs. For a fixed connected graph H, in the Weighted H-Packing problem the input is a graph G, a vertex-weight function w: V (G) → N, and positive integers k, t. The question is whether there exist k vertex-disjoint subgraphs H 1, ⋯, H k of G such that H i is isomorphic to H for each i ∈ [k] and the total weight of these k · |V (H)| vertices is at least t. It is known that the (unweighted) H-Packing problem admits a kernel with O(k |V (H)|-1) vertices on general graphs, and a linear kernel on planar graphs and graphs of bounded genus. In this work, we focus on case that H is a clique on h ≥ 3 vertices (which captures Triangle Packing) and present a linear-vertex kernel for Weighted Kh-Packing on graphs of bounded expansion, along with a kernel with O(k 1+ϵ) vertices on nowhere-dense graphs for all ϵ &gt; 0. To obtain these results, we combine two powerful ingredients in a novel way: the Erdos-Rado Sunflower lemma and the theory of sparsity.</p

Fine-grained parameterized complexity analysis of graph coloring problems

The q-COLORING problem asks whether the vertices of a graph can be properly colored with q colors. In this paper we perform a fine-grained analysis of the complexity of q-COLORING with respect to a hierarchy of structural parameters. We show that unless the Exponential Time Hypothesis fails, there is no constant θ such that q-COLORING parameterized by the size k of a vertex cover can be solved in O ∗(θ k) time for all fixed q. We prove that there are O ∗((q−ɛ) k) time algorithms where k is the vertex deletion distance to several graph classes for which q-COLORING is known to be solvable in polynomial time, including all graph classes F whose (q+1)-colorable members have bounded treedepth. In contrast, we prove that if F is the class of paths – some of the simplest graphs of unbounded treedepth – then no such algorithm can exist unless the Strong Exponential Time Hypothesis fails.</p

Sunflowers Meet Sparsity: A Linear-Vertex Kernel for Weighted Clique-Packing on Sparse Graphs

We study the kernelization complexity of the Weighted H-Packing problem on sparse graphs. For a fixed connected graph H, in the Weighted H-Packing problem the input is a graph G, a vertex-weight function w: V (G) → N, and positive integers k, t. The question is whether there exist k vertex-disjoint subgraphs H 1, ⋯, H k of G such that H i is isomorphic to H for each i ∈ [k] and the total weight of these k · |V (H)| vertices is at least t. It is known that the (unweighted) H-Packing problem admits a kernel with O(k |V (H)|-1) vertices on general graphs, and a linear kernel on planar graphs and graphs of bounded genus. In this work, we focus on case that H is a clique on h ≥ 3 vertices (which captures Triangle Packing) and present a linear-vertex kernel for Weighted Kh-Packing on graphs of bounded expansion, along with a kernel with O(k 1+ϵ) vertices on nowhere-dense graphs for all ϵ &gt; 0. To obtain these results, we combine two powerful ingredients in a novel way: the Erdos-Rado Sunflower lemma and the theory of sparsity.</p

Fine-grained parameterized complexity analysis of graph coloring problems

The q-COLORING problem asks whether the vertices of a graph can be properly colored with q colors. In this paper we perform a fine-grained analysis of the complexity of q-COLORING with respect to a hierarchy of structural parameters. We show that unless the Exponential Time Hypothesis fails, there is no constant θ such that q-COLORING parameterized by the size k of a vertex cover can be solved in O ∗(θ k) time for all fixed q. We prove that there are O ∗((q−ɛ) k) time algorithms where k is the vertex deletion distance to several graph classes for which q-COLORING is known to be solvable in polynomial time, including all graph classes F whose (q+1)-colorable members have bounded treedepth. In contrast, we prove that if F is the class of paths – some of the simplest graphs of unbounded treedepth – then no such algorithm can exist unless the Strong Exponential Time Hypothesis fails.</p

Magnetism and heterogeneity of Co in anatase Co:TiO₂ magnetic semiconductor

Using x-ray magnetic circular dichroism XMCD, x-ray absorption spectroscopy XAS, and energy filtered transmission electron microscopy, we provide evidence for a heterogeneous Co distribution in anatase Co:TiO2 magnetic semiconductor having a low Co concentration 1.4 at. %. Multiplet structure due to Co2+ is observed in XAS spectra, but suppressed due to the coexistence of metallic Co clusters and substitutional Co ions, whereas XMCD spectra resemble metallic Co. The presence of Co2+ can be correlated with earlier observations of impurity band conduction and Kondo behavior, whereas metallic Co clusters contribute to the ferromagnetism and anomalous Hall effect

