A new balance index for phylogenetic trees

Several indices that measure the degree of balance of a rooted phylogenetic tree have been proposed so far in the literature. In this work we define and study a new index of this kind, which we call the total cophenetic index: the sum, over all pairs of different leaves, of the depth of their least common ancestor. This index makes sense for arbitrary trees, can be computed in linear time and it has a larger range of values and a greater resolution power than other indices like Colless' or Sackin's. We compute its maximum and minimum values for arbitrary and binary trees, as well as exact formulas for its expected value for binary trees under the Yule and the uniform models of evolution. As a byproduct of this study, we obtain an exact formula for the expected value of the Sackin index under the uniform model, a result that seems to be new in the literature.Comment: 24 pages, 2 figures, preliminary version presented at the JBI 201

Identification of functionally related enzymes by learning-to-rank methods

Enzyme sequences and structures are routinely used in the biological sciences as queries to search for functionally related enzymes in online databases. To this end, one usually departs from some notion of similarity, comparing two enzymes by looking for correspondences in their sequences, structures or surfaces. For a given query, the search operation results in a ranking of the enzymes in the database, from very similar to dissimilar enzymes, while information about the biological function of annotated database enzymes is ignored. In this work we show that rankings of that kind can be substantially improved by applying kernel-based learning algorithms. This approach enables the detection of statistical dependencies between similarities of the active cleft and the biological function of annotated enzymes. This is in contrast to search-based approaches, which do not take annotated training data into account. Similarity measures based on the active cleft are known to outperform sequence-based or structure-based measures under certain conditions. We consider the Enzyme Commission (EC) classification hierarchy for obtaining annotated enzymes during the training phase. The results of a set of sizeable experiments indicate a consistent and significant improvement for a set of similarity measures that exploit information about small cavities in the surface of enzymes

The Decomposition Theorem and the topology of algebraic maps

We give a motivated introduction to the theory of perverse sheaves, culminating in the Decomposition Theorem of Beilinson, Bernstein, Deligne and Gabber. A goal of this survey is to show how the theory develops naturally from classical constructions used in the study of topological properties of algebraic varieties. While most proofs are omitted, we discuss several approaches to the Decomposition Theorem, indicate some important applications and examples.Comment: 117 pages. New title. Major structure changes. Final version of a survey to appear in the Bulletin of the AM

Towards Stratification Learning through Homology Inference

A topological approach to stratification learning is developed for point cloud data drawn from a stratified space. Given such data, our objective is to infer which points belong to the same strata. First we define a multi-scale notion of a stratified space, giving a stratification for each radius level. We then use methods derived from kernel and cokernel persistent homology to cluster the data points into different strata, and we prove a result which guarantees the correctness of our clustering, given certain topological conditions; some geometric intuition for these topological conditions is also provided. Our correctness result is then given a probabilistic flavor: we give bounds on the minimum number of sample points required to infer, with probability, which points belong to the same strata. Finally, we give an explicit algorithm for the clustering, prove its correctness, and apply it to some simulated data.Comment: 48 page

Type-safe two-level data transformation

A two-level data transformation consists of a type-level transformation of a data format coupled with value-level transformations of data instances corresponding to that format. Examples of two-level data transformations include XML schema evolution coupled with document migration, and data mappings used for interoperability and persistence. We provide a formal treatment of two-level data transformations that is type-safe in the sense that the well-formedness of the value-level transformations with respect to the type-level transformation is guarded by a strong type system. We rely on various techniques for generic functional programming to implement the formalization in Haskell. The formalization addresses various two-level transformation scenarios, covering fully automated as well as user-driven transformations, and allowing transformations that are information-preserving or not. In each case, two-level transformations are disciplined by one-step transformation rules and type-level transformations induce value-level transformations. We demonstrate an example hierarchical-relational mapping and subsequent migration of relational data induced by hierarchical format evolution.Fundação para a Ciência e a Tecnologia (FCT

Spacetime and Physical Equivalence

In this essay I begin to lay out a conceptual scheme for: (i) analysing dualities as cases of theoretical equivalence; (ii) assessing when cases of theoretical equivalence are also cases of physical equivalence. The scheme is applied to gauge/gravity dualities. I expound what I argue to be their contribution to questions about: (iii) the nature of spacetime in quantum gravity; (iv) broader philosophical and physical discussions of spacetime. (i)-(ii) proceed by analysing duality through four contrasts. A duality will be a suitable isomorphism between models: and the four relevant contrasts are as follows: (a) Bare theory: a triple of states, quantities, and dynamics endowed with appropriate structures and symmetries; vs. interpreted theory: which is endowed with, in addition, a suitable pair of interpretative maps. (b) Extendable vs. unextendable theories: which can, respectively cannot, be extended as regards their domains of application. (c) External vs. internal intepretations: which are constructed, respectively, by coupling the theory to another interpreted theory vs. from within the theory itself. (d) Theoretical vs. physical equivalence: which contrasts formal equivalence with the equivalence of fully interpreted theories. I apply this scheme to answering questions (iii)-(iv) for gauge/gravity dualities. I argue that the things that are physically relevant are those that stand in a bijective correspondence under duality: the common core of the two models. I therefore conclude that most of the mathematical and physical structures that we are familiar with, in these models, are largely, though crucially never entirely, not part of that common core. Thus, the interpretation of dualities for theories of quantum gravity compels us to rethink the roles that spacetime, and many other tools in theoretical physics, play in theories of spacetime.Comment: 25 pages. Winner of the essay contest "Space and Time After Quantum Gravity" of the University of Illinois at Chicago and the University of Genev

Isomorphisms of types in the presence of higher-order references

We investigate the problem of type isomorphisms in a programming language with higher-order references. We first recall the game-theoretic model of higher-order references by Abramsky, Honda and McCusker. Solving an open problem by Laurent, we show that two finitely branching arenas are isomorphic if and only if they are geometrically the same, up to renaming of moves (Laurent's forest isomorphism). We deduce from this an equational theory characterizing isomorphisms of types in a finitary language with higher order references. We show however that Laurent's conjecture does not hold on infinitely branching arenas, yielding a non-trivial type isomorphism in the extension of this language with natural numbers.Comment: Twenty-Sixth Annual IEEE Symposium on Logic In Computer Science (LICS 2011), Toronto : Canada (2011

Isomorphisms of types in the presence of higher-order references (extended version)

We investigate the problem of type isomorphisms in the presence of higher-order references. We first introduce a finitary programming language with sum types and higher-order references, for which we build a fully abstract games model following the work of Abramsky, Honda and McCusker. Solving an open problem by Laurent, we show that two finitely branching arenas are isomorphic if and only if they are geometrically the same, up to renaming of moves (Laurent's forest isomorphism). We deduce from this an equational theory characterizing isomorphisms of types in our language. We show however that Laurent's conjecture does not hold on infinitely branching arenas, yielding new non-trivial type isomorphisms in a variant of our language with natural numbers