Towards Deep Learning Approaches for Quantitative Analysis of High-Throughput DLD

2021 ◽  
Author(s):  
Eric Gioe ◽  
Xiaolin Chen ◽  
Jong-Hoon Kim
Keyword(s):  
Deep Learning ◽  
Quantitative Analysis ◽  
High Throughput ◽  
Learning Approaches

scholarly journals PARROT is a flexible recurrent neural network framework for analysis of large protein datasets

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Daniel Griffith ◽  
Alex S Holehouse
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Deep Learning ◽  
High Throughput ◽  
Recurrent Neural Network ◽  
Transcriptional Activation ◽  
Network Architecture ◽  
Learning Approaches ◽  
Large Protein ◽  
Protein Datasets

The rise of high-throughput experiments has transformed how scientists approach biological questions. The ubiquity of large-scale assays that can test thousands of samples in a day has necessitated the development of new computational approaches to interpret this data. Among these tools, machine learning approaches are increasingly being utilized due to their ability to infer complex nonlinear patterns from high-dimensional data. Despite their effectiveness, machine learning (and in particular deep learning) approaches are not always accessible or easy to implement for those with limited computational expertise. Here we present PARROT, a general framework for training and applying deep learning-based predictors on large protein datasets. Using an internal recurrent neural network architecture, PARROT is capable of tackling both classification and regression tasks while only requiring raw protein sequences as input. We showcase the potential uses of PARROT on three diverse machine learning tasks: predicting phosphorylation sites, predicting transcriptional activation function of peptides generated by high-throughput reporter assays, and predicting the fibrillization propensity of amyloid beta with data generated by deep mutational scanning. Through these examples, we demonstrate that PARROT is easy to use, performs comparably to state-of-the-art computational tools, and is applicable for a wide array of biological problems.

scholarly journals Outdoor Plant Segmentation With Deep Learning for High-Throughput Field Phenotyping on a Diverse Wheat Dataset

2022 ◽  
Vol 12 ◽  
Author(s):  
Radek Zenkl ◽  
Radu Timofte ◽  
Norbert Kirchgessner ◽  
Lukas Roth ◽  
Andreas Hund ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
High Throughput ◽  
Developmental Stages ◽  
Agricultural Practices ◽  
Support Vector ◽  
Learning Approaches ◽  
Support Vector Classifier ◽  
Wide Range ◽  
Field Phenotyping

Robust and automated segmentation of leaves and other backgrounds is a core prerequisite of most approaches in high-throughput field phenotyping. So far, the possibilities of deep learning approaches for this purpose have not been explored adequately, partly due to a lack of publicly available, appropriate datasets. This study presents a workflow based on DeepLab v3+ and on a diverse annotated dataset of 190 RGB (350 x 350 pixels) images. Images of winter wheat plants of 76 different genotypes and developmental stages have been acquired throughout multiple years at high resolution in outdoor conditions using nadir view, encompassing a wide range of imaging conditions. Inconsistencies of human annotators in complex images have been quantified, and metadata information of camera settings has been included. The proposed approach achieves an intersection over union (IoU) of 0.77 and 0.90 for plants and soil, respectively. This outperforms the benchmarked machine learning methods which use Support Vector Classifier and/or Random Forrest. The results show that a small but carefully chosen and annotated set of images can provide a good basis for a powerful segmentation pipeline. Compared to earlier methods based on machine learning, the proposed method achieves better performance on the selected dataset in spite of using a deep learning approach with limited data. Increasing the amount of publicly available data with high human agreement on annotations and further development of deep neural network architectures will provide high potential for robust field-based plant segmentation in the near future. This, in turn, will be a cornerstone of data-driven improvement in crop breeding and agricultural practices of global benefit.

