Do you want to publish a course? Click here

Characterising menotactic behaviours in movement data using hidden Markov models

134   0   0.0 ( 0 )
 Added by Ron Togunov
 Publication date 2021
  fields Biology
and research's language is English




Ask ChatGPT about the research

1. Movement is the primary means by which animals obtain resources and avoid hazards. Most movement exhibits directional bias that is related to environmental features (taxis), such as the location of food patches, predators, ocean currents, or wind. Numerous behaviours with directional bias can be characterized by maintaining orientation at an angle relative to the environmental stimuli (menotaxis), including navigation relative to sunlight or magnetic fields and energy-conserving flight across wind. However, no statistical methods exist to flexibly classify and characterise such directional bias. 2. We propose a biased correlated random walk model that can identify menotactic behaviours by predicting turning angle as a trade-off between directional persistence and directional bias relative to environmental stimuli without making a priori assumptions about the angle of bias. We apply the model within the framework of a multi-state hidden Markov model (HMM) and describe methods to remedy information loss associated with coarse environmental data to improve the classification and parameterization of directional bias. 3. Using simulation studies, we illustrate how our method more accurately classifies behavioural states compared to conventional correlated random walk HMMs that do not incorporate directional bias. We illustrate the application of these methods by identifying cross wind olfactory foraging and drifting behaviour mediated by wind-driven sea ice drift in polar bears (Ursus maritimus) from movement data collected by satellite telemetry. 4. The extensions we propose can be readily applied to movement data to identify and characterize behaviours with directional bias toward any angle, and open up new avenues to investigate more mechanistic relationships between animal movement and the environment.



rate research

Read More

162 - A. Kovalev , N. Zarrabi , F. Werz 2009
The conformational kinetics of enzymes can be reliably revealed when they are governed by Markovian dynamics. Hidden Markov Models (HMMs) are appropriate especially in the case of conformational states that are hardly distinguishable. However, the evolution of the conformational states of proteins mostly shows non-Markovian behavior, recognizable by non-monoexponential state dwell time histograms. The application of a Hidden Markov Model technique to a cyclic system demonstrating semi-Markovian dynamics is presented in this paper and the required extension of the model design is discussed. As standard ranking criteria of models cannot deal with these systems properly, a new approach is proposed considering the shape of the dwell time histograms. We observed the rotational kinetics of a single F1-ATPase alpha3beta3gamma sub-complex over six orders of magnitude of different ATP to ADP and Pi concentration ratios, and established a general model describing the kinetics for the entire range of concentrations. The HMM extension described here is applicable in general to the accurate analysis of protein dynamics.
Spatial memory plays a role in the way animals perceive their environments, resulting in memory-informed movement patterns that are observable to ecologists. Developing mathematical techniques to understand how animals use memory in their environments allows for an increased understanding of animal cognition. Here we describe a model that accounts for the memory of seasonal or ephemeral qualities of an animals environment. The model captures multiple behaviors at once by allowing for resource selection in the present time as well as long-distance navigations to previously visited locations within an animals home range. We performed a set of analyses on simulated data to test our model, determining that it can provide informative results from as little as one year of discrete-time location data. We also show that the accuracy of model selection and parameter estimation increases with more location data. This model has potential to identify cognitive mechanisms for memory in a variety of ecological systems where periodic or seasonal revisitation patterns within a home range may take place.
Motivated by applications in systems biology, we seek a probabilistic framework based on Markov processes to represent intracellular processes. We review the formal relationships between different stochastic models referred to in the systems biology literature. As part of this review, we present a novel derivation of the differential Chapman-Kolmogorov equation for a general multidimensional Markov process made up of both continuous and jump processes. We start with the definition of a time-derivative for a probability density but place no restrictions on the probability distribution, in particular, we do not assume it to be confined to a region that has a surface (on which the probability is zero). In our derivation, the master equation gives the jump part of the Markov process while the Fokker-Planck equation gives the continuous part. We thereby sketch a {}``family tree for stochastic models in systems biology, providing explicit derivations of their formal relationship and clarifying assumptions involved.
The identification of factors associated with mental and behavioral disorders in early childhood is critical both for psychopathology research and the support of primary health care practices. Motivated by the Millennium Cohort Study, in this paper we study the effect of a comprehensive set of covariates on childrens emotional and behavioural trajectories in England. To this end, we develop a Quantile Mixed Hidden Markov Model for joint estimation of multiple quantiles in a linear regression setting for multivariate longitudinal data. The novelty of the proposed approach is based on the Multivariate Asymmetric Laplace distribution which allows to jointly estimate the quantiles of the univariate conditional distributions of a multivariate response, accounting for possible correlation between the outcomes. Sources of unobserved heterogeneity and serial dependency due to repeated measures are modeled through the introduction of individual-specific, time-constant random coefficients and time-varying parameters evolving over time with a Markovian structure, respectively. The inferential approach is carried out through the construction of a suitable Expectation-Maximization algorithm without parametric assumptions on the random effects distribution.
The Baum-Welsh algorithm together with its derivatives and variations has been the main technique for learning Hidden Markov Models (HMM) from observational data. We present an HMM learning algorithm based on the non-negative matrix factorization (NMF) of higher order Markovian statistics that is structurally different from the Baum-Welsh and its associated approaches. The described algorithm supports estimation of the number of recurrent states of an HMM and iterates the non-negative matrix factorization (NMF) algorithm to improve the learned HMM parameters. Numerical examples are provided as well.
comments
Fetching comments Fetching comments
mircosoft-partner

هل ترغب بارسال اشعارات عن اخر التحديثات في شمرا-اكاديميا