scholarly journals Atomistic Line Graph Neural Network for improved materials property predictions

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Kamal Choudhary ◽  
Brian DeCost
Keyword(s):  
Neural Network ◽  
Message Passing ◽  
Line Graph ◽  
Interatomic Bond ◽  
Distance Information ◽  
Bond Angles ◽  
Atomic Structures ◽  
Performance Improvements ◽  
Improved Performance ◽  
Model Training

AbstractGraph neural networks (GNN) have been shown to provide substantial performance improvements for atomistic material representation and modeling compared with descriptor-based machine learning models. While most existing GNN models for atomistic predictions are based on atomic distance information, they do not explicitly incorporate bond angles, which are critical for distinguishing many atomic structures. Furthermore, many material properties are known to be sensitive to slight changes in bond angles. We present an Atomistic Line Graph Neural Network (ALIGNN), a GNN architecture that performs message passing on both the interatomic bond graph and its line graph corresponding to bond angles. We demonstrate that angle information can be explicitly and efficiently included, leading to improved performance on multiple atomistic prediction tasks. We ALIGNN models for predicting 52 solid-state and molecular properties available in the JARVIS-DFT, Materials project, and QM9 databases. ALIGNN can outperform some previously reported GNN models on atomistic prediction tasks by up to 85% in accuracy with better or comparable model training speed.

scholarly journals AI-based localization and classification of skin disease with erythema

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ha Min Son ◽  
Wooho Jeon ◽  
Jinhyun Kim ◽  
Chan Yeong Heo ◽  
Hye Jin Yoon ◽  
...  
Keyword(s):  
Neural Network ◽  
Skin Diseases ◽  
Classification Model ◽  
Screening Tests ◽  
Sensitivity Score ◽  
Common Skin ◽  
Novel Method ◽  
Improved Performance ◽  
High Level

AbstractAlthough computer-aided diagnosis (CAD) is used to improve the quality of diagnosis in various medical fields such as mammography and colonography, it is not used in dermatology, where noninvasive screening tests are performed only with the naked eye, and avoidable inaccuracies may exist. This study shows that CAD may also be a viable option in dermatology by presenting a novel method to sequentially combine accurate segmentation and classification models. Given an image of the skin, we decompose the image to normalize and extract high-level features. Using a neural network-based segmentation model to create a segmented map of the image, we then cluster sections of abnormal skin and pass this information to a classification model. We classify each cluster into different common skin diseases using another neural network model. Our segmentation model achieves better performance compared to previous studies, and also achieves a near-perfect sensitivity score in unfavorable conditions. Our classification model is more accurate than a baseline model trained without segmentation, while also being able to classify multiple diseases within a single image. This improved performance may be sufficient to use CAD in the field of dermatology.

Breast cancer diagnosis using multiple activation deep neural network

2021 ◽  
pp. 1063293X2110251
Author(s):  
K Vijayakumar ◽  
Vinod J Kadam ◽  
Sudhir Kumar Sharma
Keyword(s):  
Breast Cancer ◽  
Neural Network ◽  
Deep Neural Network ◽  
Breast Cancer Diagnosis ◽  
Activation Function ◽  
Linear Functions ◽  
Cancer Data ◽  
Final Layer ◽  
Improved Performance ◽  
Hidden Layer

Deep Neural Network (DNN) stands for multilayered Neural Network (NN) that is capable of progressively learn the more abstract and composite representations of the raw features of the input data received, with no need for any feature engineering. They are advanced NNs having repetitious hidden layers between the initial input and the final layer. The working principle of such a standard deep classifier is based on a hierarchy formed by the composition of linear functions and a defined nonlinear Activation Function (AF). It remains uncertain (not clear) how the DNN classifier can function so well. But it is clear from many studies that within DNN, the AF choice has a notable impact on the kinetics of training and the success of tasks. In the past few years, different AFs have been formulated. The choice of AF is still an area of active study. Hence, in this study, a novel deep Feed forward NN model with four AFs has been proposed for breast cancer classification: hidden layer 1: Swish, hidden layer, 2:-LeakyReLU, hidden layer 3: ReLU, and final output layer: naturally Sigmoidal. The purpose of the study is twofold. Firstly, this study is a step toward a more profound understanding of DNN with layer-wise different AFs. Secondly, research is also aimed to explore better DNN-based systems to build predictive models for breast cancer data with improved accuracy. Therefore, the benchmark UCI dataset WDBC was used for the validation of the framework and evaluated using a ten-fold CV method and various performance indicators. Multiple simulations and outcomes of the experimentations have shown that the proposed solution performs in a better way than the Sigmoid, ReLU, and LeakyReLU and Swish activation DNN in terms of different parameters. This analysis contributes to producing an expert and precise clinical dataset classification method for breast cancer. Furthermore, the model also achieved improved performance compared to many established state-of-the-art algorithms/models.

