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Hidden Markov models: the best models for forager movements?

ABSTRACT: One major challenge in the emerging field of movement ecology is the inference of behavioural modes from movement patterns. This has been mainly addressed through Hidden Markov models (HMMs). We propose here to evaluate two sets of alternative and state-of-the-art modelling approaches. First, we consider hidden semi-Markov models (HSMMs). They may better represent the behavioural dynamics of foragers since they explicitly model the duration of the behavioural modes. Second, we consider discriminative models which state the inference of behavioural modes as a classification issue, and may take better advantage of multivariate and non linear combinations of movement pattern descriptors. For this work, we use a dataset of >200 trips from human foragers, Peruvian fishermen targeting anchovy. Their movements were recorded through a Vessel Monitoring System (∼1 record per hour), while their behavioural modes (fishing, searching and cruising) were reported by on-board observers. We compare the efficiency of hidden Markov, hidden semi-Markov, and three discriminative models (random forests, artificial neural networks and support vector machines) for inferring the fishermen behavioural modes, using a cross-validation procedure. HSMMs show the highest accuracy (80%), significantly outperforming HMMs and discriminative models. Simulations show that data with higher temporal resolution, HSMMs reach nearly 100% of accuracy. Our results demonstrate to what extent the sequential nature of movement is critical for accurately inferring behavioural modes from a trajectory and we strongly recommend the use of HSMMs for such purpose. In addition, this work opens perspectives on the use of hybrid HSMM-discriminative models, where a discriminative setting for the observation process of HSMMs could greatly improve inference performance.

SUBMITTER: Joo R

PROVIDER: S-EPMC3751962 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:The results of two experiments are analyzed to find out how artistic expertise influences visual search. Experiment I comprised survey data of 1,065 students on self-reported visual memory skills and their ability to find three targets in four images of artwork. Experiment II comprised eye movement data of 50 Visual Literacy (VL) experts and non-experts whose eye movements during visual search were analyzed for nine images of artwork as an external validation of the assessment tasks performed in Sample I. No time constraint was set for completion of the visual search task. A latent profile analysis revealed four typical solution patterns for the students in Sample I, including a mainstream group, a group that completes easy images fast and difficult images slowly, a fast and erroneous group, and a slow working student group, depending on task completion time and on the probability of finding all three targets. Eidetic memory, performance in art education and visual imagination as self-reported visual skills have significant impact on latent class membership probability. We present a hidden Markov model (HMM) approach to uncover underlying regions of attraction that result from visual search eye-movement behavior in Experiment II. VL experts and non-experts did not significantly differ in task time and number of targets found but they did differ in their visual search process: compared to non-experts, experts showed greater precision in fixating specific prime and target regions, assessed through hidden state fixation overlap. Exploratory analysis of HMMs revealed differences between experts and non-experts in image locations of attraction (HMM states). Experts seem to focus their attention on smaller image parts whereas non-experts used wider parts of the image during their search. Differences between experts and non-experts depend on the relative saliency of targets embedded in images. HMMs can determine the effect of expertise on exploratory eye movements executed during visual search tasks. Further research on HMMs and art expertise is required to confirm exploratory results.

Project description:BackgroundRiboswitches are a type of noncoding RNA that regulate gene expression by switching from one structural conformation to another on ligand binding. The various classes of riboswitches discovered so far are differentiated by the ligand, which on binding induces a conformational switch. Every class of riboswitch is characterized by an aptamer domain, which provides the site for ligand binding, and an expression platform that undergoes conformational change on ligand binding. The sequence and structure of the aptamer domain is highly conserved in riboswitches belonging to the same class. We propose a method for fast and accurate identification of riboswitches using profile Hidden Markov Models (pHMM). Our method exploits the high degree of sequence conservation that characterizes the aptamer domain.ResultsOur method can detect riboswitches in genomic databases rapidly and accurately. Its sensitivity is comparable to the method based on the Covariance Model (CM). For six out of ten riboswitch classes, our method detects more than 99.5% of the candidates identified by the much slower CM method while being several hundred times faster. For three riboswitch classes, our method detects 97-99% of the candidates relative to the CM method. Our method works very well for those classes of riboswitches that are characterized by distinct and conserved sequence motifs.ConclusionRiboswitches play a crucial role in controlling the expression of several prokaryotic genes involved in metabolism and transport processes. As more and more new classes of riboswitches are being discovered, it is important to understand the patterns of their intra and inter genomic distribution. Understanding such patterns will enable us to better understand the evolutionary history of these genetic regulatory elements. However, a complete picture of the distribution pattern of riboswitches will emerge only after accurate identification of riboswitches across genomes. We believe that the riboswitch detection method developed in this paper will aid in that process. The significant advantage in terms of speed, of our pHMM-based approach over the method based on CM allows us to scan entire databases (rather than 5'UTRs only) in a relatively short period of time in order to accurately identify riboswitch candidates.

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Hidden Markov models: the best models for forager movements?

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