scholarly journals GPTransformer: A Transformer-Based Deep Learning Method for Predicting Fusarium Related Traits in Barley

2021 ◽  
Vol 12 ◽  
Author(s):  
Sheikh Jubair ◽  
James R. Tucker ◽  
Nathan Henderson ◽  
Colin W. Hiebert ◽  
Ana Badea ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Molecular Markers ◽  
Fusarium Head Blight ◽  
High Throughput ◽  
Genomic Prediction ◽  
Prediction Models ◽  
Spring Barley ◽  
Pearson Correlation ◽  
Head Blight

Fusarium head blight (FHB) incited by Fusarium graminearum Schwabe is a devastating disease of barley and other cereal crops worldwide. Fusarium head blight is associated with trichothecene mycotoxins such as deoxynivalenol (DON), which contaminates grains, making them unfit for malting or animal feed industries. While genetically resistant cultivars offer the best economic and environmentally responsible means to mitigate disease, parent lines with adequate resistance are limited in barley. Resistance breeding based upon quantitative genetic gains has been slow to date, due to intensive labor requirements of disease nurseries. The production of a high-throughput genome-wide molecular marker assembly for barley permits use in development of genomic prediction models for traits of economic importance to this crop. A diverse panel consisting of 400 two-row spring barley lines was assembled to focus on Canadian barley breeding programs. The panel was evaluated for FHB and DON content in three environments and over 2 years. Moreover, it was genotyped using an Illumina Infinium High-Throughput Screening (HTS) iSelect custom beadchip array of single nucleotide polymorphic molecular markers (50 K SNP), where over 23 K molecular markers were polymorphic. Genomic prediction has been demonstrated to successfully reduce FHB and DON content in cereals using various statistical models. Herein, we have studied an alternative method based on machine learning and compare it with a statistical approach. The bi-allelic SNPs represented pairs of alleles and were encoded in two ways: as categorical (–1, 0, 1) or using Hardy-Weinberg probability frequencies. This was followed by selecting essential genomic markers for phenotype prediction. Subsequently, a Transformer-based deep learning algorithm was applied to predict FHB and DON. Apart from the Transformer method, a Residual Fully Connected Neural Network (RFCNN) was also applied. Pearson correlation coefficients were calculated to compare true vs. predicted outputs. Models which included all markers generally showed marginal improvement in prediction. Hardy-Weinberg encoding generally improved correlation for FHB (6.9%) and DON (9.6%) for the Transformer network. This study suggests the potential of the Transformer based method as an alternative to the popular BLUP model for genomic prediction of complex traits such as FHB or DON, having performed equally or better than existing machine learning and statistical methods.

scholarly journals Predicting carbon nanotube forest attributes and mechanical properties using simulated images and deep learning

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Taher Hajilounezhad ◽  
Rina Bao ◽  
Kannappan Palaniappan ◽  
Filiz Bunyak ◽  
Prasad Calyam ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Carbon Nanotube ◽  
High Throughput ◽  
Self Assembly ◽  
Mechanical Performance ◽  
Physical Parameters ◽  
Structure Property ◽  
Processing Parameter ◽  
Physics Based Simulation

AbstractUnderstanding and controlling the self-assembly of vertically oriented carbon nanotube (CNT) forests is essential for realizing their potential in myriad applications. The governing process–structure–property mechanisms are poorly understood, and the processing parameter space is far too vast to exhaustively explore experimentally. We overcome these limitations by using a physics-based simulation as a high-throughput virtual laboratory and image-based machine learning to relate CNT forest synthesis attributes to their mechanical performance. Using CNTNet, our image-based deep learning classifier module trained with synthetic imagery, combinations of CNT diameter, density, and population growth rate classes were labeled with an accuracy of >91%. The CNTNet regression module predicted CNT forest stiffness and buckling load properties with a lower root-mean-square error than that of a regression predictor based on CNT physical parameters. These results demonstrate that image-based machine learning trained using only simulated imagery can distinguish subtle CNT forest morphological features to predict physical material properties with high accuracy. CNTNet paves the way to incorporate scanning electron microscope imagery for high-throughput material discovery.

scholarly journals A review of deep learning applications for genomic selection

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Osval Antonio Montesinos-López ◽  
Abelardo Montesinos-López ◽  
Paulino Pérez-Rodríguez ◽  
José Alberto Barrón-López ◽  
Johannes W. R. Martini ◽  
...  
Keyword(s):  
Deep Learning ◽  
Plant Breeding ◽  
Genomic Selection ◽  
Genomic Prediction ◽  
Mixed Model ◽  
Prediction Models ◽  
Genetic Effect ◽  
Training Data ◽  
Additive Genetic Effect ◽  
Main Body

