Impossibility results on stability of phylogenetic consensus methods

We answer two questions raised by Bryant, Francis and Steel in their work on consensus methods in phylogenetics. Consensus methods apply to every practical instance where it is desired to aggregate a set of given phylogenetic trees (say, gene evolution trees) into a resulting, "consensus" tree (say, a species tree). Various stability criteria have been explored in this context, seeking to model desirable consistency properties of consensus methods as the experimental data is updated (e.g., more taxa, or more trees, are mapped). However, such stability conditions can be incompatible with some basic regularity properties that are widely accepted to be essential in any meaningful consensus method. Here, we prove that such an incompatibility does arise in the case of extension stability on binary trees and in the case of associative stability. Our methods combine general theoretical considerations with the use of computer programs tailored to the given stability requirements

Algebraic foundations for qualitative calculi and networks

A qualitative representation $\phi$ is like an ordinary representation of a relation algebra, but instead of requiring $(a; b)^\phi = a^\phi | b^\phi$, as we do for ordinary representations, we only require that $c^\phi\supseteq a^\phi | b^\phi \iff c\geq a ; b$, for each $c$ in the algebra. A constraint network is qualitatively satisfiable if its nodes can be mapped to elements of a qualitative representation, preserving the constraints. If a constraint network is satisfiable then it is clearly qualitatively satisfiable, but the converse can fail. However, for a wide range of relation algebras including the point algebra, the Allen Interval Algebra, RCC8 and many others, a network is satisfiable if and only if it is qualitatively satisfiable. Unlike ordinary composition, the weak composition arising from qualitative representations need not be associative, so we can generalise by considering network satisfaction problems over non-associative algebras. We prove that computationally, qualitative representations have many advantages over ordinary representations: whereas many finite relation algebras have only infinite representations, every finite qualitatively representable algebra has a finite qualitative representation; the representability problem for (the atom structures of) finite non-associative algebras is NP-complete; the network satisfaction problem over a finite qualitatively representable algebra is always in NP; the validity of equations over qualitative representations is co-NP-complete. On the other hand we prove that there is no finite axiomatisation of the class of qualitatively representable algebras.Comment: 22 page

Algebraic Properties of Qualitative Spatio-Temporal Calculi

Qualitative spatial and temporal reasoning is based on so-called qualitative calculi. Algebraic properties of these calculi have several implications on reasoning algorithms. But what exactly is a qualitative calculus? And to which extent do the qualitative calculi proposed meet these demands? The literature provides various answers to the first question but only few facts about the second. In this paper we identify the minimal requirements to binary spatio-temporal calculi and we discuss the relevance of the according axioms for representation and reasoning. We also analyze existing qualitative calculi and provide a classification involving different notions of a relation algebra.Comment: COSIT 2013 paper including supplementary materia