Hierarchical compression of Caenorhabditis elegans locomotion reveals phenotypic differences in the organization of behaviour

  title={Hierarchical compression of Caenorhabditis elegans locomotion reveals phenotypic differences in the organization of behaviour},
  author={Alex Gomez-Marin and Greg J. Stephens and Andr{\'e} E. X. Brown},
  journal={Journal of the Royal Society Interface},
Regularities in animal behaviour offer insights into the underlying organizational and functional principles of nervous systems and automated tracking provides the opportunity to extract features of behaviour directly from large-scale video data. Yet how to effectively analyse such behavioural data remains an open question. Here, we explore whether a minimum description length principle can be exploited to identify meaningful behaviours and phenotypes. We apply a dictionary compression… 

Figures from this paper

Capturing the continuous complexity of behaviour in Caenorhabditis elegans

A data-driven framework based on theory of dynamical systems is applied to characterize nematode behaviour and explain its complexity through deterministic chaotic dynamics.

A context-free grammar for Caenorhabditis elegans behavior

It is shown that worm foraging is organized hierarchically —a feature not explainable via Markovian dynamics—, and derive a context-free grammar governing its behavior —which is different than a regular grammar, or a hidden Markov chain.

Hierarchical Compression Reveals Sub-Second to Day-Long Structure in Larval Zebrafish Behaviour

The organisation of larval zebrafish behaviour at multiple timescales is revealed and tools to identify structure from large-scale behavioural datasets are provided and it is demonstrated that module and motif analysis can uncover novel pharmacological and genetic mutant phenotypes.

Hierarchical Compression Reveals Sub-Second to Day-Long Structure in Larval Zebrafish Behavior

Computational tools are developed and the organization of larval zebrafish behavior at multiple timescales is revealed and tools to identify structure from large-scale behavioral datasets are provided, demonstrating that module and motif analysis can uncover novel pharmacological and genetic mutant phenotypes.

Screening by changes in stereotypical behavior during cell motility

This work uses drug treatment and genetics to demonstrate that maximum caliber descriptors can discriminate between healthy and aberrant migration, thereby showing potential applications for maximum caliber methods in automated disease screening, for example in the identification of behaviors associated with cancer metastasis.

Capturing the Continuous Complexity of Behavior in C. elegans

This work develops a behavioral state space in which the full instantaneous state is smoothly unfolded as a combination of short-time posture dynamics, tailored to multivariate observations and extends previous reconstructions through the use of maximal prediction.

Predicting path from undulations for C. elegans using linear and nonlinear resistive force theory

It is confirmed that linear resistive force theory provides a good effective model of worm crawling that can be used in applications such as whole-animal simulations and advanced tracking algorithms, but that the nature of the physical interaction between worms and their most commonly studied laboratory substrate remains unresolved.

Temporal processing and context dependency in Caenorhabditis elegans response to mechanosensation

This work investigates how the nematode Caenorhabditis elegans responds to time-varying mechanosensory signals using a high-throughput optogenetic assay and automated behavior quantification and presents a linear-nonlinear model that predicts the animal’s behavioral response to stimulus.

Minimal neuronal circuit for action command generation and motor behaviour in Caenorhabditis elegans

An experimental method to suppress the whole nervous system and then reconstitute and record activities of individual neurons or small groups of neurons, which suggests that the expression of the silencing transgene was indeed pan-neuronal, and suggests a strategy other than Cre-Lox might be useful.

A lexical approach for identifying behavioural action sequences

An unsupervised algorithm called “BASS” is designed to efficiently identify and segment conserved behavioral action sequences transiently occurring in long behavioral recordings, which can be easily incorporated into the pipelines of existing behavioral analyses across diverse species, and used as a generic algorithm for pattern recognition in low-dimensional sequential data.



A dictionary of behavioral motifs reveals clusters of genes affecting Caenorhabditis elegans locomotion

It is shown that four basic shapes, or eigenworms, previously described for wild-type worms, also capture mutant shapes, and that this representation can be used to build a dictionary of repetitive behavioral motifs in an unbiased way.

Changes in Postural Syntax Characterize Sensory Modulation and Natural Variation of C. elegans Locomotion

A quantitative understanding of the nature of behavioural variation will inform research on the function and evolution of neural circuits and enable the use of methods developed for other kinds of discrete data in bioinformatics and language processing to be harnessed for the study of behaviour.

Mechanistic analysis of the search behaviour of Caenorhabditis elegans

The results show how movement strategies arise from a balance between intrinsic and extrinsic mechanisms, that search behaviour in C. elegans is initially determined by expectations developed from previous environmental experiences, and which reorientation behaviours are modified as information is acquired from new environments.

Controlling interneuron activity in Caenorhabditis elegans to evoke chemotactic behavior

Optogenetics and new optical tools are used to manipulate neural activity directly in freely moving animals to evoke chemotactic behaviour and it is discovered that controlling the dynamics of activity in just one interneuron pair (AIY) was sufficient to force the animal to locate, turn towards and track virtual light gradients.

Emergence of long timescales and stereotyped behaviors in Caenorhabditis elegans

The stochastic dynamics of the crawling behavior of the nematode Caenorhabditis elegans are used to show that the noise amplitude decreases systematically with increasing time away from food, resulting in longer bouts of forward crawling and suggesting that worms can use noise to modify their locomotory behavior.

Dimensionality and Dynamics in the Behavior of C. elegans

It is shown that the space of shapes adopted by the nematode Caenorhabditis elegans is low dimensional, with just four dimensions accounting for 95% of the shape variance, and Stimulus-dependent correlations among the different modes suggest that one can generate more reliable behaviors by synchronizing stimuli to the state of the worm in shape space.

Systematic profiling of Caenorhabditis elegans locomotive behaviors reveals additional components in G-protein Gαq signaling

Genetic screens have been widely applied to uncover genetic mechanisms of movement disorders. However, most screens rely on human observations of qualitative differences. Here we demonstrate the

High-content behavioral analysis of Caenorhabditis elegans in precise spatiotemporal chemical environments

A microfluidic system to analyze Caenorhabditis elegans behavior in defined temporal and spatial stimulus patterns and identified both expected and unexpected responses in wild-type worms and sensory mutants by quantifying dozens of behavioral parameters.