scholarly journals A fully automated deep learning pipeline for high-throughput colony segmentation and classification

2019 ◽  
Author(s):  
Sarah H. Carl ◽  
Lea Duempelmann ◽  
Yukiko Shimada ◽  
Marc Bühler
Keyword(s):  
Neural Networks ◽  
Statistical Power ◽  
Training Data ◽  
Large Numbers ◽  
Manual Counting ◽  
Epigenetic Events ◽  
Colony Color ◽  
Automated Pipeline ◽  
Screening Assays ◽  
Experienced Researcher

AbstractBackgroundAdenine auxotrophy is a commonly used non-selective genetic marker in yeast research. It allows investigators to easily visualize and quantify various genetic and epigenetic events by simply reading out colony color. However, manual counting of large numbers of colonies is extremely time-consuming, difficult to reproduce and possibly inaccurate.ResultsUsing cutting-edge neural networks, we have developed a fully automated pipeline for colony segmentation and classification, which speeds up white/red colony quantification 100-fold over manual counting by an experienced researcher.ConclusionsOur approach uses readily available training data and can be smoothly integrated into existing protocols, vastly speeding up screening assays and increasing the statistical power of experiments that employ adenine auxotrophy.

scholarly journals A fully automated deep learning pipeline for high-throughput colony segmentation and classification

Biology Open ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. bio052936
Author(s):  
Sarah H. Carl ◽  
Lea Duempelmann ◽  
Yukiko Shimada ◽  
Marc Bühler
Keyword(s):  
Neural Networks ◽  
Statistical Power ◽  
Training Data ◽  
Large Numbers ◽  
Manual Counting ◽  
Epigenetic Events ◽  
Colony Color ◽  
Automated Pipeline ◽  
Screening Assays ◽  
Experienced Researcher

ABSTRACTAdenine auxotrophy is a commonly used non-selective genetic marker in yeast research. It allows investigators to easily visualize and quantify various genetic and epigenetic events by simply reading out colony color. However, manual counting of large numbers of colonies is extremely time-consuming, difficult to reproduce and possibly inaccurate. Using cutting-edge neural networks, we have developed a fully automated pipeline for colony segmentation and classification, which speeds up white/red colony quantification 100-fold over manual counting by an experienced researcher. Our approach uses readily available training data and can be smoothly integrated into existing protocols, vastly speeding up screening assays and increasing the statistical power of experiments that employ adenine auxotrophy.

scholarly journals Automated Classification of Bacterial Cell Sub-Populations with Convolutional Neural Networks

2020 ◽  
Author(s):  
Denis Tamiev ◽  
Paige Furman ◽  
Nigel Reuel
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Bacterial Cell ◽  
Complete Solution ◽  
Training Data ◽  
Bacterial Cells ◽  
Automated Classification ◽  
The Neural Network ◽  
Manual Counting

AbstractQuantification of phenotypic heterogeneity present amongst bacterial cells can be a challenging task. Conventionally, classification and counting of bacteria sub-populations is achieved with manual microscopy, due to the lack of alternative, high-throughput, autonomous approaches. In this work, we apply classification-type convolutional neural networks (cCNN) to classify and enumerate bacterial cell sub-populations (B. subtilis clusters). Here, we demonstrate that the accuracy of the cCNN developed in this study can be as high as 86% when trained on a relatively small dataset (81 images). We also developed a new image preprocessing algorithm, specific to fluorescent microscope images, which increases the amount of training data available for the neural network by 72 times. By summing the classified cells together, the algorithm provides a total cell count which is on parity with manual counting, but is 10.2 times more consistent and 3.8 times faster. Finally, this work presents a complete solution framework for those wishing to learn and implement cCNN in their synthetic biology work.

scholarly journals Plating and imaging of yeast colonies for segmentation and classification with neural networks

