scholarly journals A New Deep Learning Calibration Method Enhances Genome-Based Prediction of Continuous Crop Traits

2021 ◽  
Vol 12 ◽  
Author(s):  
Osval A. Montesinos-López ◽  
Abelardo Montesinos-López ◽  
Brandon A. Mosqueda-González ◽  
Alison R. Bentley ◽  
Morten Lillemo ◽  
...  
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Plant Breeding ◽  
Deep Neural Networks ◽  
Reference Population ◽  
Calibration Method ◽  
Data Sets ◽  
Simple Method ◽  
Continuous Response ◽  
Predicting Performance

Genomic selection (GS) has the potential to revolutionize predictive plant breeding. A reference population is phenotyped and genotyped to train a statistical model that is used to perform genome-enabled predictions of new individuals that were only genotyped. In this vein, deep neural networks, are a type of machine learning model and have been widely adopted for use in GS studies, as they are not parametric methods, making them more adept at capturing nonlinear patterns. However, the training process for deep neural networks is very challenging due to the numerous hyper-parameters that need to be tuned, especially when imperfect tuning can result in biased predictions. In this paper we propose a simple method for calibrating (adjusting) the prediction of continuous response variables resulting from deep learning applications. We evaluated the proposed deep learning calibration method (DL_M2) using four crop breeding data sets and its performance was compared with the standard deep learning method (DL_M1), as well as the standard genomic Best Linear Unbiased Predictor (GBLUP). While the GBLUP was the most accurate model overall, the proposed deep learning calibration method (DL_M2) helped increase the genome-enabled prediction performance in all data sets when compared with the traditional DL method (DL_M1). Taken together, we provide evidence for extending the use of the proposed calibration method to evaluate its potential and consistency for predicting performance in the context of GS applied to plant breeding.

scholarly journals Mimicry Embedding Facilitates Advanced Neural Network Training for Image-Based Pathogen Detection

mSphere ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Artur Yakimovich ◽  
Moona Huttunen ◽  
Jerzy Samolej ◽  
Barbara Clough ◽  
Nagisa Yoshida ◽  
...  
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
Network Evolution ◽  
Great Promise ◽  
Data Sets ◽  
Imaging Data ◽  
Data Set ◽  
Novel Strategy

ABSTRACT The use of deep neural networks (DNNs) for analysis of complex biomedical images shows great promise but is hampered by a lack of large verified data sets for rapid network evolution. Here, we present a novel strategy, termed “mimicry embedding,” for rapid application of neural network architecture-based analysis of pathogen imaging data sets. Embedding of a novel host-pathogen data set, such that it mimics a verified data set, enables efficient deep learning using high expressive capacity architectures and seamless architecture switching. We applied this strategy across various microbiological phenotypes, from superresolved viruses to in vitro and in vivo parasitic infections. We demonstrate that mimicry embedding enables efficient and accurate analysis of two- and three-dimensional microscopy data sets. The results suggest that transfer learning from pretrained network data may be a powerful general strategy for analysis of heterogeneous pathogen fluorescence imaging data sets. IMPORTANCE In biology, the use of deep neural networks (DNNs) for analysis of pathogen infection is hampered by a lack of large verified data sets needed for rapid network evolution. Artificial neural networks detect handwritten digits with high precision thanks to large data sets, such as MNIST, that allow nearly unlimited training. Here, we developed a novel strategy we call mimicry embedding, which allows artificial intelligence (AI)-based analysis of variable pathogen-host data sets. We show that deep learning can be used to detect and classify single pathogens based on small differences.

scholarly journals Online Deep Learning: Learning Deep Neural Networks on the Fly

2018 ◽  
Author(s):  
Doyen Sahoo ◽  
Quang Pham ◽  
Jing Lu ◽  
Steven C. H. Hoi
Keyword(s):  
Neural Networks ◽  
Online Learning ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
Large Data ◽  
Learning Task ◽  
Large Data Sets ◽  
Training Data ◽  
Data Sets ◽  
Online Setting

