8,489 research outputs found
Recommended from our members
The Swiss army knife of time series data mining: ten useful things you can do with the matrix profile and ten lines of code
Multi-Sensor Event Detection using Shape Histograms
Vehicular sensor data consists of multiple time-series arising from a number
of sensors. Using such multi-sensor data we would like to detect occurrences of
specific events that vehicles encounter, e.g., corresponding to particular
maneuvers that a vehicle makes or conditions that it encounters. Events are
characterized by similar waveform patterns re-appearing within one or more
sensors. Further such patterns can be of variable duration. In this work, we
propose a method for detecting such events in time-series data using a novel
feature descriptor motivated by similar ideas in image processing. We define
the shape histogram: a constant dimension descriptor that nevertheless captures
patterns of variable duration. We demonstrate the efficacy of using shape
histograms as features to detect events in an SVM-based, multi-sensor,
supervised learning scenario, i.e., multiple time-series are used to detect an
event. We present results on real-life vehicular sensor data and show that our
technique performs better than available pattern detection implementations on
our data, and that it can also be used to combine features from multiple
sensors resulting in better accuracy than using any single sensor. Since
previous work on pattern detection in time-series has been in the single series
context, we also present results using our technique on multiple standard
time-series datasets and show that it is the most versatile in terms of how it
ranks compared to other published results
A temporal switch model for estimating transcriptional activity in gene expression
Motivation: The analysis and mechanistic modelling of time series gene expression data provided by techniques such as microarrays, NanoString, reverse transcription–polymerase chain reaction and advanced sequencing are invaluable for developing an understanding of the variation in key biological processes. We address this by proposing the estimation of a flexible dynamic model, which decouples temporal synthesis and degradation of mRNA and, hence, allows for transcriptional activity to switch between different states.
Results: The model is flexible enough to capture a variety of observed transcriptional dynamics, including oscillatory behaviour, in a way that is compatible with the demands imposed by the quality, time-resolution and quantity of the data. We show that the timing and number of switch events in transcriptional activity can be estimated alongside individual gene mRNA stability with the help of a Bayesian reversible jump Markov chain Monte Carlo algorithm. To demonstrate the methodology, we focus on modelling the wild-type behaviour of a selection of 200 circadian genes of the model plant Arabidopsis thaliana. The results support the idea that using a mechanistic model to identify transcriptional switch points is likely to strongly contribute to efforts in elucidating and understanding key biological processes, such as transcription and degradation
Adaptive Equi-Energy Sampler : Convergence and Illustration
Markov chain Monte Carlo (MCMC) methods allow to sample a distribution known
up to a multiplicative constant. Classical MCMC samplers are known to have very
poor mixing properties when sampling multimodal distributions. The Equi-Energy
sampler is an interacting MCMC sampler proposed by Kou, Zhou and Wong in 2006
to sample difficult multimodal distributions. This algorithm runs several
chains at different temperatures in parallel, and allow lower-tempered chains
to jump to a state from a higher-tempered chain having an energy 'close' to
that of the current state. A major drawback of this algorithm is that it
depends on many design parameters and thus, requires a significant effort to
tune these parameters. In this paper, we introduce an Adaptive Equi-Energy
(AEE) sampler which automates the choice of the selection mecanism when jumping
onto a state of the higher-temperature chain. We prove the ergodicity and a
strong law of large numbers for AEE, and for the original Equi-Energy sampler
as well. Finally, we apply our algorithm to motif sampling in DNA sequences
Detecting seeded motifs in DNA sequences
The problem of detecting DNA motifs with functional relevance in real biological sequences is difficult due to a number of biological, statistical and computational issues and also because of the lack of knowledge about the structure of searched patterns. Many algorithms are implemented in fully automated processes, which are often based upon a guess of input parameters from the user at the very first step. In this paper, we present a novel method for the detection of seeded DNA motifs, composed by regions with a different extent of variability. The method is based on a multi-step approach, which was implemented in a motif searching web tool (MOST). Overrepresented exact patterns are extracted from input sequences and clustered to produce motifs core regions, which are then extended and scored to generate seeded motifs. The combination of automated pattern discovery algorithms and different display tools for the evaluation and selection of results at several analysis steps can potentially lead to much more meaningful results than complete automation can produce. Experimental results on different yeast and human real datasets proved the methodology to be a promising solution for finding seeded motifs. MOST web tool is freely available at
- …