The agreement distance of unrooted phylogenetic networks

A rearrangement operation makes a small graph-theoretical change to a phylogenetic network to transform it into another one. For unrooted phylogenetic trees and networks, popular rearrangement operations are tree bisection and reconnection (TBR) and prune and regraft (PR) (called subtree prune and regraft (SPR) on trees). Each of these operations induces a metric on the sets of phylogenetic trees and networks. The TBR-distance between two unrooted phylogenetic trees $T$ and $T'$ can be characterised by a maximum agreement forest, that is, a forest with a minimum number of components that covers both $T$ and $T'$ in a certain way. This characterisation has facilitated the development of fixed-parameter tractable algorithms and approximation algorithms. Here, we introduce maximum agreement graphs as a generalisations of maximum agreement forests for phylogenetic networks. While the agreement distance -- the metric induced by maximum agreement graphs -- does not characterise the TBR-distance of two networks, we show that it still provides constant-factor bounds on the TBR-distance. We find similar results for PR in terms of maximum endpoint agreement graphs.Comment: 23 pages, 13 figures, final journal versio

Experimental Evaluation of Book Drawing Algorithms

A $k$-page book drawing of a graph $G=(V,E)$ consists of a linear ordering of its vertices along a spine and an assignment of each edge to one of the $k$ pages, which are half-planes bounded by the spine. In a book drawing, two edges cross if and only if they are assigned to the same page and their vertices alternate along the spine. Crossing minimization in a $k$-page book drawing is NP-hard, yet book drawings have multiple applications in visualization and beyond. Therefore several heuristic book drawing algorithms exist, but there is no broader comparative study on their relative performance. In this paper, we propose a comprehensive benchmark set of challenging graph classes for book drawing algorithms and provide an extensive experimental study of the performance of existing book drawing algorithms.Comment: Appears in the Proceedings of the 25th International Symposium on Graph Drawing and Network Visualization (GD 2017

Do Attitudes and Personality Characteristics Affect Socioeconomic Outcomes? The Case of Welfare Use by Young Women

We develop and estimate a model of social-psychological determinants of entry to the Aid to Families with Dependent Children (AFDC) program, the primary cash welfare program in the United States for 60 years until replaced in 1996. The structural model holds that attitudes and personality characteristics influence a woman’s likelihood of becoming demographically and financially eligible for welfare and her willingness to bear the stigma of receiving benefits. These factors, in turn, affect the likelihood of actually going on welfare. We test for a relationship between social-psychological variables and welfare participation using data from the youngest cohorts of women in the National Longitudinal Survey of Youth. We estimate logit models of the probability of ever participating in AFDC up to age 25 and hazard models of the timing until first use of AFDC. The attitudes and personality characteristics in the empirical model are self-esteem, locus of control, attitudes toward school, attitudes toward women’s work and family roles, commitment to work, and aversion to accepting public assistance. We find strong associations between welfare use and several attitudes and personality characteristics, but most of the associations are not robust to the inclusion of exogenous personal and family background characteristics. Consistent, strong evidence suggests that more positive attitudes toward school lower the likelihood of using welfare and increase duration until first receipt.

Impressionist Characterization in \u3cem\u3eWomen in Love \u3c/em\u3e

Writers with new techniques for creating prose often find themselves on the outskirts of critical acceptance, their voice attacked, their method questioned, their work disdained. Only a consummate belief in the validity of their experimentation and the joy of their own creative efforts keep such writers intent on championing their revolutionary language. D.H. Lawrence pioneered a new method of characterization in novels like Women in Love that elicited strongly negative criticism, but if his attackers had been sensitive to and appreciative of his earlier experiments with metaphoric prose, they might have understood sooner the genius of his methods. It was only after sustained attacks, however, that Lawrence came to be heralded for a method of revealing character that today seems to have been in the mainstream of those experiments with color and line that the French impressionists had developed generations before him

The agreement distance of rooted phylogenetic networks

The minimal number of rooted subtree prune and regraft (rSPR) operations needed to transform one phylogenetic tree into another one induces a metric on phylogenetic trees - the rSPR-distance. The rSPR-distance between two phylogenetic trees $T$ and $T'$ can be characterised by a maximum agreement forest; a forest with a minimum number of components that covers both $T$ and $T'$. The rSPR operation has recently been generalised to phylogenetic networks with, among others, the subnetwork prune and regraft (SNPR) operation. Here, we introduce maximum agreement graphs as an explicit representations of differences of two phylogenetic networks, thus generalising maximum agreement forests. We show that maximum agreement graphs induce a metric on phylogenetic networks - the agreement distance. While this metric does not characterise the distances induced by SNPR and other generalisations of rSPR, we prove that it still bounds these distances with constant factors.Comment: 24 pages, 16 figure