Reconstructing phylogenies from noisy quartets in polynomial time with a high success probability

<p>Abstract</p> <p>Background</p> <p>In recent years, quartet-based phylogeny reconstruction methods have received considerable attentions in the computational biology community. Traditionally, the accuracy of a phylogeny reconstruction method is measured by simulations on synthetic datasets with known "true" phylogenies, while little theoretical analysis has been done. In this paper, we present a new model-based approach to measuring the accuracy of a quartet-based phylogeny reconstruction method. Under this model, we propose three efficient algorithms to reconstruct the "true" phylogeny with a high success probability.</p> <p>Results</p> <p>The first algorithm can reconstruct the "true" phylogeny from the input quartet topology set without quartet errors in <it>O</it>(<it>n</it>²) time by querying at most (<it>n </it>- 4) log(<it>n </it>- 1) quartet topologies, where <it>n </it>is the number of the taxa. When the input quartet topology set contains errors, the second algorithm can reconstruct the "true" phylogeny with a probability approximately 1 - <it>p </it>in <it>O</it>(<it>n</it>⁴log <it>n</it>) time, where <it>p </it>is the probability for a quartet topology being an error. This probability is improved by the third algorithm to approximately <inline-formula><m:math name="1748-7188-3-1-i1" xmlns:m="http://www.w3.org/1998/Math/MathML"><m:semantics><m:mrow><m:mfrac><m:mn>1</m:mn><m:mrow><m:mn>1</m:mn><m:mo>+</m:mo><m:msup><m:mi>q</m:mi><m:mn>2</m:mn></m:msup><m:mo>+</m:mo><m:mfrac><m:mn>1</m:mn><m:mn>2</m:mn></m:mfrac><m:msup><m:mi>q</m:mi><m:mn>4</m:mn></m:msup><m:mo>+</m:mo><m:mfrac><m:mn>1</m:mn><m:mrow><m:mn>16</m:mn></m:mrow></m:mfrac><m:msup><m:mi>q</m:mi><m:mn>5</m:mn></m:msup></m:mrow></m:mfrac></m:mrow><m:annotation encoding="MathType-MTEF"> MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaqcfa4aaSaaaeaacqaIXaqmaeaacqaIXaqmcqGHRaWkcqWGXbqCdaahaaqabeaacqaIYaGmaaGaey4kaSYaaSaaaeaacqaIXaqmaeaacqaIYaGmaaGaemyCae3aaWbaaeqabaGaeGinaqdaaiabgUcaRmaalaaabaGaeGymaedabaGaeGymaeJaeGOnaydaaiabdghaXnaaCaaabeqaaiabiwda1aaaaaaaaa@3D5A@</m:annotation></m:semantics></m:math></inline-formula>, where <inline-formula><m:math name="1748-7188-3-1-i2" xmlns:m="http://www.w3.org/1998/Math/MathML"><m:semantics><m:mrow><m:mi>q</m:mi><m:mo>=</m:mo><m:mfrac><m:mi>p</m:mi><m:mrow><m:mn>1</m:mn><m:mo>−</m:mo><m:mi>p</m:mi></m:mrow></m:mfrac></m:mrow><m:annotation encoding="MathType-MTEF"> MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaGaemyCaeNaeyypa0tcfa4aaSaaaeaacqWGWbaCaeaacqaIXaqmcqGHsislcqWGWbaCaaaaaa@3391@</m:annotation></m:semantics></m:math></inline-formula>, with running time of <it>O</it>(<it>n</it>⁵), which is at least 0.984 when <it>p </it>< 0.05.</p> <p>Conclusion</p> <p>The three proposed algorithms are mathematically guaranteed to reconstruct the "true" phylogeny with a high success probability. The experimental results showed that the third algorithm produced phylogenies with a higher probability than its aforementioned theoretical lower bound and outperformed some existing phylogeny reconstruction methods in both speed and accuracy.</p

Using GRASP and GA to design resilient and cost-effective IP/MPLS networks

The main objective of this thesis is to find good quality solutions for representative instances of the problem of designing a resilient and low cost IP/MPLS network, to be deployed over an existing optical transport network. This research is motivated by two complementary real-world application cases, which comprise the most important commercial and academic networks of Uruguay. To achieve this goal, we performed an exhaustive analysis of existing models and technologies. From all of them we took elements that were contrasted with the particular requirements of our counterparts. We highlight among these requirements, the need of getting solutions transparently implementable over a heterogeneous network environment, which limit us to use widely standardized features of related technologies. We decided to create new models more suitable to fit these needs. These models are intrinsically hard to solve (NP-Hard). Thus we developed metaheuristic based algorithms to find solutions to these real-world instances. Evolutionary Algorithms and Greedy Randomized Adaptive Search Procedures obtained the best results. As it usually happens, real-world planning problems are surrounded by uncertainty. Therefore, we have worked closely with our counterparts to reduce the fuzziness upon data to a set of representative cases. They were combined with different strategies of design to get to scenarios, which were translated into instances of these problems. Finally, the algorithms were fed with this information, and from their outcome we derived our results and conclusions

Algorithmic Graph Theory

The main focus of this workshop was on mathematical techniques needed for the development of efficient solutions and algorithms for computationally difficult graph problems. The techniques studied at the workshhop included: the probabilistic method and randomized algorithms, approximation and optimization, structured families of graphs and approximation algorithms for large problems. The workshop Algorithmic Graph Theory was attended by 46 participants, many of them being young researchers. In 15 survey talks an overview of recent developments in Algorithmic Graph Theory was given. These talks were supplemented by 10 shorter talks and by two special sessions

A Polyhedral Study of Mixed 0-1 Set

We consider a variant of the well-known single node fixed charge network flow set with constant capacities. This set arises from the relaxation of more general mixed integer sets such as lot-sizing problems with multiple suppliers. We provide a complete polyhedral characterization of the convex hull of the given set

On the Implementation of Purely Functional Data Structures for the Linearisation case of Dynamic Trees

Dynamic trees, originally described by Sleator and Tarjan, have been studied in detail for non persistent structures providing O(log n) time for update and lookup operations as shown in theory and practice by Werneck. However, there are two gaps in current theory. First, how the most common dynamic tree operations (link and cut) are computed over a purely functional data structure has not been studied in detail. Second, even in the imperative case, when checking whether two vertices u and v are connected (i.e. in the same component), it is taken for granted that the corresponding location indices (i.e. pointers, which are not allowed in purely functional programming) are known a priori and do not need to be computed, yet this is rarely the case in practice. In this thesis we address these omissions by formally introducing two new data structures, Full and Top, which we use to represent trees in a functionally efficient manner. Based on a primitive version of finger trees – the de facto sequence data structure for the purely lazy-evaluation programming language Haskell – they are augmented with collection (i.e. set-based) data structures in order to manage efficiently k-ary trees for the so-called linearisation case of the dynamic trees problem. Different implementations are discussed, and their performance is measured. Our results suggest that relative timings for our proposed structures perform sublinear time per operation once the forest is generated. Furthermore, Full and Top implementations show simplicity and preserve purity under a common interface