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

Continuous Nearest Neighbor Queries over Sliding Windows

Abstract—This paper studies continuous monitoring of nearest neighbor (NN) queries over sliding window streams. According to this model, data points continuously stream in the system, and they are considered valid only while they belong to a sliding window that contains 1) the W most recent arrivals (count-based) or 2) the arrivals within a fixed interval W covering the most recent time stamps (time-based). The task of the query processor is to constantly maintain the result of long-running NN queries among the valid data. We present two processing techniques that apply to both count-based and time-based windows. The first one adapts conceptual partitioning, the best existing method for continuous NN monitoring over update streams, to the sliding window model. The second technique reduces the problem to skyline maintenance in the distance-time space and precomputes the future changes in the NN set. We analyze the performance of both algorithms and extend them to variations of NN search. Finally, we compare their efficiency through a comprehensive experimental evaluation. The skyline-based algorithm achieves lower CPU cost, at the expense of slightly larger space overhead. Index Terms—Location-dependent and sensitive, spatial databases, query processing, nearest neighbors, data streams, sliding windows.

FAST: FAST Analysis of Sequences Toolbox.

FAST (FAST Analysis of Sequences Toolbox) provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data. Modeled after the GNU (GNU's Not Unix) Textutils such as grep, cut, and tr, FAST tools such as fasgrep, fascut, and fastr make it easy to rapidly prototype expressive bioinformatic workflows in a compact and generic command vocabulary. Compact combinatorial encoding of data workflows with FAST commands can simplify the documentation and reproducibility of bioinformatic protocols, supporting better transparency in biological data science. Interface self-consistency and conformity with conventions of GNU, Matlab, Perl, BioPerl, R, and GenBank help make FAST easy and rewarding to learn. FAST automates numerical, taxonomic, and text-based sorting, selection and transformation of sequence records and alignment sites based on content, index ranges, descriptive tags, annotated features, and in-line calculated analytics, including composition and codon usage. Automated content- and feature-based extraction of sites and support for molecular population genetic statistics make FAST useful for molecular evolutionary analysis. FAST is portable, easy to install and secure thanks to the relative maturity of its Perl and BioPerl foundations, with stable releases posted to CPAN. Development as well as a publicly accessible Cookbook and Wiki are available on the FAST GitHub repository at https://github.com/tlawrence3/FAST. The default data exchange format in FAST is Multi-FastA (specifically, a restriction of BioPerl FastA format). Sanger and Illumina 1.8+ FastQ formatted files are also supported. FAST makes it easier for non-programmer biologists to interactively investigate and control biological data at the speed of thought

Streaming Similarity Self-Join

We introduce and study the problem of computing the similarity self-join in a streaming context (SSSJ), where the input is an unbounded stream of items arriving continuously. The goal is to find all pairs of items in the stream whose similarity is greater than a given threshold. The simplest formulation of the problem requires unbounded memory, and thus, it is intractable. To make the problem feasible, we introduce the notion of time-dependent similarity: the similarity of two items decreases with the difference in their arrival time. By leveraging the properties of this time-dependent similarity function, we design two algorithmic frameworks to solve the sssj problem. The first one, MiniBatch (MB), uses existing index-based filtering techniques for the static version of the problem, and combines them in a pipeline. The second framework, Streaming (STR), adds time filtering to the existing indexes, and integrates new time-based bounds deeply in the working of the algorithms. We also introduce a new indexing technique (L2), which is based on an existing state-of-the-art indexing technique (L2AP), but is optimized for the streaming case. Extensive experiments show that the STR algorithm, when instantiated with the L2 index, is the most scalable option across a wide array of datasets and parameters