Fully automated contrast and non-contrast cardiac view detection in echocardiography a multi-centre, multi-vendor study

2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
S Gao ◽  
D Stojanovski ◽  
A Parker ◽  
P Marques ◽  
S Heitner ◽  
...  
Keyword(s):  
Neural Network ◽  
Training Data ◽  
Classification Model ◽  
Validation Dataset ◽  
Funding Source ◽  
Private Company ◽  
Validation Data ◽  
Independent Test ◽  
Model Training ◽  
Confusion Matrices

Abstract Background Correctly identifying views acquired in a 2D echocardiographic examination is paramount to post-processing and quantification steps often performed as part of most clinical workflows. In many exams, particularly in stress echocardiography, microbubble contrast is used which greatly affects the appearance of the cardiac views. Here we present a bespoke, fully automated convolutional neural network (CNN) which identifies apical 2, 3, and 4 chamber, and short axis (SAX) views acquired with and without contrast. The CNN was tested in a completely independent, external dataset with the data acquired in a different country than that used to train the neural network. Methods Training data comprised of 2D echocardiograms was taken from 1014 subjects from a prospective multisite, multi-vendor, UK trial with the number of frames in each view greater than 17,500. Prior to view classification model training, images were processed using standard techniques to ensure homogenous and normalised image inputs to the training pipeline. A bespoke CNN was built using the minimum number of convolutional layers required with batch normalisation, and including dropout for reducing overfitting. Before processing, the data was split into 90% for model training (211,958 frames), and 10% used as a validation dataset (23,946 frames). Image frames from different subjects were separated out entirely amongst the training and validation datasets. Further, a separate trial dataset of 240 studies acquired in the USA was used as an independent test dataset (39,401 frames). Results Figure 1 shows the confusion matrices for both validation data (left) and independent test data (right), with an overall accuracy of 96% and 95% for the validation and test datasets respectively. The accuracy for the non-contrast cardiac views of >99% exceeds that seen in other works. The combined datasets included images acquired across ultrasound manufacturers and models from 12 clinical sites. Conclusion We have developed a CNN capable of automatically accurately identifying all relevant cardiac views used in “real world” echo exams, including views acquired with contrast. Use of the CNN in a routine clinical workflow could improve efficiency of quantification steps performed after image acquisition. This was tested on an independent dataset acquired in a different country to that used to train the model and was found to perform similarly thus indicating the generalisability of the model. Figure 1. Confusion matrices Funding Acknowledgement Type of funding source: Private company. Main funding source(s): Ultromics Ltd.

Study on Rapid Archival Technology of Bullets Based on Graph Convolutional Neural Network

2021 ◽  
Author(s):  
Shi-bo Pan ◽  
Di-lin Pan ◽  
Nan Pan ◽  
Xiao Ye ◽  
Miaohan Zhang
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Neural Network Model ◽  
Dynamic Time Warping ◽  
Large Scale ◽  
Line Graph ◽  
High Accuracy ◽  
Time Warping ◽  
Large Numbers ◽  
Dynamic Time

Traditional gun archiving methods are mostly carried out through bullets’ physics or photography, which are inefficient and difficult to trace, and cannot meet the needs of large-scale archiving. Aiming at such problems, a rapid archival technology of bullets based on graph convolutional neural network has been studied and developed. First, the spot laser is used to take the circle points of the bullet rifling traces. The obtained data is filtered and noise-reduced to make the corresponding line graph, and then the dynamic time warping (DTW) algorithm convolutional neural network model is used to perform the processing on the processed data. Not only is similarity matched, the rapid matching of the rifling of the bullet is also accomplished. Comparison of experimental results shows that this technology has the advantages of rapid archiving and high accuracy. Furthermore, it can be carried out in large numbers at the same time, and is more suitable for practical promotion and application.