Deep Neural Networks (DNNs) are typically trained by backpropagation in a batch setting, requiring the entire training data to be made available prior to the learning task. This is not scalable for many real-world scenarios where new data arrives sequentially in a stream. We aim to address an open challenge of ``Online Deep Learning" (ODL) for learning DNNs on the fly in an online setting. Unlike traditional online learning that often optimizes some convex objective function with respect to a shallow model (e.g., a linear/kernel-based hypothesis), ODL is more challenging as the optimization objective is non-convex, and regular DNN with standard backpropagation does not work well in practice for online settings. We present a new ODL framework that attempts to tackle the challenges by learning DNN models which dynamically adapt depth from a sequence of training data in an online learning setting. Specifically, we propose a novel Hedge Backpropagation (HBP) method for online updating the parameters of DNN effectively, and validate the efficacy on large data sets (both stationary and concept drifting scenarios).

scholarly journals Automatic Detection of Arrhythmia Based on Multi-Resolution Representation of ECG Signal

Sensors ◽  
2020 ◽  
Vol 20 (6) ◽  
pp. 1579
Author(s):  
Dongqi Wang ◽  
Qinghua Meng ◽  
Dongming Chen ◽  
Hupo Zhang ◽  
Lisheng Xu
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
Channel Model ◽  
Expert Knowledge ◽  
Automatic Detection ◽  
Data Representation ◽  
Learning Technology ◽  
Arrhythmia Detection ◽  
Automatic Feature Extraction

Automatic detection of arrhythmia is of great significance for early prevention and diagnosis of cardiovascular disease. Traditional feature engineering methods based on expert knowledge lack multidimensional and multi-view information abstraction and data representation ability, so the traditional research on pattern recognition of arrhythmia detection cannot achieve satisfactory results. Recently, with the increase of deep learning technology, automatic feature extraction of ECG data based on deep neural networks has been widely discussed. In order to utilize the complementary strength between different schemes, in this paper, we propose an arrhythmia detection method based on the multi-resolution representation (MRR) of ECG signals. This method utilizes four different up to date deep neural networks as four channel models for ECG vector representations learning. The deep learning based representations, together with hand-crafted features of ECG, forms the MRR, which is the input of the downstream classification strategy. The experimental results of big ECG dataset multi-label classification confirm that the F1 score of the proposed method is 0.9238, which is 1.31%, 0.62%, 1.18% and 0.6% higher than that of each channel model. From the perspective of architecture, this proposed method is highly scalable and can be employed as an example for arrhythmia recognition.

scholarly journals Enabling deeper learning on big data for materials informatics applications

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dipendra Jha ◽  
Vishu Gupta ◽  
Logan Ward ◽  
Zijiang Yang ◽  
Christopher Wolverton ◽  
...  
Keyword(s):  
Neural Networks ◽  
Big Data ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
Materials Science ◽  
Prediction Models ◽  
Model Performance ◽  
Materials Informatics ◽  
Learning Framework ◽  
Significant Attention

AbstractThe application of machine learning (ML) techniques in materials science has attracted significant attention in recent years, due to their impressive ability to efficiently extract data-driven linkages from various input materials representations to their output properties. While the application of traditional ML techniques has become quite ubiquitous, there have been limited applications of more advanced deep learning (DL) techniques, primarily because big materials datasets are relatively rare. Given the demonstrated potential and advantages of DL and the increasing availability of big materials datasets, it is attractive to go for deeper neural networks in a bid to boost model performance, but in reality, it leads to performance degradation due to the vanishing gradient problem. In this paper, we address the question of how to enable deeper learning for cases where big materials data is available. Here, we present a general deep learning framework based on Individual Residual learning (IRNet) composed of very deep neural networks that can work with any vector-based materials representation as input to build accurate property prediction models. We find that the proposed IRNet models can not only successfully alleviate the vanishing gradient problem and enable deeper learning, but also lead to significantly (up to 47%) better model accuracy as compared to plain deep neural networks and traditional ML techniques for a given input materials representation in the presence of big data.

scholarly journals Representing Deep Neural Networks Latent Space Geometries with Graphs

