Skyline queries are used to find the Pareto optimal solution from datasets containing multi-dimensional data points. In this paper, we propose a new type of skyline queries whose evaluation is constrained by a multi-cost transportation network (MCTN) and whose answers are off the network. This type of skyline queries is useful in many applications. For example, a person wants to find an apartment by considering not only the price and the surrounding area of the apartment, but also the transportation cost, time, and distance between the apartment and his/her work place. Most existing works that evaluate skyline queries on multi-cost networks (MCNs), which are either MCTNs or road networks, find interesting objects that locate on edges of the networks. Formally, our new type of skyline queries takes as input an MCTN, a query point q, and a set of objects of interest D with spatial information, where q and the objects in D are off the network. The answers to such queries are objects in D that are not dominated by other D objects when considering the multiple attributes of these objects and the multiple network cost from q to the solution objects. To evaluate such queries, we propose an exact search algorithm and its improved version by implementing several properties. The space of the exact skyline solutions is huge and can easily reach the order of thousands and incur long evaluation time. We further design much more efficient heuristic methods to find approximate solutions. We run extensive experiments using both real and synthetic datasets to test the effectiveness and efficiency of our proposed approaches. The results show that the exact search algorithm can be dramatically improved by utilizing several properties. The heuristic approaches to find approximate answers can largely reduce the query time and retrieve results that are comparable to the exact solutions.
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New algorithms for detecting multi-effect and multi-way epistatic interactions
Epistasis, which is the phenomenon of genetic interactions, plays a central role in many scientific discoveries. However, due to the combinatorial nature of the problem, it is extremely challenging to decipher the exact combinations of genes that trigger the epistatic effects. Many existing methods only focus on two-way interactions. Some of the most effective methods used machine learning techniques, but many were designed for special case-and-control studies or suffer from overfitting. We propose three new algorithms for multi-effect and multi-way epistases detection, with one guaranteeing global optimality and the other two being local optimization oriented heuristics.
The computational performance of the proposed heuristic algorithm was compared with several state-of-the-art methods using a yeast dataset. Results suggested that searching for the global optimal solution could be extremely time consuming, but the proposed heuristic algorithm was much more effective and efficient than others at finding a close-to-optimal solution. Moreover, it was able to provide biological insight on the exact configurations of epistases, besides achieving a higher prediction accuracy than the state-of-the-art methods.
Data source was publicly available and details are provided in the text.
- NSF-PAR ID:
- 10117571
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Bioinformatics
- ISSN:
- 1367-4803
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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