scholarly journals Alternative shoe closure designs alter biomechanical performance during agility-based movements

2020 ◽  
Author(s):  
Moira Pryhoda ◽  
Rachel Wathen ◽  
Jay Dicharry ◽  
Kevin Shelburne ◽  
Bradley Davidson
Keyword(s):  
Mechanical Properties ◽  
Performance Measures ◽  
Performance Measure ◽  
Male Athletes ◽  
Impaired Performance ◽  
Performance Improvements ◽  
Two Measures ◽  
Ground Contact Time ◽  
Improved Performance ◽  
Consistent Performance

The objective of this research was to determine if three alternative shoe upper closures improve biomechanical performance measures relative to a standard lace closure in court-based movements. NCAA Division 1 and club-level male athletes recruited from lacrosse, soccer, tennis, and rugby performed four court-based movements: Lateral Skater Jump repeats (LSJ), Countermovement Jump repeats (CMJ), Triangle Drop Step drill (TDS), and Anterior-Posterior drill (AP). Each athlete performed the movements in four shoe upper closures: Standard Closure, Lace Replacement, Y Wrap, and Tri Strap. Ground contact time, peak eccentric rate of force development (RFD), peak concentric GRF, peak concentric COM power, eccentric work, concentric work, and movement completion time were measured. Tri Strap saw improvements in four of seven biomechanical variables during CMJ and LSJ and one variable during TDS. Lace Replacement delivered improvements in one performance measure during CMJ, LSJ, and AP, and two variables in TDS. Y Wrap improved performance in three performance measures during LSJ and impaired performance in two measures during CMJ and three measures during AP. Tri Strap provided the most consistent performance improvements across all movements. This study allowed for the mechanical properties of the shoe lower to remain consistent across designs to examine if an alternative shoe upper closure could enhance performance. Our results indicate that increased proprioception and/or mechanical properties due to the alternative closures, especially Tri Strap, improves athlete performance, which concludes that the design of the shoe upper is an essential consideration in shoe design.

scholarly journals AI-MHC: an allele-integrated deep learning framework for improving Class I & Class II HLA-binding predictions

2018 ◽  
Author(s):  
John-William Sidhom ◽  
Drew Pardoll ◽  
Alexander Baras
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Immune System ◽  
State Of The Art ◽  
Class Ii ◽  
Class I ◽  
Binding Prediction ◽  
Translational Invariance ◽  
Mhc Molecules ◽  
Improved Performance

AbstractMotivationThe immune system has potential to present a wide variety of peptides to itself as a means of surveillance for pathogenic invaders. This means of surveillances allows the immune system to detect peptides derives from bacterial, viral, and even oncologic sources. However, given the breadth of the epitope repertoire, in order to study immune responses to these epitopes, investigators have relied on in-silico prediction algorithms to help narrow down the list of candidate epitopes, and current methods still have much in the way of improvement.ResultsWe present Allele-Integrated MHC (AI-MHC), a deep learning architecture with improved performance over the current state-of-the-art algorithms in human Class I and Class II MHC binding prediction. Our architecture utilizes a convolutional neural network that improves prediction accuracy by 1) allowing one neural network to be trained on all peptides for all alleles of a given class of MHC molecules by making the allele an input to the net and 2) introducing a global max pooling operation with an optimized kernel size that allows the architecture to achieve translational invariance in MHC-peptide binding analysis, making it suitable for sequence analytics where a frame of interest needs to be learned in a longer, variable length sequence. We assess AI-MHC against internal independent test sets and compare against all algorithms in the IEDB automated server benchmarks, demonstrating our algorithm achieves state-of-the-art for both Class I and Class II prediction.Availability and ImplementationAI-MHC can be used via web interface at baras.pathology.jhu.edu/[email protected]

scholarly journals An Improved Fully Convolutional Network Based on Post-Processing with Global Variance Equalization and Noise-Aware Training for Speech Enhancement

2021 ◽  
Vol 25 (1) ◽  
pp. 130-137
Author(s):  
Wenlong Li ◽  
◽  
Kaoru Hirota ◽  
Yaping Dai ◽  
Zhiyang Jia
Keyword(s):  
Neural Network ◽  
Speech Enhancement ◽  
Deep Neural Network ◽  
Voice Conversion ◽  
Post Processing ◽  
Generalization Capability ◽  
Convolutional Network ◽  
Fully Convolutional Network ◽  
Subjective Score ◽  
Model Training

