Abstract: "String alignment by dynamic programming is generalized to include simultaneous computation of optimal alignment cost and corresponding rotation for strings representing cyclic patterns. A guided search algorithm is devised that is based on iterative extraction of submatrices from an initial dynamic programming matrix. The algorithm uses bounds derived for actual alignment costs from these submatrices for any rotation of the test string. Algorithmic complexity is analyzed for major stages in the search. Applicability of the method is illustrated with satellite DNA sequences and circularly permuted protein sequences."

Abstract: "Stochastic context-free grammars are an important tool in syntactic pattern analysis and in other applications as well. This paper discusses major results in single-type and multitype branching processes used to study a grammar's stochastic derivations. Probability generating functions are used extensively."

Abstract: "This paper applies structural pattern analysis to an aspect of automation in cytogenetics, specifically, to the classification of G-banded human metaphase chromosomes by type. The method uses probabilistic Markov networks that represent band pattern sequences and are inferred directly from learning data without supervision. This work investigates a new cost function for dynamic programming used to align networks, a refined form of inferred networks, and reducing the size of networks after inference. Limit experimental work with simultaneous alignment of multiple networks is also reported."

Abstract: "A version of parallel computation in dynamic programming for optimal string-to-network alignments is discussed. The specific application is pattern analysis in which Markov networks are used as models of classes of strings. The dynamic programming computes maximum probability string-to-network alignments with a cost function based on relative frequencies. The concurrent-processor computer is a Sequent Balance, a machine with processors, memory modules, and I/O controllers connected to a single, high-speed bus. The implementation and experimental results are described."