scholarly journals Zebrafish Larvae Phenotype Classification from Bright-field Microscopic Images Using a Two-Tier Deep-Learning Pipeline

2020 ◽  
Vol 10 (4) ◽  
pp. 1247 ◽  
Author(s):  
Shang Shang ◽  
Sijie Lin ◽  
Fengyu Cong
Keyword(s):  
Deep Learning ◽  
Environmental Influence ◽  
Training Data ◽  
Convolutional Network ◽  
Training Images ◽  
Zebrafish Larvae ◽  
Machine Learning Methods ◽  
Phenotype Classification ◽  
Convolution Kernels

Classification of different zebrafish larvae phenotypes is useful for studying the environmental influence on embryo development. However, the scarcity of well-annotated training images and fuzzy inter-phenotype differences hamper the application of machine-learning methods in phenotype classification. This study develops a deep-learning approach to address these challenging problems. A convolutional network model with compressed separable convolution kernels is adopted to address the overfitting issue caused by insufficient training data. A two-tier classification pipeline is designed to improve the classification accuracy based on fuzzy phenotype features. Our method achieved an averaged accuracy of 91% for all the phenotypes and maximum accuracy of 100% for some phenotypes (e.g., dead and chorion). We also compared our method with the state-of-the-art methods based on the same dataset. Our method obtained dramatic accuracy improvement up to 22% against the existing method. This study offers an effective deep-learning solution for classifying difficult zebrafish larvae phenotypes based on very limited training data.

scholarly journals Leaf Segmentation and Classification with a Complicated Background Using Deep Learning

Agronomy ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1721 ◽  
Author(s):  
Kunlong Yang ◽  
Weizhen Zhong ◽  
Fengguo Li
Keyword(s):  
Deep Learning ◽  
Misclassification Error ◽  
Training Set ◽  
Convolutional Network ◽  
Training Images ◽  
Average Accuracy ◽  
Phenotype Analysis ◽  
Leaf Segmentation ◽  
Leaf Image

The segmentation and classification of leaves in plant images are a great challenge, especially when several leaves are overlapping in images with a complicated background. In this paper, the segmentation and classification of leaf images with a complicated background using deep learning are studied. First, more than 2500 leaf images with a complicated background are collected and artificially labeled with target pixels and background pixels. Two-thousand of them are fed into a Mask Region-based Convolutional Neural Network (Mask R-CNN) to train a model for leaf segmentation. Then, a training set that contains more than 1500 training images of 15 species is fed into a very deep convolutional network with 16 layers (VGG16) to train a model for leaf classification. The best hyperparameters for these methods are found by comparing a variety of parameter combinations. The results show that the average Misclassification Error (ME) of 80 test images using Mask R-CNN is 1.15%. The average accuracy value for the leaf classification of 150 test images using VGG16 is up to 91.5%. This indicates that these methods can be used to segment and classify the leaf image with a complicated background effectively. It could provide a reference for the phenotype analysis and automatic classification of plants.

Deep Learning based Tomato’s Ripe and Unripe Classification System

2022 ◽  
Vol 10 (1) ◽  
pp. 0-0
Keyword(s):  
Deep Learning ◽  
Classification Accuracy ◽  
Ccd Camera ◽  
Agricultural Products ◽  
Training Data ◽  
Maturity Level ◽  
Agriculture Sector ◽  
The Past ◽  
State Of Art

Effective productivity estimates of fresh produced crops are very essential for efficient farming, commercial planning, and logistical support. In the past ten years, machine learning (ML) algorithms have been widely used for grading and classification of agricultural products in agriculture sector. However, the precise and accurate assessment of the maturity level of tomatoes using ML algorithms is still a quite challenging to achieve due to these algorithms being reliant on hand crafted features. Hence, in this paper we propose a deep learning based tomato maturity grading system that helps to increase the accuracy and adaptability of maturity grading tasks with less amount of training data. The performance of proposed system is assessed on the real tomato datasets collected from the open fields using Nikon D3500 CCD camera. The proposed approach achieved an average maturity classification accuracy of 99.8 % which seems to be quite promising in comparison to the other state of art methods.

