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

Efficient chain structure for high-utility sequential pattern mining

High-utility sequential pattern mining (HUSPM) is an emerging topic in data mining, which considers both utility and sequence factors to derive the set of high-utility sequential patterns (HUSPs) from the quantitative databases. Several works have been presented to reduce the computational cost by variants of pruning strategies. In this paper, we present an efficient sequence-utility (SU)-chain structure, which can be used to store more relevant information to improve mining performance. Based on the SU-Chain structure, the existing pruning strategies can also be utilized here to early prune the unpromising candidates and obtain the satisfied HUSPs. Experiments are then compared with the state-of-the-art HUSPM algorithms and the results showed that the SU-Chain-based model can efficiently improve the efficiency performance than the existing HUSPM algorithms in terms of runtime and number of the determined candidates

Constraint-based Sequential Pattern Mining with Decision Diagrams

Constrained sequential pattern mining aims at identifying frequent patterns on a sequential database of items while observing constraints defined over the item attributes. We introduce novel techniques for constraint-based sequential pattern mining that rely on a multi-valued decision diagram representation of the database. Specifically, our representation can accommodate multiple item attributes and various constraint types, including a number of non-monotone constraints. To evaluate the applicability of our approach, we develop an MDD-based prefix-projection algorithm and compare its performance against a typical generate-and-check variant, as well as a state-of-the-art constraint-based sequential pattern mining algorithm. Results show that our approach is competitive with or superior to these other methods in terms of scalability and efficiency.Comment: AAAI201