Best-case and worst-case sparsifiability of Boolean CSPs

We continue the investigation of polynomial-time sparsification for NP-complete Boolean Constraint Satisfaction Problems (CSPs). The goal in sparsification is to reduce the number of constraints in a problem instance without changing the answer, such that a bound on the number of resulting constraints can be given in terms of the number of variables n. We investigate how the worst-case sparsification size depends on the types of constraints allowed in the problem formulation (the constraint language). Two algorithmic results are presented. The first result essentially shows that for any arity k, the only constraint type for which no nontrivial sparsification is possible has exactly one falsifying assignment, and corresponds to logical OR (up to negations). Our second result concerns linear sparsification, that is, a reduction to an equivalent instance with O(n) constraints. Using linear algebra over rings of integers modulo prime powers, we give an elegant necessary and sufficient condition for a constraint type to be captured by a degree-1 polynomial over such a ring, which yields linear sparsifications. The combination of these algorithmic results allows us to prove two characterizations that capture the optimal sparsification sizes for a range of Boolean CSPs. For NP-complete Boolean CSPs whose constraints are symmetric (the satisfaction depends only on the number of 1 values in the assignment, not on their positions), we give a complete characterization of which constraint languages allow for a linear sparsification. For Boolean CSPs in which every constraint has arity at most three, we characterize the optimal size of sparsifications in terms of the largest OR that can be expressed by the constraint language

Finding k-secluded trees faster

We revisit the k-SECLUDED TREE problem. Given a vertex-weighted undirected graph G, its objective is to find a maximum-weight induced subtree T whose open neighborhood has size at most k. We present a fixed-parameter tractable algorithm that solves the problem in time 2 O(klog⁡k)⋅n O(1), improving on a double-exponential running time from earlier work by Golovach, Heggernes, Lima, and Montealegre. Starting from a single vertex, our algorithm grows a k-secluded tree by branching on vertices in the open neighborhood of the current tree T. To bound the branching depth, we prove a structural result that can be used to identify a vertex that belongs to the neighborhood of any k-secluded supertree T ′⊇T once the open neighborhood of T becomes sufficiently large. We extend the algorithm to enumerate compact descriptions of all maximum-weight k-secluded trees, which allows us to count them as well.</p

Finding k-secluded trees faster

We revisit the k-SECLUDED TREE problem. Given a vertex-weighted undirected graph G, its objective is to find a maximum-weight induced subtree T whose open neighborhood has size at most k. We present a fixed-parameter tractable algorithm that solves the problem in time 2 O(klog⁡k)⋅n O(1), improving on a double-exponential running time from earlier work by Golovach, Heggernes, Lima, and Montealegre. Starting from a single vertex, our algorithm grows a k-secluded tree by branching on vertices in the open neighborhood of the current tree T. To bound the branching depth, we prove a structural result that can be used to identify a vertex that belongs to the neighborhood of any k-secluded supertree T ′⊇T once the open neighborhood of T becomes sufficiently large. We extend the algorithm to enumerate compact descriptions of all maximum-weight k-secluded trees, which allows us to count them as well.</p

Sparsification Lower Bounds for List H-Coloring

We investigate the List H-Coloring problem, the generalization of graph coloring that asks whether an input graph G admits a homomorphism to the undirected graph H (possibly with loops), such that each vertex v ∈ V (G) is mapped to a vertex on its list L(v) ⊆ V (H). An important result by Feder, Hell, and Huang [JGT 2003] states that List H-Coloring is polynomial-time solvable if H is a so-called bi-arc graph, and NP-complete otherwise. We investigate the NP-complete cases of the problem from the perspective of polynomial-time sparsification: can an n-vertex instance be efficiently reduced to an equivalent instance of bitsize O(n 2−ε ) for some ε &gt; 0? We prove that if H is not a bi-arc graph, then List H-Coloring does not admit such a sparsification algorithm unless NP ⊆ coNP/poly. Our proofs combine techniques from kernelization lower bounds with a study of the structure of graphs H which are not bi-graphs.</p