Fast Searching for Andrews–Curtis Trivializations

Fast Searching for Andrews-Curtis Trivializations

Fast String Searching

Since the Boyer-Moore algorithm was described in 1977, it has been the standard benchmark for the practical string search literature. Yet this yardstick compares badly with current practice. We describe two algorithms that perform 47% fewer comparisons and are about 4.5 times faster across a wide range of architectures and compilers. These new variants are members of a family of algorithms base...

Generic trivializations of geometric theories

We study the theory T ∗ of the structure induced by parameter free formulas on a dense algebraically independent subset of a model of a geometric theory T . We show that while being a trivial geometric theory, T ∗ inherits most of the model theoretic complexity of T related to stability, simplicity, rosiness, NIP and NTP2. In particular, we show that T is strongly minimal, supersimple of SU-ran...

Compression of nucleotide databases for fast searching

MOTIVATION International sequencing efforts are creating huge nucleotide databases, which are used in searching applications to locate sequences homologous to a query sequence. In such applications, it is desirable that databases are stored compactly, that sequences can be accessed independently of the order in which they were stored, and that data can be rapidly retrieved from secondary storag...

Effective Query Filtering for Fast Homology Searching

To improve the accuracy of rapid homology searching it is common practice to filter all queries to mask low complexity regions prior to searching. We show in this paper, through a large-scale study of querying the PIR database, that applying popular filtering techniques unselectively to all queries may reduce retrieval effectiveness. We also show that masking queries with our new technique, caf...