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

EXMOTIF: efficient structured motif extraction

BACKGROUND: Extracting motifs from sequences is a mainstay of bioinformatics. We look at the problem of mining structured motifs, which allow variable length gaps between simple motif components. We propose an efficient algorithm, called EXMOTIF, that given some sequence(s), and a structured motif template, extracts all frequent structured motifs that have quorum q. Potential applications of our method include the extraction of single/composite regulatory binding sites in DNA sequences. RESULTS: EXMOTIF is efficient in terms of both time and space and is shown empirically to outperform RISO, a state-of-the-art algorithm. It is also successful in finding potential single/composite transcription factor binding sites. CONCLUSION: EXMOTIF is a useful and efficient tool in discovering structured motifs, especially in DNA sequences. The algorithm is available as open-source at:

Mining Patterns and Rules for Software Specification Discovery

Proceedings of the VLDB Endowment121609-161

CCPM: A Scalable and Noise-Resistant Closed Contiguous Sequential Patterns Mining Algorithm

International audienceMining closed contiguous sequential patterns has been addressed in the literature only recently, through the CCSpan algorithm. CCSpan mines a set of patterns that contains the same information than traditional sets of closed sequential patterns, while being more compact due to the contiguity. Although CCSpan outperforms closed sequential pattern mining algorithms in the general case, it does not scale well on large datasets with long sequences. Moreover, in the context of noisy datasets, the contiguity constraint prevents from mining a relevant result set. Inspired by BIDE, that has proven to be one of the most efficient closed sequential pattern mining algorithm, we propose CCPM that mines closed contiguous sequential patterns, while being scalable. Furthermore , CCPM introduces usable wildcards that address the problem of mining noisy data. Experiments show that CCPM greatly outperforms CCSpan, especially on large datasets with long sequences. In addition, they show that the wildcards allows to efficiently tackle the problem of noisy data

Periodic subgraph mining in dynamic networks

La tesi si prefigge di scoprire interazioni periodiche frequenti tra i membri di una popolazione il cui comportamento viene studiato in un certo arco di tempo. Le interazioni tra i membri della popolazione sono rappresentate da archi E tra vertici V di un grafo. Una rete dinamica consiste in una serie di T timestep per ciascuno dei quali esiste un grafo che rappresenta le interazioni attive in quel dato istante. Questa tesi presenta ListMiner, un algoritmo per il problema dell’estrazione di sottografi periodici. La complessità computazionale di tale algoritmo è O((V+E) T2 ln (T /σ)), dove σ è il minimo numero di ripetizioni periodiche necessarie per riportare il sottografo estratto in output. Questa complessità propone un miglioramento di un fattore T rispetto l’unico algoritmo noto in letteratura, PSEMiner. Nella tesi sono inoltre presenti un’analisi dei risultati ottenuti e una presentazione di una variante del problem

C3Ro: An efficient mining algorithm of extende d-close d contiguous robust sequential patterns in noisy data

International audienceSequential pattern mining has been the focus of many works, but still faces a tough challenge in the mining of large databases for both efficiency and apprehensibility of its resulting set. To overcome these issues, the most promising direction taken by the literature relies on the use of constraints, including the well-known closedness constraint. However, such a mining is not resistant to noise in data, a characteristic of most real-world data. The main research question raised in this paper is thus: how to efficiently mine an apprehensible set of sequential patterns from noisy data? In order to address this research question, we introduce 1) two original constraints designed for the mining of noisy data: the robustness and the extended-closedness constraints, 2) a generic pattern mining algorithm, C3Ro, designed to mine a wide range of sequential patterns, going from closed or maximal contiguous sequential patterns to closed or maximal regular sequential patterns. C3Ro is dedicated to practitioners and is able to manage their multiple constraints. C3Ro also is the first sequential pattern mining algorithm to be as generic and parameterizable. Extensive experiments have been conducted and reveal the high efficiency of C3Ro, especially in large datasets, over well-known algorithms from the literature. Additional experiments have been conducted on a real-world job offers noisy dataset, with the goal to mine activities. This experiment offers a more thorough insight into C3Ro algorithm: job market experts confirm that the constraints we introduced actually have a significant positive impact on the apprehensibility of the set of mined activities