2019 ◽  
Author(s):  
Marc Bühler ◽  
Lea Dümpelmann ◽  
Sarah Carl
Keyword(s):  
Neural Networks ◽  
High Accuracy ◽  
Research Community ◽  
Epigenetic Mechanisms ◽  
Reporter Assay ◽  
Standardized Protocol ◽  
Colony Color ◽  
Automated Pipeline ◽  
Manual Classification ◽  
Imaging Conditions

Abstract The yeast research community commonly makes use of a simple and powerful color reporter assay, based on adenine auxotrophy, to study genetic and epigenetic mechanisms. Manual classification and quantification of colony color in high numbers is tedious, immensely time consuming, can be erroneous and irreproducible. To overcome these problems, we have established an automated pipeline to quantify and classify yeast colonies from images of entire plates with high accuracy (98.6%). Having the same plating and imaging conditions as used for training of the network is key to this high accuracy. Here we provide a standardized protocol for plating of yeast and imaging within 5-7 days, compatible with the classification pipeline described in Carl et al (bioRxiv; doi: https://doi.org/10.1101/801845).

Operational Determination of the Activated Sludge Process Using Neural Networks

1992 ◽  
Vol 26 (9-11) ◽  
pp. 2461-2464 ◽  
Author(s):  
R. D. Tyagi ◽  
Y. G. Du
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Steady State ◽  
Activated Sludge ◽  
Feedforward Neural Network ◽  
Training Data ◽  
Activated Sludge Process

A steady-statemathematical model of an activated sludgeprocess with a secondary settler was developed. With a limited number of training data samples obtained from the simulation at steady state, a feedforward neural network was established which exhibits an excellent capability for the operational prediction and determination.

scholarly journals U-Infuse: Democratization of Customizable Deep Learning for Object Detection

Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2611
Author(s):  
Andrew Shepley ◽  
Greg Falzon ◽  
Christopher Lawson ◽  
Paul Meek ◽  
Paul Kwan
Keyword(s):  
Deep Learning ◽  
Intellectual Property ◽  
Object Detection ◽  
Image Data ◽  
Learning Technologies ◽  
Training Data ◽  
Learning Models ◽  
Ecological Data ◽  
Single Class ◽  
Large Numbers

Image data is one of the primary sources of ecological data used in biodiversity conservation and management worldwide. However, classifying and interpreting large numbers of images is time and resource expensive, particularly in the context of camera trapping. Deep learning models have been used to achieve this task but are often not suited to specific applications due to their inability to generalise to new environments and inconsistent performance. Models need to be developed for specific species cohorts and environments, but the technical skills required to achieve this are a key barrier to the accessibility of this technology to ecologists. Thus, there is a strong need to democratize access to deep learning technologies by providing an easy-to-use software application allowing non-technical users to train custom object detectors. U-Infuse addresses this issue by providing ecologists with the ability to train customised models using publicly available images and/or their own images without specific technical expertise. Auto-annotation and annotation editing functionalities minimize the constraints of manually annotating and pre-processing large numbers of images. U-Infuse is a free and open-source software solution that supports both multiclass and single class training and object detection, allowing ecologists to access deep learning technologies usually only available to computer scientists, on their own device, customised for their application, without sharing intellectual property or sensitive data. It provides ecological practitioners with the ability to (i) easily achieve object detection within a user-friendly GUI, generating a species distribution report, and other useful statistics, (ii) custom train deep learning models using publicly available and custom training data, (iii) achieve supervised auto-annotation of images for further training, with the benefit of editing annotations to ensure quality datasets. Broad adoption of U-Infuse by ecological practitioners will improve ecological image analysis and processing by allowing significantly more image data to be processed with minimal expenditure of time and resources, particularly for camera trap images. Ease of training and use of transfer learning means domain-specific models can be trained rapidly, and frequently updated without the need for computer science expertise, or data sharing, protecting intellectual property and privacy.

scholarly journals Improving Semi-Supervised Learning for Audio Classification with FixMatch

