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 Algorithm for Mining Frequent Sequence with Constraint Programming

The main advantage of Constraint Programming (CP) approaches for sequential pattern mining (SPM) is their modularity, which includes the ability to add new constraints (regular expressions, length restrictions, etc). The current best CP approach for SPM uses a global constraint (module) that computes the projected database and enforces the minimum frequency; it does this with a filtering algorithm similar to the PrefixSpan method. However, the resulting system is not as scalable as some of the most advanced mining systems like Zaki's cSPADE. We show how, using techniques from both data mining and CP, one can use a generic constraint solver and yet outperform existing specialized systems. This is mainly due to two improvements in the module that computes the projected frequencies: first, computing the projected database can be sped up by pre-computing the positions at which an symbol can become unsupported by a sequence, thereby avoiding to scan the full sequence each time; and second by taking inspiration from the trailing used in CP solvers to devise a backtracking-aware data structure that allows fast incremental storing and restoring of the projected database. Detailed experiments show how this approach outperforms existing CP as well as specialized systems for SPM, and that the gain in efficiency translates directly into increased efficiency for other settings such as mining with regular expressions.Comment: frequent sequence mining, constraint programmin

Data Mining Approach for Amino Acid Sequence Classification

Computerized applications are employed all around the world, an enormous amount of data is collected. The essential information contained in large amounts of data is attracting scholars from a variety of disciplines to examine how to extract the hidden knowledge inside them. The technique of obtaining or mining usable and valuable knowledge from enormous amounts of data is known as data mining. Text mining, picture mining, sequential pattern mining, web mining, and so on are all examples of data mining fields. Sequencing mining is one of the most important technologies in this field, as it aids in the discovery of sequential connections in data. Sequence mining is used in a variety of applications, including customers' buying trends analysis, web access trends analysis, atmospheric observation, amino acid sequences, Gene sequencing, and so on. Sequence mining techniques are utilized in protein and DNA analysis for sequence alignment, pattern searching, and pattern categorization. Researchers are exhibiting an interest in the subject of amino acid sequence categorization in the field of amino acid sequence analysis. It has the ability to find recurrent patterns in homologous proteins. This study describes the numerous methods used by numerous studies to categories proteins and gives an overview of the most important sequence classification techniques

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

Efficient Mining of Sequential Patterns in a Sequence Database with Weight Constraint

Sequence pattern mining is one of the essential data mining tasks with broad applications. Many sequence mining algorithms have been developed to find a set of frequent sub-sequences satisfying the support threshold in a sequence database. The main problem in most of these algorithms is they generate huge number of sequential patterns when the support threshold is low and all the sequence patterns are treated uniformly while real sequential patterns have different importance. In this paper, we propose an algorithm which aims to find more interesting sequential patterns, considering the different significance of each data element in a sequence database. Unlike the conventional weighted sequential pattern mining, where the weights of items are preassigned according to the priority or importance, in our approach the weights are set according to the real data and during the mining process not only the supports but also weights of patterns are considered. The experimental results show that the algorithm is efficient and effective in generating more interesting patterns