scholarly journals Shape-to-graph Mapping Method for Efficient Characterization and Classification of Complex Geometries in Biological Images

2020 ◽  
Author(s):  
William Pilcher ◽  
Xingyu Yang ◽  
Anastasia Zhurikhina ◽  
Olga Chernaya ◽  
Yinghan Xu ◽  
...  
Keyword(s):  
Machine Learning ◽  
Quantitative Information ◽  
Mapping Method ◽  
Terminal Point ◽  
Small Data ◽  
Imaging Data ◽  
Biophysical Parameters ◽  
Biological Images ◽  
Complex Shapes

AbstractWith the ever-increasing quality and quantity of imaging data in biomedical research comes the demand for computational methodologies that enable efficient and reliable automated extraction of the quantitative information contained within these images. One of the challenges in providing such methodology is the need for tailoring algorithms to the specifics of the data, limiting their areas of application. Here we present a broadly applicable approach to quantification and classification of complex shapes and patterns in biological or other multi-component formations. This approach integrates the mapping of all shape boundaries within an image onto a global information-rich graph and machine learning on the multidimensional measures of the graph. We demonstrated the power of this method by (1) extracting subtle structural differences from visually indistinguishable images in our phenotype rescue experiments using the endothelial tube formations assay, (2) training the algorithm to identify biophysical parameters underlying the formation of different multicellular networks in our simulation model of collective cell behavior, and (3) analyzing the response of U2OS cell cultures to a broad array of small molecule perturbations.Author SummaryIn this paper, we present a methodology that is based on mapping an arbitrary set of outlines onto a complete, strictly defined structure, in which every point representing the shape becomes a terminal point of a global graph. Because this mapping preserves the whole complexity of the shape, it allows for extracting the full scope of geometric features of any scale. Importantly, an extensive set of graph-based metrics in each image makes integration with machine learning routines highly efficient even for a small data sets and provide an opportunity to backtrack the subtle morphological features responsible for the automated distinction into image classes. The resulting tool provides efficient, versatile, and robust quantification of complex shapes and patterns in experimental images.

scholarly journals Optimizing automatic morphological classification of galaxies with machine learning and deep learning using Dark Energy Survey imaging

2020 ◽  
Vol 493 (3) ◽  
pp. 4209-4228 ◽  
Author(s):  
Ting-Yun Cheng ◽  
Christopher J Conselice ◽  
Alfonso Aragón-Salamanca ◽  
Nan Li ◽  
Asa F L Bluck ◽  
...  
Keyword(s):  
Machine Learning ◽  
Imaging Data ◽  
Morphological Classification ◽  
Learning Methods ◽  
Visual Classification ◽  
Machine Learning Methods ◽  
Dark Energy Survey ◽  
Galaxy Classification ◽  
Energy Survey

ABSTRACT There are several supervised machine learning methods used for the application of automated morphological classification of galaxies; however, there has not yet been a clear comparison of these different methods using imaging data, or an investigation for maximizing their effectiveness. We carry out a comparison between several common machine learning methods for galaxy classification [Convolutional Neural Network (CNN), K-nearest neighbour, logistic regression, Support Vector Machine, Random Forest, and Neural Networks] by using Dark Energy Survey (DES) data combined with visual classifications from the Galaxy Zoo 1 project (GZ1). Our goal is to determine the optimal machine learning methods when using imaging data for galaxy classification. We show that CNN is the most successful method of these ten methods in our study. Using a sample of ∼2800 galaxies with visual classification from GZ1, we reach an accuracy of ∼0.99 for the morphological classification of ellipticals and spirals. The further investigation of the galaxies that have a different ML and visual classification but with high predicted probabilities in our CNN usually reveals the incorrect classification provided by GZ1. We further find the galaxies having a low probability of being either spirals or ellipticals are visually lenticulars (S0), demonstrating that supervised learning is able to rediscover that this class of galaxy is distinct from both ellipticals and spirals. We confirm that ∼2.5 per cent galaxies are misclassified by GZ1 in our study. After correcting these galaxies’ labels, we improve our CNN performance to an average accuracy of over 0.99 (accuracy of 0.994 is our best result).

scholarly journals Shape-to-graph mapping method for efficient characterization and classification of complex geometries in biological images

