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

Modelling epistasis in genetic disease using Petri nets, evolutionary computation and frequent itemset mining

Petri nets are useful for mathematically modelling disease-causing genetic epistasis. A Petri net model of an interaction has the potential to lead to biological insight into the cause of a genetic disease. However, defining a Petri net by hand for a particular interaction is extremely difficult because of the sheer complexity of the problem and degrees of freedom inherent in a Petri net’s architecture. We propose therefore a novel method, based on evolutionary computation and data mining, for automatically constructing Petri net models of non-linear gene interactions. The method comprises two main steps. Firstly, an initial partial Petri net is set up with several repeated sub-nets that model individual genes and a set of constraints, comprising relevant common sense and biological knowledge, is also defined. These constraints characterise the class of Petri nets that are desired. Secondly, this initial Petri net structure and the constraints are used as the input to a genetic algorithm. The genetic algorithm searches for a Petri net architecture that is both a superset of the initial net, and also conforms to all of the given constraints. The genetic algorithm evaluation function that we employ gives equal weighting to both the accuracy of the net and also its parsimony. We demonstrate our method using an epistatic model related to the presence of digital ulcers in systemic sclerosis patients that was recently reported in the literature. Our results show that although individual “perfect” Petri nets can frequently be discovered for this interaction, the true value of this approach lies in generating many different perfect nets, and applying data mining techniques to them in order to elucidate common and statistically significant patterns of interaction

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

CloSpan Sequential Pattern Mining for Books Recommendation System in Petra Christian University Library

Petra Christian University (PCU) Library has been using website for their books search system. To further improve the service, it is necessary to develop the automatic system which can recommends the book or the correlation or the book which often being lend at the same time or sequentially by prospective borrowers. The algorithm used to explore the lending sequential patterns is CloSpan Sequential Mining algorithm. The output generated by this application is closed sequential pattern rules and the tree of sequential patterns. They can be used as a reference to establish a list of recommended related books. From the test results it can be concluded that the more data and smaller minimum support, the longer the process takes, and the more patterns that is produced. From the questionnaire outcome that are distributed to employees and users of the library can be concluded that the system can create right recommendations and useful

Discovering unbounded episodes in sequential data

One basic goal in the analysis of time-series data is to find frequent interesting episodes, i.e, collections of events occurring frequently together in the input sequence. Most widely-known work decide the interestingness of an episode from a fixed user-specified window width or interval, that bounds the subsequent sequential association rules. We present in this paper, a more intuitive definition that allows, in turn, interesting episodes to grow during the mining without any user-specified help. A convenient algorithm to efficiently discover the proposed unbounded episodes is also implemented. Experimental results confirm that our approach results useful and advantageous.Postprint (published version