Abstract Background Several conventional genomic Bayesian (or no Bayesian) prediction methods have been proposed including the standard additive genetic effect model for which the variance components are estimated with mixed model equations. In recent years, deep learning (DL) methods have been considered in the context of genomic prediction. The DL methods are nonparametric models providing flexibility to adapt to complicated associations between data and output with the ability to adapt to very complex patterns. Main body We review the applications of deep learning (DL) methods in genomic selection (GS) to obtain a meta-picture of GS performance and highlight how these tools can help solve challenging plant breeding problems. We also provide general guidance for the effective use of DL methods including the fundamentals of DL and the requirements for its appropriate use. We discuss the pros and cons of this technique compared to traditional genomic prediction approaches as well as the current trends in DL applications. Conclusions The main requirement for using DL is the quality and sufficiently large training data. Although, based on current literature GS in plant and animal breeding we did not find clear superiority of DL in terms of prediction power compared to conventional genome based prediction models. Nevertheless, there are clear evidences that DL algorithms capture nonlinear patterns more efficiently than conventional genome based. Deep learning algorithms are able to integrate data from different sources as is usually needed in GS assisted breeding and it shows the ability for improving prediction accuracy for large plant breeding data. It is important to apply DL to large training-testing data sets.

Accuracy of within- and among-family genomic prediction for Fusarium head blight and Septoria tritici blotch in winter wheat

2018 ◽  
Vol 132 (4) ◽  
pp. 1121-1135 ◽  
Author(s):  
Cathérine Pauline Herter ◽  
Erhard Ebmeyer ◽  
Sonja Kollers ◽  
Viktor Korzun ◽  
Tobias Würschum ◽  
...  
Keyword(s):  
Winter Wheat ◽  
Fusarium Head Blight ◽  
Genomic Prediction ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Head Blight

scholarly journals APMFT: Anamoly Prediction Model for Financial Transactions Using Learning Methods in Machine Learning and Deep Learning

2021 ◽  
Author(s):  
R. Priyadarshini ◽  
K. Anuratha ◽  
N. Rajendran ◽  
S. Sujeetha
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Prediction Models ◽  
General Pattern ◽  
High Dimensional ◽  
Learning Methods ◽  
Data Points ◽  
The Times ◽  
Financial Transactions ◽  
Journal Entries

Anamoly is an uncommon and it represents an outlier i.e, a nonconforming case. According to Oxford Dictionary of Mathematics anamoly is defined as an unusal and erroneous observation that usually doesn’t follow the general pattern of drawn population. The process of detecting the anmolies is a process of data mining and it aims at finding the data points or patterns that do not adapt with the actual complete pattern of the data.The study on anamoly behavior and its impact has been done on areas such as Network Security, Finance, Healthcare and Earth Sciences etc. The proper detection and prediction of anamolies are of great importance as these rare observations may carry siginificant information. In today’s finanicial world, the enterprise data is digitized and stored in the cloudand so there is a significant need to detect the anaomalies in financial data which will help the enterprises to deal with the huge amount of auditing The corporate and enterprise is conducting auidts on large number of ledgers and journal entries. The monitoring of those kinds of auidts is performed manually most of the times. There should be proper anamoly detection in the high dimensional data published in the ledger format for auditing purpose. This work aims at analyzing and predicting unusal fraudulent financial transations by emplyoing few Machine Learning and Deep Learning Methods. Even if any of the anamoly like manipulation or tampering of data detected, such anamolies and errors can be identified and marked with proper proof with the help of the machine learning based algorithms. The accuracy of the prediction is increased by 7% by implementing the proposed prediction models.

scholarly journals Application of Bioactivity Profile Based Fingerprints for Building Machine Learning Models

2018 ◽  
Author(s):  
Noé Sturm ◽  
Jiangming Sun ◽  
Yves Vandriessche ◽  
Andreas Mayr ◽  
Günter Klambauer ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
High Throughput ◽  
Scaffold Hopping ◽  
Learning Models ◽  
Industrial Data ◽  
Structural Descriptors ◽  
Bioactivity Profile ◽  
Machine Learning Models

<div>This article describes an application of high-throughput fingerprints (HTSFP) built upon industrial data accumulated over the years. </div><div>The fingerprint was used to build machine learning models (multi-task deep learning + SVM) for compound activity predictions towards a panel of 131 targets. </div><div>Quality of the predictions and the scaffold hopping potential of the HTSFP were systematically compared to traditional structural descriptors ECFP. </div><div><br></div>

scholarly journals Generalized Prediction of Shock in Intensive Care Units using Deep Learning

