On finding bicliques in bipartite graphs: a novel algorithm and its application to the integration of diverse biological data types

BACKGROUND: Integrating and analyzing heterogeneous genome-scale data is a huge algorithmic challenge for modern systems biology. Bipartite graphs can be useful for representing relationships across pairs of disparate data types, with the interpretation of these relationships accomplished through an enumeration of maximal bicliques. Most previously-known techniques are generally ill-suited to this foundational task, because they are relatively inefficient and without effective scaling. In this paper, a powerful new algorithm is described that produces all maximal bicliques in a bipartite graph. Unlike most previous approaches, the new method neither places undue restrictions on its input nor inflates the problem size. Efficiency is achieved through an innovative exploitation of bipartite graph structure, and through computational reductions that rapidly eliminate non-maximal candidates from the search space. An iterative selection of vertices for consideration based on non-decreasing common neighborhood sizes boosts efficiency and leads to more balanced recursion trees. RESULTS: The new technique is implemented and compared to previously published approaches from graph theory and data mining. Formal time and space bounds are derived. Experiments are performed on both random graphs and graphs constructed from functional genomics data. It is shown that the new method substantially outperforms the best previous alternatives. CONCLUSIONS: The new method is streamlined, efficient, and particularly well-suited to the study of huge and diverse biological data. A robust implementation has been incorporated into GeneWeaver, an online tool for integrating and analyzing functional genomics experiments, available at http://geneweaver.org. The enormous increase in scalability it provides empowers users to study complex and previously unassailable gene-set associations between genes and their biological functions in a hierarchical fashion and on a genome-wide scale. This practical computational resource is adaptable to almost any applications environment in which bipartite graphs can be used to model relationships between pairs of heterogeneous entities. BMC Bioinformatics 2014; 15(1):110

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

Efficient Temporal Synopsis of Social Media Streams

Search and summarization of streaming social media, such as Twitter, requires the ongoing analysis of large volumes of data with dynamically changing characteristics. Tweets are short and repetitious -- lacking context and structure -- making it difficult to generate a coherent synopsis of events within a given time period. Although some established algorithms for frequent itemset analysis might provide an efficient foundation for synopsis generation, the unmodified application of standard methods produces a complex mass of rules, dominated by common language constructs and many trivial variations on topically related results. Moreover, these results are not necessarily specific to events within the time period of interest. To address these problems, we build upon the Linear time Closed itemset Mining (LCM) algorithm, which is particularly suited to the large and sparse vocabulary of tweets. LCM generates only closed itemsets, providing an immediate reduction in the number of trivial results. To reduce the impact of function words and common language constructs, we apply a filltering step that preserves these terms only when they may form part of a relevant collocation. To further reduce trivial results, we propose a novel strengthening of the closure condition of LCM to retain only those results that exceed a threshold of distinctiveness. Finally, we perform temporal ranking, based on information gain, to identify results that are particularly relevant to the time period of interest. We evaluate our work over a collection of tweets gathered in late 2012, exploring the efficiency and filtering characteristic of each processing step, both individually and collectively. Based on our experience, the resulting synopses from various time periods provide understandable and meaningful pictures of events within those periods, with potential application to tasks such as temporal summarization and query expansion for search

Multipartite Graph Algorithms for the Analysis of Heterogeneous Data

The explosive growth in the rate of data generation in recent years threatens to outpace the growth in computer power, motivating the need for new, scalable algorithms and big data analytic techniques. No field may be more emblematic of this data deluge than the life sciences, where technologies such as high-throughput mRNA arrays and next generation genome sequencing are routinely used to generate datasets of extreme scale. Data from experiments in genomics, transcriptomics, metabolomics and proteomics are continuously being added to existing repositories. A goal of exploratory analysis of such omics data is to illuminate the functions and relationships of biomolecules within an organism. This dissertation describes the design, implementation and application of graph algorithms, with the goal of seeking dense structure in data derived from omics experiments in order to detect latent associations between often heterogeneous entities, such as genes, diseases and phenotypes. Exact combinatorial solutions are developed and implemented, rather than relying on approximations or heuristics, even when problems are exceedingly large and/or difficult. Datasets on which the algorithms are applied include time series transcriptomic data from an experiment on the developing mouse cerebellum, gene expression data measuring acute ethanol response in the prefrontal cortex, and the analysis of a predicted protein-protein interaction network. A bipartite graph model is used to integrate heterogeneous data types, such as genes with phenotypes and microbes with mouse strains. The techniques are then extended to a multipartite algorithm to enumerate dense substructure in multipartite graphs, constructed using data from three or more heterogeneous sources, with applications to functional genomics. Several new theoretical results are given regarding multipartite graphs and the multipartite enumeration algorithm. In all cases, practical implementations are demonstrated to expand the frontier of computational feasibility