Mining frequent biological sequences based on bitmap without candidate sequence generation

Biological sequences carry a lot of important genetic information of organisms. Furthermore, there is an inheritance law related to protein function and structure which is useful for applications such as disease prediction. Frequent sequence mining is a core technique for association rule discovery, but existing algorithms suffer from low efficiency or poor error rate because biological sequences differ from general sequences with more characteristics. In this paper, an algorithm for mining Frequent Biological Sequence based on Bitmap, FBSB, is proposed. FBSB uses bitmaps as the simple data structure and transforms each row into a quicksort list QS-list for sequence growth. For the continuity and accuracy requirement of biological sequence mining, tested sequences used during the mining process of FBSB are real ones instead of generated candidates, and all the frequent sequences can be mined without any errors. Comparing with other algorithms, the experimental results show that FBSB can achieve a better performance on both run time and scalability

An efficient closed frequent itemset miner for the MOA stream mining system

Mining itemsets is a central task in data mining, both in the batch and the streaming paradigms. While robust, efficient, and well-tested implementations exist for batch mining, hardly any publicly available equivalent exists for the streaming scenario. The lack of an efficient, usable tool for the task hinders its use by practitioners and makes it difficult to assess new research in the area. To alleviate this situation, we review the algorithms described in the literature, and implement and evaluate the IncMine algorithm by Cheng, Ke, and Ng (2008) for mining frequent closed itemsets from data streams. Our implementation works on top of the MOA (Massive Online Analysis) stream mining framework to ease its use and integration with other stream mining tasks. We provide a PAC-style rigorous analysis of the quality of the output of IncMine as a function of its parameters; this type of analysis is rare in pattern mining algorithms. As a by-product, the analysis shows how one of the user-provided parameters in the original description can be removed entirely while retaining the performance guarantees. Finally, we experimentally confirm both on synthetic and real data the excellent performance of the algorithm, as reported in the original paper, and its ability to handle concept drift.Postprint (published version