scholarly journals TADA: phylogenetic augmentation of microbiome samples enhances phenotype classification

2019 ◽  
Vol 35 (14) ◽  
pp. i31-i40 ◽  
Author(s):  
Erfan Sayyari ◽  
Ban Kawas ◽  
Siavash Mirarab
Keyword(s):  
Machine Learning ◽  
Sample Size ◽  
Data Augmentation ◽  
Training Data ◽  
Supplementary Information ◽  
High Dimensional ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Phenotype Classification ◽  
Microbiome Data

Abstract Motivation Learning associations of traits with the microbial composition of a set of samples is a fundamental goal in microbiome studies. Recently, machine learning methods have been explored for this goal, with some promise. However, in comparison to other fields, microbiome data are high-dimensional and not abundant; leading to a high-dimensional low-sample-size under-determined system. Moreover, microbiome data are often unbalanced and biased. Given such training data, machine learning methods often fail to perform a classification task with sufficient accuracy. Lack of signal is especially problematic when classes are represented in an unbalanced way in the training data; with some classes under-represented. The presence of inter-correlations among subsets of observations further compounds these issues. As a result, machine learning methods have had only limited success in predicting many traits from microbiome. Data augmentation consists of building synthetic samples and adding them to the training data and is a technique that has proved helpful for many machine learning tasks. Results In this paper, we propose a new data augmentation technique for classifying phenotypes based on the microbiome. Our algorithm, called TADA, uses available data and a statistical generative model to create new samples augmenting existing ones, addressing issues of low-sample-size. In generating new samples, TADA takes into account phylogenetic relationships between microbial species. On two real datasets, we show that adding these synthetic samples to the training set improves the accuracy of downstream classification, especially when the training data have an unbalanced representation of classes. Availability and implementation TADA is available at https://github.com/tada-alg/TADA. Supplementary information Supplementary data are available at Bioinformatics online.

Qualitative classification of waste textiles based on near infrared spectroscopy and the convolutional network

2019 ◽  
Vol 90 (9-10) ◽  
pp. 1057-1066 ◽  
Author(s):  
Zhengdong Liu ◽  
Wenxia Li ◽  
Zihan Wei
Keyword(s):  
Deep Learning ◽  
Infrared Spectroscopy ◽  
Near Infrared Spectroscopy ◽  
Near Infrared ◽  
Convolutional Network ◽  
The Sustainable Development ◽  
Softmax Classifier ◽  
Qualitative Classification ◽  
Reliable Classification

The recycling of waste textiles has become a growth point for the sustainable development of the textile and clothing industry. In addition, sorting is a key link in the follow-up recycling process. Since different fabrics are required to be processed by different technologies, manual sorting not only takes time and effort but also cannot achieve accurate and reliable classification. Based on the analysis of near infrared spectroscopy, the theory and methods of deep learning are used for the qualitative classification of waste textiles in order to complete the automatic fabric composition recognition in the sorting process. Firstly, a standard sample set is established by waveform clipping and normalization, and a Textile Recycling Net deep web suitable for near infrared spectroscopy is established. Then, a pixilated layer is used to facilitate the deep learning of features, and the multidimensional features of the spectrum are extracted by using the multi-layer convolutional and pooling layers. Finally, the softmax classifier is adopted to complete the qualitative classification. Experimental results show that the convolutional network classification method using normalized and pixelated near infrared spectroscopy can realize the automatic classification of several common textiles, such as cotton and polyester, and effectively improve the detection level and speed of fabric components.

scholarly journals Investigasi Pengaruh Skema Stride dan Step Training untuk Deteksi Jari Pada Region-based Fully Convolutional Network (R-FCN) dalam Teknologi Augmented Reality

