Distinct movement patterns generate stages of spider web-building

The geometric complexity and stereotypy of spider webs have long generated interest in their algorithmic origin. Like other examples of animal architecture, web construction is the result of several assembly phases that are driven by distinct behavioral stages coordinated to build a successful structure. Manual observations have revealed a range of sensory cues and movement patterns used during web construction, but methods to systematically quantify the dynamics of these sensorimotor patterns are lacking. Here, we apply an analytical pipeline to quantify web-making behavior of the orb-weaver Uloborus diversus. Position tracking revealed stereotyped stages of construction that could occur in typical or atypical progressions across individuals. Using an unsupervised clustering approach, we identified general and stage-specific leg movements. A Hierarchical Hidden Markov Model revealed that stages of web-building are characterized by stereotyped sequences of actions largely shared across individuals, regardless of whether these stages progress in a typical or atypical fashion. Web stages could be predicted based on action-sequences alone, revealing that web-stages are a physical manifestation of underlying behavioral phases.

Context-Aware Smart Door Lock with Activity Recognition Using Hierarchical Hidden Markov Model

Context-Aware Security demands a security system such as a Smart Door Lock to be flexible in determining security levels. The context can be in various forms; a person’s activity in the house is one of them and is proposed in this research. Several learning methods, such as Naïve Bayes, have been used previously to provide context-aware security systems, using related attributes. However conventional learning methods cannot be implemented directly to a Context-Aware system if the attribute of the learning process is low level. In the proposed system, attributes are in forms of movement data obtained from a PIR Sensor Network. Movement data is considered low level because it is not related directly to the desired context, which is activity. To solve the problem, the research proposes a hierarchical learning method, namely Hierarchical Hidden Markov Model (HHMM). HHMM will first transform the movement data into activity data through the first hierarchy, hence obtaining high level attributes through Activity Recognition. The second hierarchy will determine the security level through the activity pattern. To prove the success rate of the proposed method a comparison is made between HHMM, Naïve Bayes, and HMM. Through experiments created in a limited area with real sensed activity, the results show that HHMM provides a higher F1-Measure than Naïve Bayes and HMM in determining the desired context in the proposed system. Besides that, the accuracies obtained respectively are 88% compared to 75% and 82%.

Detecting and Localizing Anomalies in Container Clusters Using Markov Models

Detecting the location of performance anomalies in complex distributed systems is critical to ensuring the effective operation of a system, in particular, if short-lived container deployments are considered, adding challenges to anomaly detection and localization. In this paper, we present a framework for monitoring, detecting and localizing performance anomalies for container-based clusters using the hierarchical hidden Markov model (HHMM). The model aims at detecting and localizing the root cause of anomalies at runtime in order to maximize the system availability and performance. The model detects response time variations in containers and their hosting cluster nodes based on their resource utilization and tracks the root causes of variations. To evaluate the proposed framework, experiments were conducted for container orchestration, with different performance metrics being used. The results show that HHMMs are able to accurately detect and localize performance anomalies in a timely fashion.

Statistical structure of locomotion and its modulation by odors

Most behaviors such as making tea are not stereotypical but have an obvious structure. However, analytical methods to objectively extract structure from non-stereotyped behaviors are immature. In this study, we analyze the locomotion of fruit flies and show that this non-stereotyped behavior is well-described by a Hierarchical Hidden Markov Model (HHMM). HHMM shows that a fly's locomotion can be decomposed into a few locomotor features, and odors modulate locomotion by altering the time a fly spends performing different locomotor features. Importantly, although all flies in our dataset use the same set of locomotor features, individual flies vary considerably in how often they employ a given locomotor feature, and how this usage is modulated by odor. This variation is so large that the behavior of individual flies is best understood as being grouped into at least three to five distinct clusters, rather than variations around an average fly.

Statistical structure of locomotion and its modulation by odors

Most behaviors such as making tea are not stereotypical but have an obvious structure. However, analytical methods to objectively extract structure from non-stereotyped behaviors are immature. In this study, we analyze the locomotion of fruit flies and show that this non-stereotyped behavior is well-described by a Hierarchical Hidden Markov Model (HHMM). HHMM shows that a fly’s locomotion can be decomposed into a small number of locomotor features, and odors modulate locomotion by altering the time a fly spends performing different locomotor features. Importantly, although all flies in our dataset use the same set of locomotor features, individual flies vary considerably in how often they employ a given locomotor feature, and how this usage is modulated by odor. This variation is so large that the behavior of individual flies is best understood as being grouped into at least 3-5 distinct clusters, rather than variations around an average fly.

Bayesian-estimated hierarchical HMMs enable robust analysis of single-molecule kinetic heterogeneity

ABSTRACTSingle-molecule kinetic experiments allow the reaction trajectories of individual biomolecules to be directly observed, eliminating the effects of population averaging and providing a powerful approach for elucidating the kinetic mechanisms of biomolecular processes. A major challenge to the analysis and interpretation of these experiments, however, is the kinetic heterogeneity that almost universally complicates the recorded single-molecule signal versus time trajectories (i.e., signal trajectories). Such heterogeneity manifests as changes and/or differences in the transition rates that are observed within individual signal trajectories or across a population of signal trajectories. Although characterizing kinetic heterogeneity can provide critical mechanistic information, there are currently no computational methods available that effectively and/or comprehensively enable such analysis. To address this gap, we have developed a computational algorithm and software program, hFRET, that uses the variational approximation for Bayesian inference to estimate the parameters of a hierarchical hidden Markov model, thereby enabling robust identification and characterization of kinetic heterogeneity. Using simulated signal trajectories, we demonstrate the ability of hFRET to accurately and precisely characterize kinetic heterogeneity. In addition, we use hFRET to analyze experimentally recorded signal trajectories reporting on the conformational dynamics of ribosomal pre-translocation (PRE) complexes. The results of our analyses demonstrate that PRE complexes exhibit kinetic heterogeneity, reveal the physical origins of this heterogeneity, and allow us to expand the current model of PRE complex dynamics. The methods described here can be applied to signal trajectories generated using any type of signal and can be easily extended to the analysis of signal trajectories exhibiting more complex kinetic behaviors. Moreover, variations of our approach can be easily developed to integrate kinetic data obtained from different experimental constructs and/or from molecular dynamics simulations of a biomolecule of interest. The hFRET source code, graphical user interface, and user manual can be downloaded as freeware at https://github.com/GonzalezBiophysicsLab/hFRET.

MONITORING FARMLAND LOSS CAUSED BY URBANIZATION IN BEIJING FROM MODIS TIME SERIES USING HIERARCHICAL HIDDEN MARKOV MODEL

In this study, we proposed a method to map urban encroachment onto farmland using satellite image time series (SITS) based on the hierarchical hidden Markov model (HHMM). In this method, the farmland change process is decomposed into three hierarchical levels, i.e., the land cover level, the vegetation phenology level, and the SITS level. Then a three-level HHMM is constructed to model the multi-level semantic structure of farmland change process. Once the HHMM is established, a change from farmland to built-up could be detected by inferring the underlying state sequence that is most likely to generate the input time series. The performance of the method is evaluated on MODIS time series in Beijing. Results on both simulated and real datasets demonstrate that our method improves the change detection accuracy compared with the HMM-based method.