Electronics ◽  
2021 ◽  
Vol 10 (15) ◽  
pp. 1807
Author(s):  
Sascha Grollmisch ◽  
Estefanía Cano
Keyword(s):  
Neural Networks ◽  
Supervised Learning ◽  
Transfer Learning ◽  
Data Transfer ◽  
State Of The Art ◽  
Training Data ◽  
Audio Classification ◽  
Image Domain ◽  
Full Dataset ◽  
Audio Data

Including unlabeled data in the training process of neural networks using Semi-Supervised Learning (SSL) has shown impressive results in the image domain, where state-of-the-art results were obtained with only a fraction of the labeled data. The commonality between recent SSL methods is that they strongly rely on the augmentation of unannotated data. This is vastly unexplored for audio data. In this work, SSL using the state-of-the-art FixMatch approach is evaluated on three audio classification tasks, including music, industrial sounds, and acoustic scenes. The performance of FixMatch is compared to Convolutional Neural Networks (CNN) trained from scratch, Transfer Learning, and SSL using the Mean Teacher approach. Additionally, a simple yet effective approach for selecting suitable augmentation methods for FixMatch is introduced. FixMatch with the proposed modifications always outperformed Mean Teacher and the CNNs trained from scratch. For the industrial sounds and music datasets, the CNN baseline performance using the full dataset was reached with less than 5% of the initial training data, demonstrating the potential of recent SSL methods for audio data. Transfer Learning outperformed FixMatch only for the most challenging dataset from acoustic scene classification, showing that there is still room for improvement.

scholarly journals Experiments with Neural Networks in the Identification and Control of a Magnetic Levitation System Using a Low-Cost Platform

2021 ◽  
Vol 11 (6) ◽  
pp. 2535
Author(s):  
Bruno E. Silva ◽  
Ramiro S. Barbosa
Keyword(s):  
Neural Networks ◽  
Neural Control ◽  
Magnetic Levitation ◽  
Low Cost ◽  
Training Data ◽  
Neural Controllers ◽  
Levitation System ◽  
Internal Model Controller ◽  
Magnetic Levitation System ◽  
And Performance

In this article, we designed and implemented neural controllers to control a nonlinear and unstable magnetic levitation system composed of an electromagnet and a magnetic disk. The objective was to evaluate the implementation and performance of neural control algorithms in a low-cost hardware. In a first phase, we designed two classical controllers with the objective to provide the training data for the neural controllers. After, we identified several neural models of the levitation system using Nonlinear AutoRegressive eXogenous (NARX)-type neural networks that were used to emulate the forward dynamics of the system. Finally, we designed and implemented three neural control structures: the inverse controller, the internal model controller, and the model reference controller for the control of the levitation system. The neural controllers were tested on a low-cost Arduino control platform through MATLAB/Simulink. The experimental results proved the good performance of the neural controllers.

scholarly journals Autonomous flight cycles and extreme landings of airliners beyond the current limits and capabilities using artificial neural networks

2021 ◽  
Author(s):  
Haitham Baomar ◽  
Peter J. Bentley
Keyword(s):  
Neural Networks ◽  
Artificial Neural Networks ◽  
Weather Conditions ◽  
Extreme Weather ◽  
Training Data ◽  
Aviation Industry ◽  
Control Models ◽  
Novel Approach ◽  
Network Modules ◽  
Artificial Neural

