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

Content warehouses

Nowadays, content management systems are an established technology. Based on the experiences from several application scenarios we discuss the points of contact between content management systems and other disciplines of information systems engineering like data warehouses, data mining, and data integration. We derive a system architecture called "content warehouse" that integrates these technologies and defines a more general and more sophisticated view on content management. As an example, a system for the collection, maintenance, and evaluation of biological content like survey data or multimedia resources is shown as a case study

A survey of temporal knowledge discovery paradigms and methods

With the increase in the size of data sets, data mining has recently become an important research topic and is receiving substantial interest from both academia and industry. At the same time, interest in temporal databases has been increasing and a growing number of both prototype and implemented systems are using an enhanced temporal understanding to explain aspects of behavior associated with the implicit time-varying nature of the universe. This paper investigates the confluence of these two areas, surveys the work to date, and explores the issues involved and the outstanding problems in temporal data mining

Periodic Pattern Mining a Algorithms and Applications

Owing to a large number of applications periodic pattern mining has been extensively studied for over a decade Periodic pattern is a pattern that repeats itself with a specific period in a give sequence Periodic patterns can be mined from datasets like biological sequences continuous and discrete time series data spatiotemporal data and social networks Periodic patterns are classified based on different criteria Periodic patterns are categorized as frequent periodic patterns and statistically significant patterns based on the frequency of occurrence Frequent periodic patterns are in turn classified as perfect and imperfect periodic patterns full and partial periodic patterns synchronous and asynchronous periodic patterns dense periodic patterns approximate periodic patterns This paper presents a survey of the state of art research on periodic pattern mining algorithms and their application areas A discussion of merits and demerits of these algorithms was given The paper also presents a brief overview of algorithms that can be applied for specific types of datasets like spatiotemporal data and social network

Cooperation between expert knowledge and data mining discovered knowledge: Lessons learned

Expert systems are built from knowledge traditionally elicited from the human expert. It is precisely knowledge elicitation from the expert that is the bottleneck in expert system construction. On the other hand, a data mining system, which automatically extracts knowledge, needs expert guidance on the successive decisions to be made in each of the system phases. In this context, expert knowledge and data mining discovered knowledge can cooperate, maximizing their individual capabilities: data mining discovered knowledge can be used as a complementary source of knowledge for the expert system, whereas expert knowledge can be used to guide the data mining process. This article summarizes different examples of systems where there is cooperation between expert knowledge and data mining discovered knowledge and reports our experience of such cooperation gathered from a medical diagnosis project called Intelligent Interpretation of Isokinetics Data, which we developed. From that experience, a series of lessons were learned throughout project development. Some of these lessons are generally applicable and others pertain exclusively to certain project types

A novel computational framework for fast, distributed computing and knowledge integration for microarray gene expression data analysis

The healthcare burden and suffering due to life-threatening diseases such as cancer would be significantly reduced by the design and refinement of computational interpretation of micro-molecular data collected by bioinformaticians. Rapid technological advancements in the field of microarray analysis, an important component in the design of in-silico molecular medicine methods, have generated enormous amounts of such data, a trend that has been increasing exponentially over the last few years. However, the analysis and handling of these data has become one of the major bottlenecks in the utilization of the technology. The rate of collection of these data has far surpassed our ability to analyze the data for novel, non-trivial, and important knowledge. The high-performance computing platform, and algorithms that utilize its embedded computing capacity, has emerged as a leading technology that can handle such data-intensive knowledge discovery applications. In this dissertation, we present a novel framework to achieve fast, robust, and accurate (biologically-significant) multi-class classification of gene expression data using distributed knowledge discovery and integration computational routines, specifically for cancer genomics applications. The research presents a unique computational paradigm for the rapid, accurate, and efficient selection of relevant marker genes, while providing parametric controls to ensure flexibility of its application. The proposed paradigm consists of the following key computational steps: (a) preprocess, normalize the gene expression data; (b) discretize the data for knowledge mining application; (c) partition the data using two proposed methods: partitioning with overlapped windows and adaptive selection; (d) perform knowledge discovery on the partitioned data-spaces for association rule discovery; (e) integrate association rules from partitioned data and knowledge spaces on distributed processor nodes using a novel knowledge integration algorithm; and (f) post-analysis and functional elucidation of the discovered gene rule sets. The framework is implemented on a shared-memory multiprocessor supercomputing environment, and several experimental results are demonstrated to evaluate the algorithms. We conclude with a functional interpretation of the computational discovery routines for enhanced biological physiological discovery from cancer genomics datasets, while suggesting some directions for future research

New Approaches to Frequent and Incremental Frequent Pattern Mining

Data Mining (DM) is a process for extracting interesting patterns from large volumes of data. It is one of the crucial steps in Knowledge Discovery in Databases (KDD). It involves various data mining methods that mainly fall into predictive and descriptive models. Descriptive models look for patterns, rules, relationships and associations within data. One of the descriptive methods is association rule analysis, which represents co-occurrence of items or events. Association rules are commonly used in market basket analysis. An association rule is in the form of X → Y and it shows that X and Y co-occur with a given level of support and confidence. Association rule mining is a common technique used in discovering interesting frequent patterns in large datasets acquired in various application domains. Having petabytes of data finding its way into data storages in perhaps every day, made many researchers look for efficient methods for analyzing these large datasets. Many algorithms have been proposed for searching for frequent patterns. The search space combinatorically explodes as the size of the source data increases. Simply using more powerful computers, or even super-computers to handle ever-increasing size of large data sets is not sufficient. Hence, incremental algorithms have been developed and used to improve the efficiency of frequent pattern mining. One of the challenges of frequent itemset mining is long running times of the algorithms. Two major costs of long running times of frequent itemset mining are due to the number of database scans and the number of candidates generated (the latter one requires memory, and the more the number of candidates there are the more memory space is needed. When the candidates do not fit in memory then page swapping will occur which will increase the running time of the algorithms). In this dissertation we propose a new implementation of Apriori algorithm, NCLAT (Near Candidate-less Apriori with Tidlists), which scans the database only once and creates candidates only for level one (1-itemsets) which is equivalent to the total number of unique items in the database. In addition, we also show the results of choice of data structures used whether they are probabilistic or not, whether the datasets are horizontal or vertical, how counting is done, whether the algorithms are computed single or parallel way. We implement, explore and devise incremental algorithm UWEP with single as well as parallel computation. We have also cleaned a minor bug in UWEP and created a more efficient version UWEP2, which reduces the number of candidates created and the number of database scans. We have run all of our tests against three datasets with different features for different minimum support levels. We show both frequent and incremental frequent itemset mining implementation test results and comparison to each other. While there has been a lot of work done on frequent itemset mining on structured data, very little work has been done on the unstructured data. So, we have created a new hybrid pattern search algorithm, Double-Hash, which performed better for all of our test scenarios than the known pattern search algorithms. Double-Hash can potentially be used in frequent itemset mining on unstructured data in the future. We will be presenting our work and test results on this as well