Algorithms for Visualizing Phylogenetic Networks

We study the problem of visualizing phylogenetic networks, which are extensions of the Tree of Life in biology. We use a space filling visualization method, called DAGmaps, in order to obtain clear visualizations using limited space. In this paper, we restrict our attention to galled trees and galled networks and present linear time algorithms for visualizing them as DAGmaps.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

Computing k-Modal Embeddings of Planar Digraphs

Given a planar digraph G and a positive even integer k, an embedding of G in the plane is k-modal, if every vertex of G is incident to at most k pairs of consecutive edges with opposite orientations, i.e., the incoming and the outgoing edges at each vertex are grouped by the embedding into at most k sets of consecutive edges with the same orientation. In this paper, we study the k-Modality problem, which asks for the existence of a k-modal embedding of a planar digraph. This combinatorial problem is at the very core of a variety of constrained embedding questions for planar digraphs and flat clustered networks. First, since the 2-Modality problem can be easily solved in linear time, we consider the general k-Modality problem for any value of k>2 and show that the problem is NP-complete for planar digraphs of maximum degree Delta <= k+3. We relate its computational complexity to that of two notions of planarity for flat clustered networks: Planar Intersection-Link and Planar NodeTrix representations. This allows us to answer in the strongest possible way an open question by Di Giacomo [https://doi.org/10.1007/978-3-319-73915-1_37], concerning the complexity of constructing planar NodeTrix representations of flat clustered networks with small clusters, and to address a research question by Angelini et al. [https://doi.org/10.7155/jgaa.00437], concerning intersection-link representations based on geometric objects that determine complex arrangements. On the positive side, we provide a simple FPT algorithm for partial 2-trees of arbitrary degree, whose running time is exponential in k and linear in the input size. Second, motivated by the recently-introduced planar L-drawings of planar digraphs [https://doi.org/10.1007/978-3-319-73915-1_36], which require the computation of a 4-modal embedding, we focus our attention on k=4. On the algorithmic side, we show a complexity dichotomy for the 4-Modality problem with respect to Delta, by providing a linear-time algorithm for planar digraphs with Delta <= 6. This algorithmic result is based on decomposing the input digraph into its blocks via BC-trees and each of these blocks into its triconnected components via SPQR-trees. In particular, we are able to show that the constraints imposed on the embedding by the rigid triconnected components can be tackled by means of a small set of reduction rules and discover that the algorithmic core of the problem lies in special instances of NAESAT, which we prove to be always NAE-satisfiable - a result of independent interest that improves on Porschen et al. [https://doi.org/10.1007/978-3-540-24605-3_14]. Finally, on the combinatorial side, we consider outerplanar digraphs and show that any such a digraph always admits a k-modal embedding with k=4 and that this value of k is best possible for the digraphs in this family

Two-dimensional state sum models and spin structures

The state sum models in two dimensions introduced by Fukuma, Hosono and Kawai are generalised by allowing algebraic data from a non-symmetric Frobenius algebra. Without any further data, this leads to a state sum model on the sphere. When the data is augmented with a crossing map, the partition function is defined for any oriented surface with a spin structure. An algebraic condition that is necessary for the state sum model to be sensitive to spin structure is determined. Some examples of state sum models that distinguish topologically-inequivalent spin structures are calculated.Comment: 43 pages. Mathematica script in ancillary file. v2: nomenclature of models and their properties changed, some proofs simplified, more detailed explanations. v3: extended introduction, presentational improvements; final versio

Upward Book Embeddings of st-Graphs

We study k-page upward book embeddings (kUBEs) of st-graphs, that is, book embeddings of single-source single-sink directed acyclic graphs on k pages with the additional requirement that the vertices of the graph appear in a topological ordering along the spine of the book. We show that testing whether a graph admits a kUBE is NP-complete for k >= 3. A hardness result for this problem was previously known only for k = 6 [Heath and Pemmaraju, 1999]. Motivated by this negative result, we focus our attention on k=2. On the algorithmic side, we present polynomial-time algorithms for testing the existence of 2UBEs of planar st-graphs with branchwidth b and of plane st-graphs whose faces have a special structure. These algorithms run in O(f(b)* n+n^3) time and O(n) time, respectively, where f is a singly-exponential function on b. Moreover, on the combinatorial side, we present two notable families of plane st-graphs that always admit an embedding-preserving 2UBE

Extensions of some classical local moves on knot diagrams

In the present paper, we consider local moves on classical and welded diagrams: (self-)crossing change, (self-)virtualization, virtual conjugation, Delta, fused, band-pass and welded band-pass moves. Interrelationship between these moves is discussed and, for each of these move, we provide an algebraic classification. We address the question of relevant welded extensions for classical moves in the sense that the classical quotient of classical object embeds into the welded quotient of welded objects. As a by-product, we obtain that all of the above local moves are unknotting operations for welded (long) knots. We also mention some topological interpretations for these combinatorial quotients.Comment: 18 pages; this paper is an entirely new version of "On forbidden moves and the Delta move": the exposition has been totally revised, and several new results have been added; to appear in Michigan Math.