Towards Deep Learning Approaches for Quantitative Analysis of High-Throughput DLD

2020 ◽  
Author(s):  
Eric A. Gioe ◽  
Xiaolin Chen ◽  
Jong-Hoon Kim
Keyword(s):  
Deep Learning ◽  
High Throughput ◽  
Lateral Displacement ◽  
Great Promise ◽  
Learning Approaches ◽  
Timely Manner ◽  
Particle Detection ◽  
New Techniques ◽  
Deterministic Lateral Displacement ◽  
Total Particle

Abstract Microfluidics has shown great promise for the sorting or separation of biological cells such as circulating tumor cells since the first studies came out a few decades ago. With recent advances in high-throughput microfluidics, analysis of massive amounts of data needs to be completed in an iterative, timely manner. However, the majority of analysis is either performed manually or through the use of superimposing multiple images to define the flow of the particles, taking a significant amount of time to complete. The objective of the work is to increase the efficiency and repeatability of particle detection in a high-throughput deterministic lateral displacement (DLD) device. The program proposed is in the early stages of development, but shows promise. The average time it takes to analyze over a gigabyte of video is 24.21 seconds. The average percent error of the total particle detection was 21.42%. The assumptions made for the initial version of the program affect the accuracy of the particle in wall detection, so new techniques that do not follow the assumptions will need to be investigated. More work will be completed to implement machine learning or deep learning to assist in the development of DLD devices.

Deep learning approaches for quantitative analysis of ultrasound backscattered signals

2019 ◽  
Vol 146 (4) ◽  
pp. 2810-2810
Author(s):  
Aiguo Han ◽  
Andrew S. Boehringer ◽  
Vivian Montes ◽  
Michael P. Andre ◽  
John W. Erdman ◽  
...  
Keyword(s):  
Deep Learning ◽  
Quantitative Analysis ◽  
Learning Approaches ◽  
Backscattered Signals

scholarly journals PARROT: a flexible recurrent neural network framework for analysis of large protein datasets

2021 ◽  
Author(s):  
Daniel Griffith ◽  
Alex S Holehouse
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Deep Learning ◽  
High Throughput ◽  
Recurrent Neural Network ◽  
Transcriptional Activation ◽  
Network Architecture ◽  
Learning Approaches ◽  
Large Protein ◽  
Protein Datasets

The rise of high-throughput experiments has transformed how scientists approach biological questions. The ubiquity of large-scale assays that can test thousands of samples in a day has necessitated the development of new computational approaches to interpret this data. Among these tools, machine learning approaches are increasingly being utilized due to their ability to infer complex non-linear patterns from high-dimensional data. Despite their effectiveness, machine learning (and in particular deep learning) approaches are not always accessible or easy to implement for those with limited computational expertise. Here we present PARROT, a general framework for training and applying deep learning-based predictors on large protein datasets. Using an internal recurrent neural network architecture, PARROT is capable of tackling both classification and regression tasks while only requiring raw protein sequences as input. We showcase the potential uses of PARROT on three diverse machine learning tasks: predicting phosphorylation sites, predicting transcriptional activation function of peptides generated by high-throughput reporter assays, and predicting the fibrillization propensity of amyloid-beta with data generated by deep mutational scanning. Through these examples, we demonstrate that PARROT is easy to use, performs comparably to state-of-the-art computational tools, and is applicable for a wide array of biological problems.

scholarly journals A Quantitative Analysis Platform for PD-L1 Immunohistochemistry based on Point-level Supervision Model

2019 ◽  
Author(s):  
Haibo Mi ◽  
Kele Xu ◽  
Yang Xiang ◽  
Yulin He ◽  
Dawei Feng ◽  
...  
Keyword(s):  
Deep Learning ◽  
Quantitative Analysis ◽  
Medical Image Analysis ◽  
Learning Approaches ◽  
Cell Nuclei ◽  
Object Locations ◽  
Accurate Quantitative Analysis ◽  
Supervision Model ◽  
Analysis Platform ◽  
Point Level

Recently, deep learning has witnessed dramatic progress in the medical image analysis field. In the precise treatment of cancer immunotherapy, the quantitative analysis of PD-L1 immunohistochemistry is of great importance. It is quite common that pathologists manually quantify the cell nuclei. This process is very time-consuming and error-prone. In this paper, we describe the development of a platform for PD-L1 pathological image quantitative analysis using deep learning approaches. As point-level annotations can provide a rough estimate of the object locations and classifications, this platform adopts a point-level supervision model to classify, localize, and count the PD-L1 cells nuclei. Presently, this platform has achieved an accurate quantitative analysis of PD-L1 for two types of carcinoma, and it is deployed in one of the first-class hospitals in China.