An improved fully convolutional network based on post-processing with global variance (GV) equalization and noise-aware training (PN-FCN) for speech enhancement model is proposed. It aims at reducing the complexity of the speech improvement system, and it solves overly smooth speech signal spectrogram problem and poor generalization capability. The PN-FCN is fed with the noisy speech samples augmented with an estimate of the noise. In this way, the PN-FCN uses additional online noise information to better predict the clean speech. Besides, PN-FCN uses the global variance information, which improve the subjective score in a voice conversion task. Finally, the proposed framework adopts FCN, and the number of parameters is one-seventh of deep neural network (DNN). Results of experiments on the Valentini-Botinhaos dataset demonstrate that the proposed framework achieves improvements in both denoising effect and model training speed.

scholarly journals JAMPI: Efficient Matrix Multiplication in Spark Using Barrier Execution Mode

2020 ◽  
Author(s):  
Tamas Foldi ◽  
Chris von Csefalvay ◽  
Nicolas A. Perez
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Message Passing ◽  
Matrix Multiplication ◽  
Map Reduce ◽  
Distributed Training ◽  
Learning Tasks ◽  
Memory Footprint ◽  
Asynchronous Network ◽  
Execution Mode

The new barrier mode in Apache Spark allows embedding distributed deep learning training as a Spark stage to simplify the distributed training workflow. In Spark, a task in a stage doesn’t depend on any other tasks in the same stage, and hence it can be scheduled independently. However, several algorithms require more sophisticated inter-task communications, similar to the MPI paradigm. By combining distributed message passing (using asynchronous network IO), OpenJDK’s new auto-vectorization and Spark’s barrier execution mode, we can add non-map/reduce based algorithms, such as Cannon’s distributed matrix multiplication to Spark. We document an efficient distributed matrix multiplication using Cannon’s algorithm, which improves significantly on the performance of the existing MLlib implementation. Used within a barrier task, the algorithm described herein results in an up to 24% performance increase on a 10,000x10,000 square matrix with a significantly lower memory footprint. Applications of efficient matrix multiplication include, among others, accelerating the training and implementation of deep convolutional neural network based workloads, and thus such efficient algorithms can play a ground-breaking role in faster, more efficient execution of even the most complicated machine learning tasks

Matrix inference and estimation in multi-layer models*

2021 ◽  
Vol 2021 (12) ◽  
pp. 124004
Author(s):  
Parthe Pandit ◽  
Mojtaba Sahraee-Ardakan ◽  
Sundeep Rangan ◽  
Philip Schniter ◽  
Alyson K Fletcher
Keyword(s):  
Neural Network ◽  
Message Passing ◽  
Hidden Variables ◽  
Signal Recovery ◽  
Inference Problem ◽  
Neural Network Learning ◽  
Approximate Message Passing ◽  
Message Passing Algorithm ◽  
Training Samples ◽  
Mixed Regression

Abstract We consider the problem of estimating the input and hidden variables of a stochastic multi-layer neural network (NN) from an observation of the output. The hidden variables in each layer are represented as matrices with statistical interactions along both rows as well as columns. This problem applies to matrix imputation, signal recovery via deep generative prior models, multi-task and mixed regression, and learning certain classes of two-layer NNs. We extend a recently-developed algorithm—multi-layer vector approximate message passing, for this matrix-valued inference problem. It is shown that the performance of the proposed multi-layer matrix vector approximate message passing algorithm can be exactly predicted in a certain random large-system limit, where the dimensions N × d of the unknown quantities grow as N → ∞ with d fixed. In the two-layer neural-network learning problem, this scaling corresponds to the case where the number of input features as well as training samples grow to infinity but the number of hidden nodes stays fixed. The analysis enables a precise prediction of the parameter and test error of the learning.

Optimasi Akurasi Metode Convolutional Neural Network untuk Identifikasi Jenis Sampah

2021 ◽  
Vol 5 (2) ◽  
pp. 312-318
Author(s):  
Rima Dias Ramadhani ◽  
Afandi Nur Aziz Thohari ