Self-organizing tuple reconstruction in column-stores

Column-stores gained popularity as a promising physical design alternative. Each attribute of a relation is physically stored as a separate column allowing queries to load only the required attributes. The overhead incurred is on-the-fly tuple reconstruction for multi-attribute queries. Each tuple reconstruction is a join of two columns based on tuple IDs, making it a significant cost component. The ultimate physical design is to have multiple presorted copies of each base table such that tuples are already appropriately organized in multiple different orders across the various columns. This requires the ability to predict the workload, idle time to prepare, and infrequent updates. In this paper, we propose a novel design, \emph{partial sideways cracking}, that minimizes the tuple rec

Performance comparison between k-tuple distance and four model-based distances in phylogenetic tree reconstruction

Phylogenetic tree reconstruction requires construction of a multiple sequence alignment (MSA) from sequences. Computationally, it is difficult to achieve an optimal MSA for many sequences. Moreover, even if an optimal MSA is obtained, it may not be the true MSA that reflects the evolutionary history of the underlying sequences. Therefore, errors can be introduced during MSA construction which in turn affects the subsequent phylogenetic tree construction. In order to circumvent this issue, we extend the application of the k-tuple distance to phylogenetic tree reconstruction. The k-tuple distance between two sequences is the sum of the differences in frequency, over all possible tuples of length k, between the sequences and can be estimated without MSAs. It has been traditionally used to build a fast ‘guide tree’ to assist the construction of MSAs. Using the 1470 simulated sets of sequences generated under different evolutionary scenarios, the neighbor-joining trees and BioNJ trees, we compared the performance of the k-tuple distance with four commonly used distance estimators including Jukes–Cantor, Kimura, F84 and Tamura–Nei. These four distance estimators fall into the category of model-based distance estimators, as each of them takes account of a specific substitution model in order to compute the distance between a pair of already aligned sequences. Results show that trees constructed from the k-tuple distance are more accurate than those from other distances most time; when the divergence between underlying sequences is high, the tree accuracy could be twice or higher using the k-tuple distance than other estimators. Furthermore, as the k-tuple distance voids the need for constructing an MSA, it can save tremendous amount of time for phylogenetic tree reconstructions when the data include a large number of sequences

A counterexample to the reconstruction of ω\omega-categorical structures from their endomorphism monoids

We present an example of two countable $\omega$-categorical structures, one of which has a finite relational language, whose endomorphism monoids are isomorphic as abstract monoids, but not as topological monoids -- in other words, no isomorphism between these monoids is a homeomorphism. For the same two structures, the automorphism groups and polymorphism clones are isomorphic, but not topologically isomorphic. In particular, there exists a countable $\omega$-categorical structure in a finite relational language which can neither be reconstructed up to first-order bi-interpretations from its automorphism group, nor up to existential positive bi-interpretations from its endomorphism monoid, nor up to primitive positive bi-interpretations from its polymorphism clone.Comment: 17 page