scholarly journals Generalising from Conventional Pipelines: A Case Study in Deep Learning-Based for High-Throughput Screening

2021 ◽  
Author(s):  
Beatriz García Santa Cruz ◽  
Jan Sölter ◽  
Gemma Gomez Giro ◽  
Claudia Saraiva ◽  
Sonia Sabaté-Soler ◽  
...  
Keyword(s):  
Computer Vision ◽  
Image Analysis ◽  
Image Segmentation ◽  
Deep Learning ◽  
High Throughput ◽  
High Throughput Screening ◽  
New Technologies ◽  
Learning Approaches ◽  
Noisy Labels

Abstract The study of complex diseases relies on large amounts of data to build models toward precision medicine. Such data acquisition is feasible in the context of high-throughput screening, in which the quality of the results relies on the accuracy of the image analysis. Although state-of-the-art solutions for image segmentation employ deep learning approaches, the high cost of manually generating ground truth labels for model training hampers the day-to-day application in experimental laboratories. Alternatively, traditional computer vision-based solutions do not need expensive labels for their implementation. Our work combines both approaches by training a deep learning network using weak training labels automatically generated with conventional computer vision methods. Our network surpasses the conventional segmentation quality by generalising beyond noisy labels, providing a 25 % increase of mean intersection over union, and simultaneously reducing the development and inference times. Our solution was embedded into an easy-to-use graphical user interface that allows researchers to assess the predictions and correct potential inaccuracies with minimal human input. To demonstrate the feasibility of training a deep learning solution on a large dataset of noisy labels automatically generated by a conventional pipeline, we compared our solution against the common approach of training a model from a small manually curated dataset by several experts. Our work suggests that humans perform better in context interpretation, such as error assessment, while computers outperform in pixel-by-pixel fine segmentation. Such pipelines are illustrated with a case study on image segmentation for autophagy events. This work aims for better translation of new technologies to real-world settings in microscopy-image analysis.

Deep Learning Approaches for Whiteboard Image Quality Enhancement

2019 ◽  
Vol 2019 (1) ◽  
pp. 360-368
Author(s):  
Mekides Assefa Abebe ◽  
Jon Yngve Hardeberg
Keyword(s):  
Deep Learning ◽  
Image Quality ◽  
Image Data ◽  
Quality Enhancement ◽  
Network Architectures ◽  
Learning Approaches ◽  
Data Set ◽  
Image Quality Enhancement ◽  
Processing Techniques ◽  
White Balancing

Different whiteboard image degradations highly reduce the legibility of pen-stroke content as well as the overall quality of the images. Consequently, different researchers addressed the problem through different image enhancement techniques. Most of the state-of-the-art approaches applied common image processing techniques such as background foreground segmentation, text extraction, contrast and color enhancements and white balancing. However, such types of conventional enhancement methods are incapable of recovering severely degraded pen-stroke contents and produce artifacts in the presence of complex pen-stroke illustrations. In order to surmount such problems, the authors have proposed a deep learning based solution. They have contributed a new whiteboard image data set and adopted two deep convolutional neural network architectures for whiteboard image quality enhancement applications. Their different evaluations of the trained models demonstrated their superior performances over the conventional methods.

Convolutional Neural Network of Atomic Surface Structures to Predict Binding Energies for High-Throughput Screening of Catalysts

2019 ◽  
Author(s):  
Seoin Back ◽  
Junwoong Yoon ◽  
Nianhan Tian ◽  
Wen Zhong ◽  
Kevin Tran ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
High Throughput ◽  
High Throughput Screening ◽  
Binding Energies ◽  
Surface Structures ◽  
Voronoi Polyhedra ◽  
Atomic Surface

We present an application of deep-learning convolutional neural network of atomic surface structures using atomic and Voronoi polyhedra-based neighbor information to predict adsorbate binding energies for the application in catalysis.

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