Algorithms ◽  
2021 ◽  
Vol 14 (2) ◽  
pp. 39
Author(s):  
Carlos Lassance ◽  
Vincent Gripon ◽  
Antonio Ortega
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Objective Function ◽  
Learning Process ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
The Core ◽  
Learning Tasks ◽  
Latent Space

Deep Learning (DL) has attracted a lot of attention for its ability to reach state-of-the-art performance in many machine learning tasks. The core principle of DL methods consists of training composite architectures in an end-to-end fashion, where inputs are associated with outputs trained to optimize an objective function. Because of their compositional nature, DL architectures naturally exhibit several intermediate representations of the inputs, which belong to so-called latent spaces. When treated individually, these intermediate representations are most of the time unconstrained during the learning process, as it is unclear which properties should be favored. However, when processing a batch of inputs concurrently, the corresponding set of intermediate representations exhibit relations (what we call a geometry) on which desired properties can be sought. In this work, we show that it is possible to introduce constraints on these latent geometries to address various problems. In more detail, we propose to represent geometries by constructing similarity graphs from the intermediate representations obtained when processing a batch of inputs. By constraining these Latent Geometry Graphs (LGGs), we address the three following problems: (i) reproducing the behavior of a teacher architecture is achieved by mimicking its geometry, (ii) designing efficient embeddings for classification is achieved by targeting specific geometries, and (iii) robustness to deviations on inputs is achieved via enforcing smooth variation of geometry between consecutive latent spaces. Using standard vision benchmarks, we demonstrate the ability of the proposed geometry-based methods in solving the considered problems.

scholarly journals Off-the-shelf deep learning is not enough, and requires parsimony, Bayesianity, and causality

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Rama K. Vasudevan ◽  
Maxim Ziatdinov ◽  
Lukas Vlcek ◽  
Sergei V. Kalinin
Keyword(s):  
Neural Networks ◽  
Computer Vision ◽  
Deep Learning ◽  
Bayesian Methods ◽  
Deep Neural Networks ◽  
Applied Research ◽  
Modern Science ◽  
Generative Models ◽  
Knowledge Development ◽  
Physical Constraints

AbstractDeep neural networks (‘deep learning’) have emerged as a technology of choice to tackle problems in speech recognition, computer vision, finance, etc. However, adoption of deep learning in physical domains brings substantial challenges stemming from the correlative nature of deep learning methods compared to the causal, hypothesis driven nature of modern science. We argue that the broad adoption of Bayesian methods incorporating prior knowledge, development of solutions with incorporated physical constraints and parsimonious structural descriptors and generative models, and ultimately adoption of causal models, offers a path forward for fundamental and applied research.

scholarly journals Diversity oriented Deep Reinforcement Learning for targeted molecule generation

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Tiago Pereira ◽  
Maryam Abbasi ◽  
Bernardete Ribeiro ◽  
Joel P. Arrais
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Reinforcement Learning ◽  
Deep Neural Networks ◽  
Chemical Space ◽  
Biological Properties ◽  
Training Process ◽  
Training Strategy ◽  
Inhibitory Power ◽  
Exploratory Strategy

AbstractIn this work, we explore the potential of deep learning to streamline the process of identifying new potential drugs through the computational generation of molecules with interesting biological properties. Two deep neural networks compose our targeted generation framework: the Generator, which is trained to learn the building rules of valid molecules employing SMILES strings notation, and the Predictor which evaluates the newly generated compounds by predicting their affinity for the desired target. Then, the Generator is optimized through Reinforcement Learning to produce molecules with bespoken properties. The innovation of this approach is the exploratory strategy applied during the reinforcement training process that seeks to add novelty to the generated compounds. This training strategy employs two Generators interchangeably to sample new SMILES: the initially trained model that will remain fixed and a copy of the previous one that will be updated during the training to uncover the most promising molecules. The evolution of the reward assigned by the Predictor determines how often each one is employed to select the next token of the molecule. This strategy establishes a compromise between the need to acquire more information about the chemical space and the need to sample new molecules, with the experience gained so far. To demonstrate the effectiveness of the method, the Generator is trained to design molecules with an optimized coefficient of partition and also high inhibitory power against the Adenosine $$A_{2A}$$ A 2 A and $$\kappa$$ κ opioid receptors. The results reveal that the model can effectively adjust the newly generated molecules towards the wanted direction. More importantly, it was possible to find promising sets of unique and diverse molecules, which was the main purpose of the newly implemented strategy.

