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Clustering sequence sets for motif discovery

Neural Information Processing Systems

Most of existing methods for DNA motif discovery consider only a single set of sequences to find an over-represented motif. In contrast, we consider multiple sets of sequences where we group sets associated with the same motif into a cluster, assuming that each set involves a single motif. Clustering sets of sequences yields clusters of coherent motifs, improving signal-to-noise ratio or enabling us to identify multiple motifs. We present a probabilistic model for DNA motif discovery where we identify multiple motifs through searching for patterns which are shared across multiple sets of sequences. Our model infers cluster-indicating latent variables and learns motifs simultaneously, where these two tasks interact with each other. We show that our model can handle various motif discovery problems, depending on how to construct multiple sets of sequences. Experiments on three different problems for discovering DNA motifs emphasize the useful behavior and confirm the substantial gains over existing methods where only single set of sequences is considered.


CASC: Context-Aware Segmentation and Clustering for Motif Discovery in Noisy Time Series Data

arXiv.org Artificial Intelligence

Complex systems, such as airplanes, cars, or financial markets, produce multivariate time series data consisting of system observations over a period of time. Such data can be interpreted as a sequence of segments, where each segment is associated with a certain state of the system. An important problem in this domain is to identify repeated sequences of states, known as motifs. Such motifs correspond to complex behaviors that capture common sequences of state transitions. For example, a motif of "making a turn" might manifest in sensor data as a sequence of states: slowing down, turning the wheel, and then speeding back up. However, discovering these motifs is challenging, because the individual states are unknown and need to be learned from the noisy time series. Simultaneously, the time series also needs to be precisely segmented and each segment needs to be associated with a state. Here we develop context-aware segmentation and clustering (CASC), a method for discovering common motifs in time series data. We formulate the problem of motif discovery as a large optimization problem, which we then solve using a greedy alternating minimization-based approach. CASC performs well in the presence of noise in the input data and is scalable to very large datasets. Furthermore, CASC leverages common motifs to more robustly segment the time series and assign segments to states. Experiments on synthetic data show that CASC outperforms state-of-the-art baselines by up to 38.2%, and two case studies demonstrate how our approach discovers insightful motifs in real-world time series data.


A Hierarchical Bayesian Markovian Model for Motifs in Biopolymer Sequences

Neural Information Processing Systems

We propose a dynamic Bayesian model for motifs in biopolymer sequences whichcaptures rich biological prior knowledge and positional dependencies in motif structure in a principled way. Our model posits that the position-specific multinomial parameters for monomer distribution aredistributed as a latent Dirichlet-mixture random variable, and the position-specific Dirichlet component is determined by a hidden Markov process. Model parameters can be fit on training motifs using a variational EMalgorithm within an empirical Bayesian framework. Variational inference is also used for detecting hidden motifs. Our model improves overprevious models that ignore biological priors and positional dependence. It has much higher sensitivity to motifs during detection and a notable ability to distinguish genuine motifs from false recurring patterns.


Detecting Motifs in System Call Sequences

arXiv.org Artificial Intelligence

The search for patterns or motifs in data represents an area of key interest to many researchers. In this paper we present the Motif Tracking Algorithm, a novel immune inspired pattern identification tool that is able to identify unknown motifs which repeat within time series data. The power of the algorithm is derived from its use of a small number of parameters with minimal assumptions. The algorithm searches from a completely neutral perspective that is independent of the data being analysed, and the underlying motifs. In this paper the motif tracking algorithm is applied to the search for patterns within sequences of low level system calls between the Linux kernel and the operating system's user space. The MTA is able to compress data found in large system call data sets to a limited number of motifs which summarise that data. The motifs provide a resource from which a profile of executed processes can be built. The potential for these profiles and new implications for security research are highlighted. A higher level call system language for measuring similarity between patterns of such calls is also suggested.


Motif Detection Inspired by Immune Memory

arXiv.org Artificial Intelligence

The search for patterns or motifs in data represents an area of key interest to many researchers. In this paper we present the Motif Tracking Algorithm, a novel immune inspired pattern identification tool that is able to identify variable length unknown motifs which repeat within time series data. The algorithm searches from a completely neutral perspective that is independent of the data being analysed and the underlying motifs. In this paper we test the flexibility of the motif tracking algorithm by applying it to the search for patterns in two industrial data sets. The algorithm is able to identify a population of motifs successfully in both cases, and the value of these motifs is discussed.