2021 ◽  
Author(s):  
Aditya Nagori ◽  
Anushtha Kalia ◽  
Arjun Sharma ◽  
Pradeep Singh ◽  
Harsh Bandhey ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Prediction Models ◽  
Age Groups ◽  
Receiver Operating Curve ◽  
Learning Approach ◽  
New Delhi ◽  
Model Generalization ◽  
Pediatric Icu ◽  
Geographical Context

Shock is a major killer in the ICU and machine learning based early predictions can potentially save lives. Generalization across age and geographical context is an unaddressed challenge. In this retrospective observational study, we built real-time shock prediction models generalized across age groups and continents. More than 1.5 million patient-hours of novel data from a pediatric ICU in New Delhi and 5 million patient-hours from the adult ICU MIMIC database were used to build models. We achieved model generalization through a novel fractal deep-learning approach and predicted shock up to 12 hours in advance. Our deep learning models showed a receiver operating curve (AUROC) drop from 78% (95%CI, 73-83) on MIMIC data to 66% (95%CI, 54-78) on New Delhi data, outperforming standard machine learning by nearly a 10% gap. Therefore, better representations and deep learning can partly address the generalizability-gap of ICU prediction models trained across geographies. Our data and algorithms are publicly available as a pre-configured docker environment at https://github.com/SAFE-ICU/ShoQPred.

Deep Learning-Based Mobile Application for Plant Disease Diagnosis

2019 ◽  
pp. 242-271 ◽  
Author(s):  
Shradha Verma ◽  
Anuradha Chug ◽  
Amit Prakash Singh ◽  
Shubham Sharma ◽  
Puranjay Rajvanshi
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Mobile Application ◽  
Plant Disease ◽  
Prediction Models ◽  
Disease Diagnosis ◽  
Tomato Leaf ◽  
Plant Diseases ◽  
Learning Tools ◽  
Class Labels

With the increasing computational power, areas such as machine learning, image processing, deep learning, etc. have been extensively applied in agriculture. This chapter investigates the applications of the said areas and various prediction models in plant pathology for accurate classification, identification, and quantification of plant diseases. The authors aim to automate the plant disease identification process. To accomplish this objective, CNN has been utilized for image classification. Research shows that deep learning architectures outperform other machine learning tools significantly. To this effect, the authors have implemented and trained five CNN models, namely Inception ResNet v2, VGG16, VGG19, ResNet50, and Xception, on PlantVillage dataset for tomato leaf images. The authors analyzed 18,160 tomato leaf images spread across 10 class labels. After comparing their performance measures, ResNet50 proved to be the most accurate prediction tool. It was employed to create a mobile application to classify and identify tomato plant diseases successfully.

scholarly journals Resistance to Fusarium head blight in spring barley

2011 ◽  
Vol 47 (No. 2) ◽  
pp. 58-63 ◽  
Author(s):  
J. Chrpová ◽  
V. Šíp ◽  
L. Štočková ◽  
L. Stemberková ◽  
L. Tvarůžek
Keyword(s):  
Fusarium Head Blight ◽  
Spring Barley ◽  
Fusarium Culmorum ◽  
Grain Weight ◽  
Head Blight ◽  
The Czech Republic ◽  
Disease Symptoms ◽  
Barley Cultivars ◽  
Yield And Quality ◽  
Medium Resistance

Fusarium head blight (FHB) is a fungal disease causing substantial yield and quality losses in barley. Genetic variation in deoxynivalenol (DON) content and and important yield traits in response to FHB were studied in 44 spring barley cultivars for two years following artificial inoculation with Fusarium culmorum under field conditions. The analysis of variance revealed that the largest effect on DON content and simultaneously on the reduction of thousand grain weight and grain weight per spike were due to the environmental conditions of the year, while the visual disease symptoms depended on the cultivars to a larger extent. All these traits were significantly interrelated. The most resistant cultivars Murasski mochi, Nordic, Krasnodarskij 35, Krasnodarskij 95, Nordus, and Usurijskij 8, together with the resistant check Chevron, showed the lowest DON content, the lowest expression of disease symptoms and the lowest reduction of TGW and GWS. However, most spring barley cultivars registered in the Czech Republic in recent years expressed susceptibility or medium resistance and were considerably affected by the disease. This increases the importance of breeding barley for resistance to FHB.

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