AbstractWe describe the Intelligent Autopilot System (IAS), a fully autonomous autopilot capable of piloting large jets such as airliners by learning from experienced human pilots using Artificial Neural Networks. The IAS is capable of autonomously executing the required piloting tasks and handling the different flight phases to fly an aircraft from one airport to another including takeoff, climb, cruise, navigate, descent, approach, and land in simulation. In addition, the IAS is capable of autonomously landing large jets in the presence of extreme weather conditions including severe crosswind, gust, wind shear, and turbulence. The IAS is a potential solution to the limitations and robustness problems of modern autopilots such as the inability to execute complete flights, the inability to handle extreme weather conditions especially during approach and landing where the aircraft’s speed is relatively low, and the uncertainty factor is high, and the pilots shortage problem compared to the increasing aircraft demand. In this paper, we present the work done by collaborating with the aviation industry to provide training data for the IAS to learn from. The training data is used by Artificial Neural Networks to generate control models automatically. The control models imitate the skills of the human pilot when executing all the piloting tasks required to pilot an aircraft between two airports. In addition, we introduce new ANNs trained to control the aircraft’s elevators, elevators’ trim, throttle, flaps, and new ailerons and rudder ANNs to counter the effects of extreme weather conditions and land safely. Experiments show that small datasets containing single demonstrations are sufficient to train the IAS and achieve excellent performance by using clearly separable and traceable neural network modules which eliminate the black-box problem of large Artificial Intelligence methods such as Deep Learning. In addition, experiments show that the IAS can handle landing in extreme weather conditions beyond the capabilities of modern autopilots and even experienced human pilots. The proposed IAS is a novel approach towards achieving full control autonomy of large jets using ANN models that match the skills and abilities of experienced human pilots and beyond.

scholarly journals Localization of Scattering Objects Using Neural Networks

Sensors ◽  
2020 ◽  
Vol 21 (1) ◽  
pp. 11
Author(s):  
Domonkos Haffner ◽  
Ferenc Izsák
Keyword(s):  
Neural Networks ◽  
Plane Waves ◽  
Measurement Data ◽  
Scattered Wave ◽  
Training Data ◽  
Data Set ◽  
Main Compound ◽  
Incident Plane ◽  
The Neural Networks ◽  
Simulation Package

The localization of multiple scattering objects is performed while using scattered waves. An up-to-date approach: neural networks are used to estimate the corresponding locations. In the scattering phenomenon under investigation, we assume known incident plane waves, fully reflecting balls with known diameters and measurement data of the scattered wave on one fixed segment. The training data are constructed while using the simulation package μ-diff in Matlab. The structure of the neural networks, which are widely used for similar purposes, is further developed. A complex locally connected layer is the main compound of the proposed setup. With this and an appropriate preprocessing of the training data set, the number of parameters can be kept at a relatively low level. As a result, using a relatively large training data set, the unknown locations of the objects can be estimated effectively.

scholarly journals Estimation of electrical resistivity using artificial neural networks: a case study from Lublin Basin, SE Poland

2021 ◽  
Author(s):  
Jakub Ważny ◽  
Michał Stefaniuk ◽  
Adam Cygal
Keyword(s):  
Neural Networks ◽  
Artificial Neural Networks ◽  
Training Data ◽  
Multilayer Perceptrons ◽  
Borehole Data ◽  
Geological Interpretation ◽  
Se Poland ◽  
Geological Conditions ◽  
Artificial Neural ◽  
Reliable Solution

AbstractArtificial neural networks method (ANNs) is a common estimation tool used for geophysical applications. Considering borehole data, when the need arises to supplement a missing well log interval or whole logging—ANNs provide a reliable solution. Supervised training of the network on a reliable set of borehole data values with further application of this network on unknown wells allows creation of synthetic values of missing geophysical parameters, e.g., resistivity. The main assumptions for boreholes are: representation of similar geological conditions and the use of similar techniques of well data collection. In the analyzed case, a set of Multilayer Perceptrons were trained on five separate chronostratigraphic intervals of borehole, considered as training data. The task was to predict missing deep laterolog (LLD) logging in a borehole representing the same sequence of layers within the Lublin Basin area. Correlation between well logs data exceeded 0.8. Subsequently, magnetotelluric parametric soundings were modeled and inverted on both boreholes. Analysis showed that congenial Occam 1D models had better fitting of TM mode of MT data in each case. Ipso facto, synthetic LLD log could be considered as a basis for geophysical and geological interpretation. ANNs provided solution for supplementing datasets based on this analytical approach.

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