scholarly journals Monitoring Weeder Robots and Anticipating Their Functioning by Using Advanced Topological Data Analysis

2021 ◽  
Vol 4 ◽  
Author(s):  
Tarek Frahi ◽  
Abel Sancarlos ◽  
Mathieu Galle ◽  
Xavier Beaulieu ◽  
Anne Chambard ◽  
...  
Keyword(s):  
Time Series ◽  
Data Analysis ◽  
Autonomous Robots ◽  
Topological Data Analysis ◽  
Topological Descriptors ◽  
Diagnosis And Prognosis ◽  
Robot Behavior ◽  
Before And After ◽  
Complex Trajectories ◽  
Original Approach

The present paper aims at analyzing the topological content of the complex trajectories that weeder-autonomous robots follow in operation. We will prove that the topological descriptors of these trajectories are affected by the robot environment as well as by the robot state, with respect to maintenance operations. Most of existing methodologies enabling efficient diagnosis are based on the data analysis, and in particular on some statistical quantities derived from the data. The present work explores the use of an original approach that instead of analyzing quantities derived from the data, analyzes the “shape” of the data, that is, the time series topology based on the homology persistence. We will prove that this procedure is able to extract valuable patterns able to discriminate the trajectories that the robot follows depending on the particular patch in which it operates, as well as to differentiate the robot behavior before and after undergoing a maintenance operation. Even if it is a preliminary work, and it does not pretend to compare its performances with respect to other existing technologies, this work opens new perspectives in considering quite natural and simple descriptors based on the intrinsic information that data contains, with the aim of performing efficient diagnosis and prognosis.

scholarly journals Topological Data Analysis Approaches to Uncovering the Timing of Ring Structure Onset in Filamentous Networks

2021 ◽  
Vol 83 (3) ◽  
Author(s):  
Maria-Veronica Ciocanel ◽  
Riley Juenemann ◽  
Adriana T. Dawes ◽  
Scott A. McKinley
Keyword(s):  
Time Series ◽  
Data Analysis ◽  
Actin Filaments ◽  
Time Series Data ◽  
Polymer Networks ◽  
Topological Data Analysis ◽  
Series Data ◽  
Topological Features ◽  
Topological Data

AbstractIn developmental biology as well as in other biological systems, emerging structure and organization can be captured using time-series data of protein locations. In analyzing this time-dependent data, it is a common challenge not only to determine whether topological features emerge, but also to identify the timing of their formation. For instance, in most cells, actin filaments interact with myosin motor proteins and organize into polymer networks and higher-order structures. Ring channels are examples of such structures that maintain constant diameters over time and play key roles in processes such as cell division, development, and wound healing. Given the limitations in studying interactions of actin with myosin in vivo, we generate time-series data of protein polymer interactions in cells using complex agent-based models. Since the data has a filamentous structure, we propose sampling along the actin filaments and analyzing the topological structure of the resulting point cloud at each time. Building on existing tools from persistent homology, we develop a topological data analysis (TDA) method that assesses effective ring generation in this dynamic data. This method connects topological features through time in a path that corresponds to emergence of organization in the data. In this work, we also propose methods for assessing whether the topological features of interest are significant and thus whether they contribute to the formation of an emerging hole (ring channel) in the simulated protein interactions. In particular, we use the MEDYAN simulation platform to show that this technique can distinguish between the actin cytoskeleton organization resulting from distinct motor protein binding parameters.

Inferring Temporal Phenotypes with Topological Data Analysis and Pseudo Time-Series

2019 ◽  
pp. 399-409 ◽  
Author(s):  
Arianna Dagliati ◽  
Nophar Geifman ◽  
Niels Peek ◽  
John H. Holmes ◽  
Lucia Sacchi ◽  
...  
Keyword(s):  
Time Series ◽  
Data Analysis ◽  
Topological Data Analysis ◽  
Topological Data

scholarly journals Persistent homology as a new method of the assessment of heart rate variability

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0253851
Author(s):  
Grzegorz Graff ◽  
Beata Graff ◽  
Paweł Pilarczyk ◽  
Grzegorz Jabłoński ◽  
Dariusz Gąsecki ◽  
...  
Keyword(s):  
Heart Rate ◽  
Heart Rate Variability ◽  
Data Analysis ◽  
Persistent Homology ◽  
Assessment Tools ◽  
Topological Data Analysis ◽  
Topological Descriptors ◽  
Time Interval ◽  
Analysis Tool ◽  
Frequency Domain Methods

Heart rate variability (hrv) is a physiological phenomenon of the variation in the length of the time interval between consecutive heartbeats. In many cases it could be an indicator of the development of pathological states. The classical approach to the analysis of hrv includes time domain methods and frequency domain methods. However, attempts are still being made to define new and more effective hrv assessment tools. Persistent homology is a novel data analysis tool developed in the recent decades that is rooted at algebraic topology. The Topological Data Analysis (TDA) approach focuses on examining the shape of the data in terms of connectedness and holes, and has recently proved to be very effective in various fields of research. In this paper we propose the use of persistent homology to the hrv analysis. We recall selected topological descriptors used in the literature and we introduce some new topological descriptors that reflect the specificity of hrv, and we discuss their relation to the standard hrv measures. In particular, we show that this novel approach provides a collection of indices that might be at least as useful as the classical parameters in differentiating between series of beat-to-beat intervals (RR-intervals) in healthy subjects and patients suffering from a stroke episode.

scholarly journals Topological Data Analysis for Eye Fundus Image Quality Assessment

Diagnostics ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1322
Author(s):  
Gener José Avilés-Rodríguez ◽  
Juan Iván Nieto-Hipólito ◽  
María de los Ángeles Cosío-León ◽  
Gerardo Salvador Romo-Cárdenas ◽  
Juan de Dios Sánchez-López ◽  
...  
Keyword(s):  
Data Analysis ◽  
Image Quality ◽  
Quality Assessment ◽  
Image Quality Assessment ◽  
Persistent Homology ◽  
Computational Cost ◽  
Topological Data Analysis ◽  
Topological Descriptors ◽  
Fundus Images ◽  
Topological Data

The objective of this work is to perform image quality assessment (IQA) of eye fundus images in the context of digital fundoscopy with topological data analysis (TDA) and machine learning methods. Eye health remains inaccessible for a large amount of the global population. Digital tools that automize the eye exam could be used to address this issue. IQA is a fundamental step in digital fundoscopy for clinical applications; it is one of the first steps in the preprocessing stages of computer-aided diagnosis (CAD) systems using eye fundus images. Images from the EyePACS dataset were used, and quality labels from previous works in the literature were selected. Cubical complexes were used to represent the images; the grayscale version was, then, used to calculate a persistent homology on the simplex and represented with persistence diagrams. Then, 30 vectorized topological descriptors were calculated from each image and used as input to a classification algorithm. Six different algorithms were tested for this study (SVM, decision tree, k-NN, random forest, logistic regression (LoGit), MLP). LoGit was selected and used for the classification of all images, given the low computational cost it carries. Performance results on the validation subset showed a global accuracy of 0.932, precision of 0.912 for label “quality” and 0.952 for label “no quality”, recall of 0.932 for label “quality” and 0.912 for label “no quality”, AUC of 0.980, F1 score of 0.932, and a Matthews correlation coefficient of 0.864. This work offers evidence for the use of topological methods for the process of quality assessment of eye fundus images, where a relatively small vector of characteristics (30 in this case) can enclose enough information for an algorithm to yield classification results useful in the clinical settings of a digital fundoscopy pipeline for CAD.

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