scholarly journals Fourier Ring Correlation and Anisotropic Kernel Density Estimation Improve Deep Learning Based SMLM Reconstruction of Microtubules

2021 ◽  
Vol 1 ◽  
Author(s):  
Andreas Berberich ◽  
Andreas Kurz ◽  
Sebastian Reinhard ◽  
Torsten Johann Paul ◽  
Paul Ray Burd ◽  
...  
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
Similarity Index ◽  
Kernel Density ◽  
Ground Truth ◽  
Quality Measure ◽  
Gaussian Kernel ◽  
Limiting Factor ◽  
Density Estimator

Single-molecule super-resolution microscopy (SMLM) techniques like dSTORM can reveal biological structures down to the nanometer scale. The achievable resolution is not only defined by the localization precision of individual fluorescent molecules, but also by their density, which becomes a limiting factor e.g., in expansion microscopy. Artificial deep neural networks can learn to reconstruct dense super-resolved structures such as microtubules from a sparse, noisy set of data points. This approach requires a robust method to assess the quality of a predicted density image and to quantitatively compare it to a ground truth image. Such a quality measure needs to be differentiable to be applied as loss function in deep learning. We developed a new trainable quality measure based on Fourier Ring Correlation (FRC) and used it to train deep neural networks to map a small number of sampling points to an underlying density. Smooth ground truth images of microtubules were generated from localization coordinates using an anisotropic Gaussian kernel density estimator. We show that the FRC criterion ideally complements the existing state-of-the-art multiscale structural similarity index, since both are interpretable and there is no trade-off between them during optimization. The TensorFlow implementation of our FRC metric can easily be integrated into existing deep learning workflows.

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.

scholarly journals Zero-Crossing Point Detection of Sinusoidal Signal in Presence of Noise and Harmonics Using Deep Neural Networks

Algorithms ◽  
2021 ◽  
Vol 14 (11) ◽  
pp. 329
Author(s):  
Venkataramana Veeramsetty ◽  
Bhavana Reddy Edudodla ◽  
Surender Reddy Salkuti
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
Harmonic Distortion ◽  
Sinusoidal Signal ◽  
Zero Crossing ◽  
Complete Study ◽  
Consistent Performance ◽  
Point Detection ◽  
Crossing Point

Zero-crossing point detection is necessary to establish a consistent performance in various power system applications, such as grid synchronization, power conversion and switch-gear protection. In this paper, zero-crossing points of a sinusoidal signal are detected using deep neural networks. In order to train and evaluate the deep neural network model, new datasets for sinusoidal signals having noise levels from 5% to 50% and harmonic distortion from 10% to 50% are developed. This complete study is implemented in Google Colab using deep learning framework Keras. Results shows that the proposed deep learning model is able to detect zero-crossing points in a distorted sinusoidal signal with good accuracy.

scholarly journals The Old and the New: Can Physics-Informed Deep-Learning Replace Traditional Linear Solvers?

2021 ◽  
Vol 4 ◽  
Author(s):  
Stefano Markidis
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
High Performance ◽  
Critical Role ◽  
Low Frequency ◽  
Accurate Solution ◽  
Limiting Factor ◽  
Data Set ◽  
Linear Solvers ◽  
Computational Performance

Physics-Informed Neural Networks (PINN) are neural networks encoding the problem governing equations, such as Partial Differential Equations (PDE), as a part of the neural network. PINNs have emerged as a new essential tool to solve various challenging problems, including computing linear systems arising from PDEs, a task for which several traditional methods exist. In this work, we focus first on evaluating the potential of PINNs as linear solvers in the case of the Poisson equation, an omnipresent equation in scientific computing. We characterize PINN linear solvers in terms of accuracy and performance under different network configurations (depth, activation functions, input data set distribution). We highlight the critical role of transfer learning. Our results show that low-frequency components of the solution converge quickly as an effect of the F-principle. In contrast, an accurate solution of the high frequencies requires an exceedingly long time. To address this limitation, we propose integrating PINNs into traditional linear solvers. We show that this integration leads to the development of new solvers whose performance is on par with other high-performance solvers, such as PETSc conjugate gradient linear solvers, in terms of performance and accuracy. Overall, while the accuracy and computational performance are still a limiting factor for the direct use of PINN linear solvers, hybrid strategies combining old traditional linear solver approaches with new emerging deep-learning techniques are among the most promising methods for developing a new class of linear solvers.

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