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 parallel method for mining frequent closed sequential patterns

Mining frequent closed sequential pattern (FCSPs) has attracted a great deal of research attention, because it is an important task in sequences mining. In recently, many studies have focused on mining frequent closed sequential patterns because, such patterns have proved to be more efficient and compact than frequent sequential patterns. Information can be fully extracted from frequent closed sequential patterns. In this paper, we propose an efficient parallel approach called parallel dynamic bit vector frequent closed sequential patterns (pDBV-FCSP) using multi-core processor architecture for mining FCSPs from large databases. The pDBV-FCSP divides the search space to reduce the required storage space and performs closure checking of prefix sequences early to reduce execution time for mining frequent closed sequential patterns. This approach overcomes the problems of parallel mining such as overhead of communication, synchronization, and data replication. It also solves the load balance issues of the workload between the processors with a dynamic mechanism that re-distributes the work, when some processes are out of work to minimize the idle CPU time.Web of Science5174021739

OLAP-Sequential Mining: Summarizing Trends from Historical Multidimensional Data using Closed Multidimensional Sequential Patterns

International audienceData warehouses are now well recognized as the way to store historical data that will then be available for future queries and analysis. In this context, some challenges are still open, among which the problem of mining such data. OLAP mining, introduced by J. Han in 1997, aims at coupling data mining techniques and data warehousing. These techniques have to take the specificities of such data into account. One of the specificities that is often not addressed by classical methods for data mining is the fact that data warehouses describe data through several dimensions. Moreover, the data are stored through time, and we thus argue that sequential patterns are one of the best ways to summarize the trends from such databases. Sequential pattern mining aims at discovering correlations among events through time. However, the number of patterns can become very important when taking several analysis dimensions into account, as it is the case in the framework of multidimensional databases. This is why we propose here to define a condensed representation without loss of information: closed multidimensional sequential patterns. This representation introduces properties that allow to deeply prune the search space. In this paper, we also define algorithms that do not require candidate set maintenance. Experiments on synthetic and real data are reported and emphasize the interest of our proposal

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

Implementation of an interactive pattern mining framework on electronic health record datasets

Large collections of electronic patient records contain a broad range of clinical information highly relevant for data analysis. However, they are maintained primarily for patient administration, and automated methods are required to extract valuable knowledge for predictive, preventive, personalized and participatory medicine. Sequential pattern mining is a fundamental task in data mining which can be used to find statistically relevant, non-trivial temporal dependencies of events such as disease comorbidities. This works objective is to use this mining technique to identify disease associations based on ICD-9-CM codes data of the entire Taiwanese population obtained from Taiwan’s National Health Insurance Research Database. This thesis reports the development and implementation of the Disease Pattern Miner – a pattern mining framework in a medical domain. The framework was designed as a Web application which can be used to run several state-of-the-art sequence mining algorithms on electronic health records, collect and filter the results to reduce the number of patterns to a meaningful size, and visualize the disease associations as an interactive model in a specific population group. This may be crucial to discover new disease associations and offer novel insights to explain disease pathogenesis. A structured evaluation of the data and models are required before medical data-scientist may use this application as a tool for further research to get a better understanding of disease comorbidities

Mining Closed Itemsets for Coherent Rules: An Inference Analysis Approach

Past observations have shown that a frequent item set mining algorithm are alleged to mine the closed ones because the finish offers a compact and a whole progress set and higher potency. Anyhow, the most recent closed item set mining algorithms works with candidate maintenance combined with check paradigm that is dear in runtime likewise as area usage when support threshold is a smaller amount or the item sets gets long. Here, we show, PEPP with inference analysis that could be a capable approach used for mining closed sequences for coherent rules while not candidate. It implements a unique sequence closure checking format with inference analysis that based mostly on Sequence Graph protruding by an approach labeled Parallel Edge projection and pruning in brief will refer as PEPP. We describe a novel inference analysis approach to prune patterns that tends to derive coherent rules. A whole observation having sparse and dense real-life information sets proved that PEPP with inference analysis performs larger compared to older algorithms because it takes low memory and is quicker than any algorithms those cited in literature frequently