2021 ◽  
Vol 12 (2) ◽  
pp. 138
Author(s):  
Hashfi Fadhillah ◽  
Suryo Adhi Wibowo ◽  
Rita Purnamasari
Keyword(s):  
Deep Learning ◽  
Augmented Reality ◽  
Virtual World ◽  
Training Data ◽  
Convolutional Network ◽  
Fully Convolutional Network ◽  
Connected Network ◽  
Learning Region ◽  
Centroid Point ◽  
Fully Connected

Abstract  Combining the real world with the virtual world and then modeling it in 3D is an effort carried on Augmented Reality (AR) technology. Using fingers for computer operations on multi-devices makes the system more interactive. Marker-based AR is one type of AR that uses markers in its detection. This study designed the AR system by detecting fingertips as markers. This system is designed using the Region-based Deep Fully Convolutional Network (R-FCN) deep learning method. This method develops detection results obtained from the Fully Connected Network (FCN). Detection results will be integrated with a computer pointer for basic operations. This study uses a predetermined step scheme to get the best IoU parameters, precision and accuracy. The scheme in this study uses a step scheme, namely: 25K, 50K and 75K step. High precision creates centroid point changes that are not too far away. High accuracy can improve AR performance under conditions of rapid movement and improper finger conditions. The system design uses a dataset in the form of an index finger image with a configuration of 10,800 training data and 3,600 test data. The model will be tested on each scheme using video at different distances, locations and times. This study produced the best results on the 25K step scheme with IoU of 69%, precision of 5.56 and accuracy of 96%.Keyword: Augmented Reality, Region-based Convolutional Network, Fully Convolutional Network, Pointer, Step training Abstrak Menggabungkan dunia nyata dengan dunia virtual lalu memodelkannya bentuk 3D merupakan upaya yang diusung pada teknologi Augmented Reality (AR). Menggunakan jari untuk operasi komputer pada multi-device membuat sistem yang lebih interaktif. Marker-based AR merupakan salah satu jenis AR yang menggunakan marker dalam deteksinya. Penelitian ini merancang sistem AR dengan mendeteksi ujung jari sebagai marker. Sistem ini dirancang menggunakan metode deep learning Region-based Fully Convolutional Network (R-FCN). Metode ini mengembangkan hasil deteksi yang didapat dari Fully Connected Network (FCN). Hasil deteksi akan diintegrasikan dengan pointer komputer untuk operasi dasar. Penelitian ini menggunakan skema step training yang telah ditentukan untuk mendapatkan parameter IoU, presisi dan akurasi yang terbaik. Skema pada penelitian ini menggunakan skema step yaitu: 25K, 50K dan 75K step. Presisi tinggi menciptakan perubahan titik centroid yang tidak terlalu jauh. Akurasi  yang tinggi dapat meningkatkan kinerja AR dalam kondisi pergerakan yang cepat dan kondisi jari yang tidak tepat. Perancangan sistem menggunakan dataset berupa citra jari telunjuk dengan konfigurasi 10.800 data latih dan 3.600 data uji. Model akan diuji pada tiap skema dilakukan menggunakan video pada jarak, lokasi dan waktu yang berbeda. Penelitian ini menghasilkan hasil terbaik pada skema step 25K dengan IoU sebesar 69%, presisi sebesar 5,56 dan akurasi sebesar 96%.Kata kunci: Augmented Reality, Region-based Convolutional Network, Fully Convolutional Network, Pointer, Step training 

scholarly journals A DEEP LEARNING BASED SURROGATE MODEL FOR ESTIMATING THE FLUX AND POWER DISTRIBUTION SOLVED BY DIFFUSION EQUATION

