A predicate f : {−1, 1} → {0, 1} with ρ(f) = |f −1(1)| 2k is called approximation resistant if given a near-satisfiable instance of CSP(f), it is computationally hard to find an assignment that satisfies at least ρ(f) + Ω(1) fraction of the constraints. We present a complete characterization of approximation resistant predicates under the Unique Games Conjecture. We also present characterizatio...

MOTIVATION Distance measures built on the notion of text compression have been used for the comparison and classification of entire genomes and mitochondrial genomes. The present study was undertaken in order to explore their utility in the classification of protein sequences. RESULTS We constructed compression-based distance measures (CBMs) using the Lempel-Zlv and the PPMZ compression algor...

Submitted: 3 May 2016 Accepted: 11 August 2016 doi:10.1111/zsc.12211 Dunn, C. W. & Munro, C. (2016). Comparative genomics and the diversity of life. — Zoologica Scripta, 45, 5–13. In the last decade, genomics has come to play a central role in systematics and biodiversity research. In coming years, systematics and phylogenetics will come to play an increasingly important role in genomics. Here,...

Detecting database records that are approximate duplicates, but not exact duplicates, is an important task. Databases may contain duplicate records concerning the same real-world entity because of data entry errors, because of un-standardized abbreviations, or because of diierences in the detailed schemas of records from multiple databases, among other reasons. In this paper, we present an eeci...

As multithreaded and reconfigurable logic architectures play an increasing role in high-performance computing (HPC), the scientific community is in need for new programming models for efficiently mapping existing applications to the new parallel platforms. In this paper, we show how we can effectively exploit tightly coupled fine-grained parallelism in architectures such as GPU and FPGA to spee...

On thit page it a collection of four memorandaJwhich have been of motor] importance in Psychology Professor Caroline Waterman's struggle to receive tenure. The ftnt memo we have published it a "tetter" of transmittal" or departmental recommendation, which was written by Psychology Department Chairman Richard Teevan and present*' his reasons for recommending that Waterman be deniea tenure. The l...

Interval graphs play important roles in analysis of DNA chains in Benzer [S. Benzer, On the topology of the genetic fine structure, Proceedings of the National Academy of Sciences of the United States of America 45 (1959) 1607–1620], restriction maps of DNA in Waterman and Griggs [M.S. Waterman, J.R. Griggs, Interval graphs and maps of DNA, Bulletin of Mathematical Biology 48 (2) (1986) 189–195...

MOTIVATION Efficient, accurate and automatic clustering of large protein sequence datasets, such as complete proteomes, into families, according to sequence similarity. Detection and correction of false positive and negative relationships with subsequent detection and resolution of multi-domain proteins. RESULTS A new algorithm for the automatic clustering of protein sequence datasets has bee...

MOTIVATION The urgent need for efficient and sustainable biological production of fuels and high-value chemicals has elicited a wave of in silico techniques for identifying promising novel pathways to these compounds in large putative metabolic networks. To date, these approaches have primarily used general graph search algorithms, which are prohibitively slow as putative metabolic networks may...