Minimum Cell Connection in Line Segment Arrangements

We study the complexity of the following cell connection problems in segment arrangements. Given a set of straight-line segments in the plane and two points a and b in different cells of the induced arrangement: [(i)] compute the minimum number of segments one needs to remove so that there is a path connecting a to b that does not intersect any of the remaining segments; [(ii)] compute the minimum number of segments one needs to remove so that the arrangement induced by the remaining segments has a single cell. We show that problems (i) and (ii) are NP-hard and discuss some special, tractable cases. Most notably, we provide a near-linear-time algorithm for a variant of problem (i) where the path connecting a to b must stay inside a given polygon P with a constant number of holes, the segments are contained in P, and the endpoints of the segments are on the boundary of P. The approach for this latter result uses homotopy of paths to group the segments into clusters with the property that either all segments in a cluster or none participate in an optimal solution

Studying cities to learn about minds: some possible implications of space syntax for spatial cognition

What can we learn of the human mind by examining its products? The city is a case in point. Since the beginning of cities human ideas about them have been dominated by geometric ideas, and the real history of cities has always oscillated between the geometric and the ‘organic’. Set in the context of the suggestion from cognitive neuroscience that we impose more geometric order on the world than it actually possesses, and intriguing question arises: what is the role of the geometric intuition in how we understand cities and how we create them? Here I argue, drawing on space syntax research which has sought to link the detailed spatial morphology of cities to observable functional regularities, that all cities, the organic as well as the geometric, are pervasively ordered by geometric intuition, so that neither the forms of the cities nor their functioning can be understood without insight into their distinctive and pervasive emergent geometrical forms. The city is often said to be the creation of economic and social processes, but here it is argued that these processes operate within an envelope of geometric possibility defined by the human mind in its interaction with spatial laws that govern the relations between objects and spaces in the ambient world

The genetic code for cities – is it simpler than we thought?

September 200

Maximum likelihood estimates of pairwise rearrangement distances

Accurate estimation of evolutionary distances between taxa is important for many phylogenetic reconstruction methods. In the case of bacteria, distances can be estimated using a range of different evolutionary models, from single nucleotide polymorphisms to large-scale genome rearrangements. In the case of sequence evolution models (such as the Jukes-Cantor model and associated metric) have been used to correct pairwise distances. Similar correction methods for genome rearrangement processes are required to improve inference. Current attempts at correction fall into 3 categories: Empirical computational studies, Bayesian/MCMC approaches, and combinatorial approaches. Here we introduce a maximum likelihood estimator for the inversion distance between a pair of genomes, using the group-theoretic approach to modelling inversions introduced recently. This MLE functions as a corrected distance: in particular, we show that because of the way sequences of inversions interact with each other, it is quite possible for minimal distance and MLE distance to differently order the distances of two genomes from a third. This has obvious implications for the use of minimal distance in phylogeny reconstruction. The work also tackles the above problem allowing free rotation of the genome. Generally a frame of reference is locked, and all computation made accordingly. This work incorporates the action of the dihedral group so that distance estimates are free from any a priori frame of reference.Comment: 21 pages, 7 figures. To appear in the Journal of Theoretical Biolog