2021 ◽  
Vol 247 ◽  
pp. 03013
Author(s):  
Qian Zhang ◽  
Jinchao Zhang ◽  
Liang Liang ◽  
Zhuo Li ◽  
Tengfei Zhang
Keyword(s):  
Deep Learning ◽  
Diffusion Equation ◽  
Power Distribution ◽  
Surrogate Model ◽  
High Efficiency ◽  
Reactor Core ◽  
Training Data ◽  
Diffusion Method ◽  
Convolutional Network ◽  
Learning Platform

A deep learning based surrogate model is proposed for replacing the conventional diffusion equation solver and predicting the flux and power distribution of the reactor core. Using the training data generated by the conventional diffusion equation solver, a special designed convolutional neural network inspired by the FCN (Fully Convolutional Network) is trained under the deep learning platform TensorFlow. Numerical results show that the deep learning based surrogate model is effective for estimating the flux and power distribution calculated by the diffusion method, which means it can be used for replacing the conventional diffusion equation solver with high efficiency boost.

scholarly journals HistoFlow: Label-Efficient and Interactive Deep Learning Cell Analysis

2020 ◽  
Author(s):  
Tim Henning ◽  
Benjamin Bergner ◽  
Christoph Lippert
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
User Interface ◽  
Network Architecture ◽  
Training Data ◽  
Cell Segmentation ◽  
Annotation Tool ◽  
Cell Analysis ◽  
Instance Segmentation

Instance segmentation is a common task in quantitative cell analysis. While there are many approaches doing this using machine learning, typically, the training process requires a large amount of manually annotated data. We present HistoFlow, a software for annotation-efficient training of deep learning models for cell segmentation and analysis with an interactive user interface.It provides an assisted annotation tool to quickly draw and correct cell boundaries and use biomarkers as weak annotations. It also enables the user to create artificial training data to lower the labeling effort. We employ a universal U-Net neural network architecture that allows accurate instance segmentation and the classification of phenotypes in only a single pass of the network. Transfer learning is available through the user interface to adapt trained models to new tissue types.We demonstrate HistoFlow for fluorescence breast cancer images. The models trained using only artificial data perform comparably to those trained with time-consuming manual annotations. They outperform traditional cell segmentation algorithms and match state-of-the-art machine learning approaches. A user test shows that cells can be annotated six times faster than without the assistance of our annotation tool. Extending a segmentation model for classification of epithelial cells can be done using only 50 to 1500 annotations.Our results show that, unlike previous assumptions, it is possible to interactively train a deep learning model in a matter of minutes without many manual annotations.

scholarly journals AN APPLICATION OF SEGNET FOR DETECTING LANDSLIDE AREAS BY USING FULLY POLARIMETRIC SAR DATA

2019 ◽  
Vol 13 (2) ◽  
pp. 215
Author(s):  
I Made Oka Guna Antara ◽  
Norikazu Shimizu ◽  
Takahiro Osawa ◽  
I Wayan Nuarsa
Keyword(s):  
Deep Learning ◽  
Learning Process ◽  
Training Data ◽  
Memory Usage ◽  
Polarimetric Sar ◽  
Training Images ◽  
Sar Data ◽  
Color Composite

The study location of landslide is in Hokkaido, Japan which occurred due to the Iburi Earthquake 2018. In this study the landslide has been estimated by the fully Polarimetric SAR (Pol-SAR) technique based on ALOS-2 PALSAR-2 data using the Yamaguchi’s decomposition. The Yamaguchi's decomposition is proposed by Yoshio Yamaguchi et.al. The data has been analyzed using the deep learning process with SegNet architecture with color composite. In this research, the performance of SegNet is fast and efficient in memory usage. However, the result is not good, based on the Intersection over Union (IoU) evaluation obtained the lowest value is 0.0515 and the highest value is 0.1483. That is because of difficulty to make training datasets and of a small number of datasets. The greater difference between accuracy and loss graph along with higher epochs represents overfitting. The overfitting can be caused by the limited amount of training data and failure of the network to generalize the feature set over the training images.

Sign in / Sign up

Export Citation Format

Share Document