Periodic pattern mining from spatio-temporal trajectory data

Rapid development in GPS tracking techniques produces a large number of spatio-temporal trajectory data. The analysis of these data provides us with a new opportunity to discover useful behavioural patterns. Spatio-temporal periodic pattern mining is employed to find temporal regularities for interesting places. Mining periodic patterns from spatio-temporal trajectories can reveal useful, important and valuable information about people's regular and recurrent movements and behaviours. Previous studies have been proposed to extract people's regular and repeating movement behavior from spatio-temporal trajectories. These previous approaches can target three following issues, (1) long individual trajectory; (2) spatial fuzziness; and (3) temporal fuzziness. First, periodic pattern mining is different to other pattern mining, such as association rule ming and sequential pattern mining, periodic pattern mining requires a very long trajectory from an individual so that the regular period can be extracted from this long single trajectory, for example, one month or one year period. Second, spatial fuzziness shows although a moving object can regularly move along the similar route, it is impossible for it to appear at the exactly same location. For instance, Bob goes to work everyday, and although he can follow a similar path from home to his workplace, the same location cannot be repeated across different days. Third, temporal fuzziness shows that periodicity is complicated including partial time span and multiple interleaving periods. In reality, the period is partial, it is highly impossible to occur through the whole movement of the object. Alternatively, the moving object has only a few periods, such as a daily period for work, or yearly period for holidays. However, it is insufficient to find effective periodic patterns considering these three issues only. This thesis aims to develop a new framework to extract more effective, understandable and meaningful periodic patterns by taking more features of spatio-temporal trajectories into account. The first feature is trajectory sequence, GPS trajectory data is temporally ordered sequences of geolocation which can be represented as consecutive trajectory segments, where each entry in each trajectory segment is closely related to the previous sampled point (trajectory node) and the latter one, rather than being isolated. Existing approaches disregard the important sequential nature of trajectory. Furthermore, they introduce both unwanted false positive reference spots and false negative reference spots. The second feature is spatial and temporal aspects. GPS trajectory data can be presented as triple data (x; y; t), x and y represent longitude and latitude respectively whilst t shows corresponding time in this location. Obviously, spatial and temporal aspects are two key factors. Existing methods do not consider these two aspects together in periodic pattern mining. Irregular time interval is the third feature of spatio-temporal trajectory. In reality, due to weather conditions, device malfunctions, or battery issues, the trajectory data are not always regularly sampled. Existing algorithms cannot deal with this issue but instead require a computationally expensive trajectory interpolation process, or it is assumed that trajectory is with regular time interval. The fourth feature is hierarchy of space. Hierarchy is an inherent property of spatial data that can be expressed in different levels, such as a country includes many states, a shopping mall is comprised of many shops. Hierarchy of space can find more hidden and valuable periodic patterns. Existing studies do not consider this inherent property of trajectory. Hidden background semantic information is the final feature. Aspatial semantic information is one of important features in spatio-temporal data, and it is embedded into the trajectory data. If the background semantic information is considered, more meaningful, understandable and useful periodic patterns can be extracted. However, existing methods do not consider the geographical information underlying trajectories. In addition, at times we are interested in finding periodic patterns among trajectory paths rather than trajectory nodes for different applications. This means periodic patterns should be identified and detected against trajectory paths rather than trajectory nodes for some applications. Existing approaches for periodic pattern mining focus on trajectories nodes rather than paths. To sum up, the aim of this thesis is to investigate solutions to these problems in periodic pattern mining in order to extract more meaningful, understandable periodic patterns. Each of three chapters addresses a different problem and then proposes adequate solutions to problems currently not addressed in existing studies. Finally, this thesis proposes a new framework to address all problems. First, we investigated a path-based solution which can target trajectory sequence and spatio-temporal aspects. We proposed an algorithm called Traclus (spatio-temporal) which can take spatial and temporal aspects into account at the same time instead of only considering spatial aspect. The result indicated our method produced more effective periodic patterns based on trajectory paths than existing node-based methods using two real-world trajectories. In order to consider hierarchy of space, we investigated existing hierarchical clustering approaches to obtain hierarchical reference spots (trajectory paths) for periodic pattern mining. HDBSCAN is an incremental version of DBSCAN which is able to handle clusters with different densities to generate a hierarchical clustering result using the single-linkage method, and then it automatically extracts clusters from a hierarchical tree. Thus, we modified traditional clustering method DBSCAN in Traclus (spatio-temporal) to HDBSCAN for extraction of hierarchical reference spots. The result is convincing, and reveals more periodic patterns than those of existing methods. Second, we introduced a stop/move method to annotate each spatio-temporal entry with a semantic label, such as restaurant, university and hospital. This method can enrich a trajectory with background semantic information so that we can easily infer people's repeating behaviors. In addition, existing methods use interpolation to make trajectory regular and then apply Fourier transform and autocorrelation to automatically detect period for each reference spot. An increasing number of trajectory nodes leads to an exponential increase of running time. Thus, we employed Lomb-Scargle periodogram to detect period for each reference spot based on raw trajectory without requiring any interpolation method. The results showed our method outperformed existing approaches on effectiveness and efficiency based on two real datasets. For hierarchical aspect, we extended previous work to find hierarchical semantic periodic patterns by applying HDBSCAN. The results were promising. Third, we apply our methodology to a case study, which reveals many interesting medical periodic patterns. These patterns can effectively explore human movement behaviors for positive medical outcomes. To sum up, this research proposed a new framework to gradually target the problems that existing methods cannot handle. These include: how to consider trajectory sequence, how to consider spatial temporal aspects together, how to deal with trajectory with irregular time interval, how to consider hierarchy of space and how to extract semantic information behind trajectory. After addressing all these problems, the experimental results demonstrate that our method can find more understandable, meaningful and effective periodic patterns than existing approaches