A certifying algorithm for a problem is an algorithm that provides a certificate with each answer that it produces. The certificate is an evidence that can be used to authenticate the correctness of the answer. A Hamiltonian cycle in a graph is a simple cycle in which each vertex of the graph appears exactly once. The Hamiltonian cycle problem is to determine whether or not a graph contains a Hamiltonian cycle. The best result for the Hamiltonian cycle problem on circular-arc graphs is an O(n2logn)-time algorithm, where n is the number of vertices of the input graph. In fact, the O(n2logn)-time algorithm can be modified as a certifying algorithm although it was published before the term certifying algorithms appeared in the literature. However, whether there exists an algorithm whose time complexity is better than O(n2logn) for solving the Hamiltonian cycle problem on circular-arc graphs has been opened for two decades. In this paper, we present an O(Δn)-time certifying algorithm to solve this problem, where Δ represents the maximum degree of the input graph. The certificates provided by our algorithm can be authenticated in O(n) time.

BACKGROUND: A mathematical model to understand, predict, control, or even design a real biological system is a central theme in systems biology. A dynamic biological system is always modeled as a nonlinear ordinary differential equation (ODE) system. How to simulate the dynamic behavior and dynamic parameter sensitivities of systems described by ODEs efficiently and accurately is a critical job. In many practical applications, e.g., the fed-batch fermentation systems, the system admissible input (corresponding to independent variables of the system) can be time-dependent. The main difficulty for investigating the dynamic log gains of these systems is the infinite dimension due to the time-dependent input. The classical dynamic sensitivity analysis does not take into account this case for the dynamic log gains. RESULTS: We present an algorithm with an adaptive step size control that can be used for computing the solution and dynamic sensitivities of an autonomous ODE system simultaneously. Although our algorithm is one of the decouple direct methods in computing dynamic sensitivities of an ODE system, the step size determined by model equations can be used on the computations of the time profile and dynamic sensitivities with moderate accuracy even when sensitivity equations are more stiff than model equations. To show this algorithm can perform the dynamic sensitivity analysis on very stiff ODE systems with moderate accuracy, it is implemented and applied to two sets of chemical reactions: pyrolysis of ethane and oxidation of formaldehyde. The accuracy of this algorithm is demonstrated by comparing the dynamic parameter sensitivities obtained from this new algorithm and from the direct method with Rosenbrock stiff integrator based on the indirect method. The same dynamic sensitivity analysis was performed on an ethanol fed-batch fermentation system with a time-varying feed rate to evaluate the applicability of the algorithm to realistic models with time-dependent admissible input. CONCLUSION: By combining the accuracy we show with the efficiency of being a decouple direct method, our algorithm is an excellent method for computing dynamic parameter sensitivities in stiff problems. We extend the scope of classical dynamic sensitivity analysis to the investigation of dynamic log gains of models with time-dependent admissible input.

In this paper, we solve the maximum agreement subtree problem for a set T of k rooted, leaf-labelled evolutionary trees on n leaves where T contains a binary tree. We show that the O(kn/sup 3/)-time dynamic programming algorithm proposed by Farach et al. and Bryant can be implemented in O(n/sup 2/log/sup k-1/n) and O(k/spl middot/n/sup 3-(1/k-1)/) using the k-dimensional binary search tree and the k-dimensional range search tree, respectively.

This paper introduces the idea of a deferred-query approach to design O(n) algorithms for the domatic partition, optimal path cover, Hamiltonian path, Hamiltonian circuit, and maximum matching problems on interval graphs given n endpoint-sorted intervals. The previous best-known algorithms run in O(n log log n) or O(n +m) time, where m is the number of edges in the corresponding interval graphs. © 1999 John Wiley & Sons, Inc. Networks 34: 1–10, 1999

This paper first presents a unified approach to design efficient algorithms for the weighted domination problem and its three variants, i.e., the weighted independent, connected, and total domination problems, on interval graphs. Given an interval model with endpoints sorted, these algorithms run in time O(n) or O(n log log n) where n is the number of vertices. The results are then extended to solve the same problems on circular-arc graphs in O(n + m) time where m is the number of edges of the input graph.