Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots

Although taxonomy is often used informally to evaluate the results of phylogenetic inference and find the root of phylogenetic trees, algorithmic methods to do so are lacking. In this paper we formalize these procedures and develop algorithms to solve the relevant problems. In particular, we introduce a new algorithm that solves a "subcoloring" problem for expressing the difference between the taxonomy and phylogeny at a given rank. This algorithm improves upon the current best algorithm in terms of asymptotic complexity for the parameter regime of interest; we also describe a branch-and-bound algorithm that saves orders of magnitude in computation on real data sets. We also develop a formalism and an algorithm for rooting phylogenetic trees according to a taxonomy. All of these algorithms are implemented in freely-available software.Comment: Version submitted to Algorithms for Molecular Biology. A number of fixes from previous versio

Ad auctions and cascade model: GSP inefficiency and algorithms

The design of the best economic mechanism for Sponsored Search Auctions (SSAs) is a central task in computational mechanism design/game theory. Two open questions concern the adoption of user models more accurate than that one currently used and the choice between Generalized Second Price auction (GSP) and Vickrey-Clark-Groves mechanism (VCG). In this paper, we provide some contributions to answer these questions. We study Price of Anarchy (PoA) and Price of Stability (PoS) over social welfare and auctioneer's revenue of GSP w.r.t. the VCG when the users follow the famous cascade model. Furthermore, we provide exact, randomized, and approximate algorithms, showing that in real-world settings (Yahoo! Webscope A3 dataset, 10 available slots) optimal allocations can be found in less than 1s with up to 1000 ads, and can be approximated in less than 20ms even with more than 1000 ads with an average accuracy greater than 99%.Comment: AAAI16, to appea

Open Problems in Parameterized and Exact Computation - IWPEC 2006

In September 2006, the Second International Workshop on Parameterized and Exact Computation was held in Zürich, Switzerland, as part of ALGO 2006. At the end of IWPEC 2006, a problem session was held. (Most of) the problems mentioned at this problem session, and some other problems, contributed by the participants of IWPEC 2006 are listed here

Connection Matrices and the Definability of Graph Parameters

In this paper we extend the Finite Rank Theorem for connection matrices of graph parameters definable in Monadic Second Order Logic with modular counting CMSOL of B. Godlin, T. Kotek and J.A. Makowsky (2008 and 2009), and demonstrate its vast applicability in simplifying known and new non-definability results of graph properties and finding new non-definability results for graph parameters. We also prove a Feferman-Vaught Theorem for the logic CFOL, First Order Logic with the modular counting quantifiers

Connection Matrices and the Definability of Graph Parameters

In this paper we extend and prove in detail the Finite Rank Theorem for connection matrices of graph parameters definable in Monadic Second Order Logic with counting (CMSOL) from B. Godlin, T. Kotek and J.A. Makowsky (2008) and J.A. Makowsky (2009). We demonstrate its vast applicability in simplifying known and new non-definability results of graph properties and finding new non-definability results for graph parameters. We also prove a Feferman-Vaught Theorem for the logic CFOL, First Order Logic with the modular counting quantifiers