Valentin I. Spitkovsky

A dictionary based approach for gene annotation

This paper describes a fast and fully automated dictionary-based approach to gene annotation and exon prediction. Two dictionaries are constructed, one from the nonredundant protein OWL database and the other from the dbEST database. These dictionaries are used to obtain O (1) time lookups of tuples in the dictionaries (4 tuples for the OWL database and 11 tuples for the dbEST database). These tuples can be used to rapidly find the longest matches at every position in an input sequence to the database sequences. Such matches provide very useful information pertaining to locating common segments between exons, alternative splice sites, and frequency data of long tuples for statistical purposes. These dictionaries also provide the basis for both homology determination, and statistical approaches to exon prediction.

A dictionary-based approach for gene annotation.

This paper describes a fast and fully automated dictionary-based approach to gene annotation and exon prediction. Two dictionaries are constructed, one from the nonredundant protein OWL database and the other from the dbEST database. These dictionaries are used to obtain O (1) time lookups of tuples in the dictionaries (4 tuples for the OWL database and 11 tuples for the dbEST database). These tuples can be used to rapidly find the longest matches at every position in an input sequence to the database sequences. Such matches provide very useful information pertaining to locating common segments between exons, alternative splice sites, and frequency data of long tuples for statistical purposes. These dictionaries also provide the basis for both homology determination, and statistical approaches to exon prediction.

Simulated N-Body: New Particle Physics-Based Heuristics for a Euclidean Location-Allocation Problem

The general facility location problem and its variants, including most location-allocation and P-median problems, are known to be NP-hard combinatorial optimization problems. Consequently, there is now a substantial body of literature on heuristic algorithms for a variety of location problems, among which can be found several versions of the well-known simulated annealing algorithm. This paper presents an optimization paradigm that, like simulated annealing, is based on a particle physics analogy but is markedly different from simulated annealing. Two heuristics based on this paradigm are presented and compared to simulated annealing for a capacitated facility location problem on Euclidean graphs. Experimental results based on randomly generated graphs suggest that one of the heuristics outperforms simulated annealing both in cost minimization as well as execution time. The particular version of location problem considered here, a location-allocation problem, involves determining locations and associated regions for a fixed number of facilities when the region sizes are given. Intended applications of this work include location problems with congestion costs as well as graph and network partitioning problems.