Multi-Mineral Segmentation of SEM Images Using Deep Learning Techniques

2021 ◽  
Author(s):  
Vladislav Vasilevich Alekseev ◽  
Denis Mihaylovich Orlov ◽  
Dmitry Anatolevich Koroteev
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
Pore Space ◽  
Rock Physics ◽  
Sem Images ◽  
Digital Rock Physics ◽  
Learning Techniques ◽  
Digital Core ◽  
Non Destructive

Abstract The approaches of building and methods of using the digital core are currently developing rapidly. The use of these methods makes it possible to obtain petrophysical information by non-destructive methods quickly. Digital rock physics includes two main stages: constructing models and modeling various physical processes on the obtained models. Our work proposes using deep learning methods for mineral and pore space segmentation instead of classical methods such as threshold image processing. Deep neural networks have long been able to show their advantages in many areas of computer vision. This paper proposes and tests methods that help identify different minerals in images from a scanning electron microscope. We used images of rocks of the Achimov formation, which are arkoses, as samples. We tested various deep neural networks such as LinkNet, U-Net, ResUNet, and pix2pix and identified those that performed best in segmentation.

SỬ DỤNG DEEP NEURAL NETWORKS PHÁT HIỆN GAI ĐỘNG KINH TRONG BẢN GHI EEG

2020 ◽  
pp. 77-84
Author(s):  
Xuyến
Keyword(s):  
Neural Networks ◽  
Artificial Neural Networks ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
Artificial Neural

Deep Neural Networks là một thuật toán dạy cho máy học, là phương pháp nâng cao của mạng nơ-ron nhân tạo (Artificial Neural Networks) nhiều tầng để học biểu diễn mô hình đối tượng. Bài báo trình bày phương pháp để phát hiện spike tự động, giải quyết bài toán cho các bác sỹ khi phân tích dữ liệu khổng lồ được thu thập từ bản ghi điện não để xác định một khu vực của não gây ra chứng động kinh. Hàng triệu mẫu được phân tích thủ công đã được đào tạo lại để tìm các gai liêp tiếp phát ra từ vùng não bị ảnh hưởng. Để đánh giá phương pháp đề xuất, tác giả đã xây dựng hệ thống trong đó sử dụng một số mô hình deep learning đưa vào thử nghiệm hỗ trợ các bác sỹ khám phát hiện và chẩn đoán sớm bệnh.

scholarly journals Semiotic Aggregation in Deep Learning

Entropy ◽  
2020 ◽  
Vol 22 (12) ◽  
pp. 1365
Author(s):  
Bogdan Muşat ◽  
Răzvan Andonie
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Learning ◽  
Decision Model ◽  
Deep Neural Networks ◽  
Neural Model ◽  
Network Layers ◽  
Saliency Maps ◽  
Spatial Entropy ◽  
Insight Into

Convolutional neural networks utilize a hierarchy of neural network layers. The statistical aspects of information concentration in successive layers can bring an insight into the feature abstraction process. We analyze the saliency maps of these layers from the perspective of semiotics, also known as the study of signs and sign-using behavior. In computational semiotics, this aggregation operation (known as superization) is accompanied by a decrease of spatial entropy: signs are aggregated into supersign. Using spatial entropy, we compute the information content of the saliency maps and study the superization processes which take place between successive layers of the network. In our experiments, we visualize the superization process and show how the obtained knowledge can be used to explain the neural decision model. In addition, we attempt to optimize the architecture of the neural model employing a semiotic greedy technique. To the extent of our knowledge, this is the first application of computational semiotics in the analysis and interpretation of deep neural networks.

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