Generic Subsequence Matching Framework: Modularity, Flexibility, Efficiency

Subsequence matching has appeared to be an ideal approach for solving many problems related to the fields of data mining and similarity retrieval. It has been shown that almost any data class (audio, image, biometrics, signals) is or can be represented by some kind of time series or string of symbols, which can be seen as an input for various subsequence matching approaches. The variety of data types, specific tasks and their partial or full solutions is so wide that the choice, implementation and parametrization of a suitable solution for a given task might be complicated and time-consuming; a possibly fruitful combination of fragments from different research areas may not be obvious nor easy to realize. The leading authors of this field also mention the implementation bias that makes difficult a proper comparison of competing approaches. Therefore we present a new generic Subsequence Matching Framework (SMF) that tries to overcome the aforementioned problems by a uniform frame that simplifies and speeds up the design, development and evaluation of subsequence matching related systems. We identify several relatively separate subtasks solved differently over the literature and SMF enables to combine them in straightforward manner achieving new quality and efficiency. This framework can be used in many application domains and its components can be reused effectively. Its strictly modular architecture and openness enables also involvement of efficient solutions from different fields, for instance efficient metric-based indexes. This is an extended version of a paper published on DEXA 2012.Comment: This is an extended version of a paper published on DEXA 201

KV-match: A Subsequence Matching Approach Supporting Normalization and Time Warping [Extended Version]

The volume of time series data has exploded due to the popularity of new applications, such as data center management and IoT. Subsequence matching is a fundamental task in mining time series data. All index-based approaches only consider raw subsequence matching (RSM) and do not support subsequence normalization. UCR Suite can deal with normalized subsequence match problem (NSM), but it needs to scan full time series. In this paper, we propose a novel problem, named constrained normalized subsequence matching problem (cNSM), which adds some constraints to NSM problem. The cNSM problem provides a knob to flexibly control the degree of offset shifting and amplitude scaling, which enables users to build the index to process the query. We propose a new index structure, KV-index, and the matching algorithm, KV-match. With a single index, our approach can support both RSM and cNSM problems under either ED or DTW distance. KV-index is a key-value structure, which can be easily implemented on local files or HBase tables. To support the query of arbitrary lengths, we extend KV-match to KV-match$_{DP}$, which utilizes multiple varied-length indexes to process the query. We conduct extensive experiments on synthetic and real-world datasets. The results verify the effectiveness and efficiency of our approach.Comment: 13 page

The Extended Edit Distance Metric

Similarity search is an important problem in information retrieval. This similarity is based on a distance. Symbolic representation of time series has attracted many researchers recently, since it reduces the dimensionality of these high dimensional data objects. We propose a new distance metric that is applied to symbolic data objects and we test it on time series data bases in a classification task. We compare it to other distances that are well known in the literature for symbolic data objects. We also prove, mathematically, that our distance is metric.Comment: Technical repor

A neural network for mining large volumes of time series data

Efficiently mining large volumes of time series data is amongst the most challenging problems that are fundamental in many fields such as industrial process monitoring, medical data analysis and business forecasting. This paper discusses a high-performance neural network for mining large time series data set and some practical issues on time series data mining. Examples of how this technology is used to search the engine data within a major UK eScience Grid project (DAME) for supporting the maintenance of Rolls-Royce aero-engine are presented

De Novo Assembly of Nucleotide Sequences in a Compressed Feature Space

Sequencing technologies allow for an in-depth analysis of biological species but the size of the generated datasets introduce a number of analytical challenges. Recently, we demonstrated the application of numerical sequence representations and data transformations for the alignment of short reads to a reference genome. Here, we expand out approach for de novo assembly of short reads. Our results demonstrate that highly compressed data can encapsulate the signal suffi- ciently to accurately assemble reads to big contigs or complete genomes

Feature-based time-series analysis

This work presents an introduction to feature-based time-series analysis. The time series as a data type is first described, along with an overview of the interdisciplinary time-series analysis literature. I then summarize the range of feature-based representations for time series that have been developed to aid interpretable insights into time-series structure. Particular emphasis is given to emerging research that facilitates wide comparison of feature-based representations that allow us to understand the properties of a time-series dataset that make it suited to a particular feature-based representation or analysis algorithm. The future of time-series analysis is likely to embrace approaches that exploit machine learning methods to partially automate human learning to aid understanding of the complex dynamical patterns in the time series we measure from the world.Comment: 28 pages, 9 figure