2020 ◽  
Vol 16 (9) ◽  
pp. e1007758
Author(s):  
William Pilcher ◽  
Xingyu Yang ◽  
Anastasia Zhurikhina ◽  
Olga Chernaya ◽  
Yinghan Xu ◽  
...  
Keyword(s):  
Mapping Method ◽  
Complex Geometries ◽  
Biological Images ◽  
Graph Mapping

scholarly journals Machine Classification of Transient Images

2014 ◽  
Vol 10 (S306) ◽  
pp. 288-291
Author(s):  
Lise du Buisson ◽  
Navin Sivanandam ◽  
Bruce A. Bassett ◽  
Mathew Smith
Keyword(s):  
Machine Learning ◽  
Naive Bayes ◽  
Machine Learning Techniques ◽  
Imaging Data ◽  
Transient Detection ◽  
Minimum Error ◽  
Learning Techniques ◽  
Nearest Neighbours ◽  
Transient Imaging

AbstractUsing transient imaging data from the 2nd and 3rd years of the SDSS supernova survey, we apply various machine learning techniques to the problem of classifying transients (e.g. SNe) from artefacts, one of the first steps in any transient detection pipeline, and one that is often still carried out by human scanners. Using features mostly obtained from PCA, we show that we can match human levels of classification success, and find that a K-nearest neighbours algorithm and SkyNet perform best, while the Naive Bayes, SVM and minimum error classifier have performances varying from slightly to significantly worse.

A Brief Survey on Text Classification Using Various Machine Learning Techniques

2018 ◽  
Vol 8 (1) ◽  
pp. 14
Author(s):  
Padmavathi .S ◽  
M. Chidambaram
Keyword(s):  
Machine Learning ◽  
Text Classification ◽  
Fixed Number ◽  
Machine Learning Techniques ◽  
Online Information ◽  
Rule Based ◽  
Learning Techniques ◽  
Machine Learning Approach ◽  
Rule Based Approach

Text classification has grown into more significant in managing and organizing the text data due to tremendous growth of online information. It does classification of documents in to fixed number of predefined categories. Rule based approach and Machine learning approach are the two ways of text classification. In rule based approach, classification of documents is done based on manually defined rules. In Machine learning based approach, classification rules or classifier are defined automatically using example documents. It has higher recall and quick process. This paper shows an investigation on text classification utilizing different machine learning techniques.

Classification of Observations through Combination of the Dimension Reduction and the Cluster Analysis

2017 ◽  
Vol 7 (8) ◽  
pp. 30
Author(s):  
Hyeuk Kim
Keyword(s):  
Machine Learning ◽  
Principal Component Analysis ◽  
Cluster Analysis ◽  
Unsupervised Learning ◽  
Principal Component ◽  
Component Analysis ◽  
Baseball Players ◽  
Partitioning Around Medoids ◽  
Different Characteristics

Unsupervised learning in machine learning divides data into several groups. The observations in the same group have similar characteristics and the observations in the different groups have the different characteristics. In the paper, we classify data by partitioning around medoids which have some advantages over the k-means clustering. We apply it to baseball players in Korea Baseball League. We also apply the principal component analysis to data and draw the graph using two components for axis. We interpret the meaning of the clustering graphically through the procedure. The combination of the partitioning around medoids and the principal component analysis can be used to any other data and the approach makes us to figure out the characteristics easily.

Learning and control

2018 ◽  
Author(s):  
Ivan Herreros
Keyword(s):  
Machine Learning ◽  
Reinforcement Learning ◽  
Brain Function ◽  
Control Strategies ◽  
Learning Problems ◽  
Animal Learning ◽  
Feed Forward Control ◽  
Machine Learning Applications ◽  
And Control

This chapter discusses basic concepts from control theory and machine learning to facilitate a formal understanding of animal learning and motor control. It first distinguishes between feedback and feed-forward control strategies, and later introduces the classification of machine learning applications into supervised, unsupervised, and reinforcement learning problems. Next, it links these concepts with their counterparts in the domain of the psychology of animal learning, highlighting the analogies between supervised learning and classical conditioning, reinforcement learning and operant conditioning, and between unsupervised and perceptual learning. Additionally, it interprets innate and acquired actions from the standpoint of feedback vs anticipatory and adaptive control. Finally, it argues how this framework of translating knowledge between formal and biological disciplines can serve us to not only structure and advance our understanding of brain function but also enrich engineering solutions at the level of robot learning and control with insights coming from biology.

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