Efficient algorithms for finding a longest common increasing subsequence

We study the problem of finding a longest common increasing subsequence (LCIS) of multiple sequences of numbers. The LCIS problem is a fundamental issue in various application areas, including the whole genome alignment. In this paper we give an efficient algorithm to find the LCIS of two sequences in time where n is the length of each sequence andr is the number of ordered pairs of positions at which the two sequences match, ℓ is the length of the LCIS, and Sort(n) is the time to sort n numbers. For m sequences wherem ≥ 3, we find the LCIS in Sort(n)) time where r is the total number of m-tuples of positions at which the m sequences match. The previous results find the LCIS of two sequences in O(n ²) and Sort(n)) time. Our algorithm is faster when r is relatively small, e.g., for .     

Integrated retail decisions with multiple selling periods and customer segments: Optimization and insights

Integrating retail decisions on such aspects as assortment, pricing, and inventory greatly improves profitability. We examine a multi-period selling horizon where a retailer jointly optimizes assortment planning, pricing, and inventory decisions for a product line of substitutable products, in a market with multiple customer segments. Focusing on fast-moving retail products, the problem is modeled as a mixed-integer nonlinear program where demand is driven by exogenous consumer reservation prices and endogenous assortment and pricing decisions. A mixed-integer linear reformulation is developed, which enables an exact solution to large problem instances (with up to a hundred products) in manageable times. Empirical evidence is provided in support of a classical deterministic maximum-surplus consumer choice model. Computational results and managerial insights are discussed. We find that the optimal assortment and pricing decisions do not exhibit a simple, intuitive structure that could be analytically characterized, which reflects the usefulness of optimization approaches to numerically identify attractive trade-offs for the decision-maker. We also observe that suboptimal inventory policies significantly decrease profitability, which highlights the importance of integrated decision-making. Finally, we find that the seasonality of consumer preferences and supply costs present an opportunity for boosting the profit via higher inventory levels and wider assortments.     

Alignments with non-overlapping moves,inversions and tandem duplications in <Emphasis Type="Italic">O</Emphasis>(<Emphasis Type="Italic">n</Emphasis><Superscript>4</Superscript>) time

Sequence alignment is a central problem in bioinformatics. The classical dynamic programming algorithm aligns two sequences by optimizing over possible insertions, deletions and substitutions. However, other evolutionary events can be observed, such as inversions, tandem duplications or moves (transpositions). It has been established that the extension of the problem to move operations is NP-complete. Previous work has shown that an extension restricted to non-overlapping inversions can be solved in O(n ³) with a restricted scoring scheme. In this paper, we show that the alignment problem extended to non-overlapping moves can be solved in O(n ⁵) for general scoring schemes, O(n ⁴log n) for concave scoring schemes and O(n ⁴) for restricted scoring schemes. Furthermore, we show that the alignment problem extended to non-overlapping moves, inversions and tandem duplications can be solved with the same time complexities. Finally, an example of an alignment with non-overlapping moves is provided. A preliminary version of this paper appeared in the Proceedings of COCOON 2007, LNCS, vol. 4598, pp. 151–164.