Introduction to Cross-Entropy Clustering The R Package CEC

Tabor, Jacek; Spurek, Przemysław; Kamieniecki, Konrad; Śmieja, Marek; Misztal, Krzysztof

doi:10.48550/arxiv.1508.04559

Cited by 2 publications

(4 citation statements)

References 31 publications

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“…For Figure 3, the pre-processing step involved binarizing cilia versus body masses of 350 bots (each represented in 3D via confocal Z-stack images) through CiliaQ [38] as described in the methods above. The data obtained from these 350 bots were further clustered into 3 groups with sizes of 125, 24 and 201 for clusters 1,2 and 3 respectively.…”

Section: Methodsmentioning

confidence: 99%

“…To separate the trajectory blocks into categories of similar behavior after calculating the movement metrics, a cross-entropy clustering algorithm was used, [37] and implemented in the cec function of the CEC package (version 0.10.2) for R. [38] This yielded us six categories, of which trajectories from categories numbered 3 and 4 were merged into categories numbered 1 and 2 respectively due to the difference being phenotypically minimal. In the "behavioral space" as defined by the straightness and gyration indices, cluster 3 had the same straightness index range as cluster 1 and a lower gyration range between roughly 0.65 and 0.95, which represented trajectories that were highly circular but fell short of cluster 1 which represented "prototypical circulars".…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Motile Living Biobots Self‐Construct from Adult Human Somatic Progenitor Seed Cells

Gumuskaya,

Srivastava,

Cooper

et al. 2023

Advanced Science

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Fundamental knowledge gaps exist about the plasticity of cells from adult soma and the potential diversity of body shape and behavior in living constructs derived from genetically wild‐type cells. Here anthrobots are introduced, a spheroid‐shaped multicellular biological robot (biobot) platform with diameters ranging from 30 to 500 microns and cilia‐powered locomotive abilities. Each Anthrobot begins as a single cell, derived from the adult human lung, and self‐constructs into a multicellular motile biobot after being cultured in extra cellular matrix for 2 weeks and transferred into a minimally viscous habitat. Anthrobots exhibit diverse behaviors with motility patterns ranging from tight loops to straight lines and speeds ranging from 5–50 microns s−1. The anatomical investigations reveal that this behavioral diversity is significantly correlated with their morphological diversity. Anthrobots can assume morphologies with fully polarized or wholly ciliated bodies and spherical or ellipsoidal shapes, each related to a distinct movement type. Anthrobots are found to be capable of traversing, and inducing rapid repair of scratches in, cultured human neural cell sheets in vitro. By controlling microenvironmental cues in bulk, novel structures, with new and unexpected behavior and biomedically‐relevant capabilities, can be discovered in morphogenetic processes without direct genetic editing or manual sculpting.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Motile Living Biobots Self‐Construct from Adult Human Somatic Progenitor Seed Cells

Gumuskaya,

Srivastava,

Cooper

et al. 2023

Advanced Science

View full text Add to dashboard Cite

show abstract

“…To separate the trajectory blocks into categories of similar behavior after calculating the movement metrics, a cross-entropy clustering algorithm was used, 2 and implemented in the cec function of the CEC package (version 0.10.2) for R. 3 This yielded us six categories, of which trajectories from categories numbered 3 and 4 were merged into categories numbered 1 and 2 respectively due to the difference being phenotypically minimal. In the “behavioral space” as defined by the straightness and gyration indices, cluster 3 had the same straightness index range as cluster 1 and a lower gyration range between roughly 0.65 and 0.95, which represented trajectories that were highly circular but fell short of cluster 1 which represented “prototypical circulars”.…”

Section: Supplemental Methods Informationmentioning

confidence: 99%

“…To separate the trajectory blocks into categories of similar behavior after calculating the movement metrics, a cross-entropy clustering algorithm was used 109 , and implemented in the cec function of the CEC package (version 0.10.2) for R 110 . This yielded us six categories, of which trajectories from categories numbered 3 and 4 were merged into categories numbered 1 and 2 respectively due to the difference being phenotypically minimal.…”

Section: Movement Type Analysismentioning

confidence: 99%

Motile Living Biobots Self-Construct from Adult Human Somatic Progenitor Seed Cells

Gumuskaya

Srivastava

Cooper

et al. 2022

Preprint

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Fundamental knowledge gaps exist with respect to the plasticity of cells from adult soma and the potential diversity of body shape and behavior in living constructs derived from such genetically wild-type cells. Here we introduce Anthrobots, a spheroid-shaped multicellular biological robot platform with diameters ranging from 30 to 500 microns. Anthrobots have an inherent capacity for motility in aqueous environments, via cilia covering their surface. Each Anthrobot starts out as a single cell, derived from the adult human lung, and self-construct into a multicellular motile biological machine after having been cultured in extra cellular matrix for 2 weeks, followed by a transfer into a minimally viscous and adhesive habitat. Anthrobots exhibit a wide range of behaviors with motility patterns ranging from tight loops to straight lines with speeds ranging from 5-50 microns/second. Our anatomical investigations reveal that this diversity in their movement types is significantly correlated with their diversity in morphological types. Anthrobots can assume diverse morphologies from fully polarized to wholly ciliated bodies with spherical or ellipsoidal shapes, each correlating with a distinct movement type. Anthrobots were found to be able to traverse live human tissues in various ways as a function of these different movement types. Remarkably, Anthrobots are shown to be able to induce rapid repair of wounds in human neural cell sheets in vitro. By controlling microenvironmental cues, entirely novel structure, behavior, and biomedically-relevant capabilities can be discovered in morphogenetic processes not requiring direct genetic manipulation.

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Introduction to Cross-Entropy Clustering The R Package CEC

Cited by 2 publications

References 31 publications

Motile Living Biobots Self‐Construct from Adult Human Somatic Progenitor Seed Cells

Motile Living Biobots Self‐Construct from Adult Human Somatic Progenitor Seed Cells

Motile Living Biobots Self-Construct from Adult Human Somatic Progenitor Seed Cells

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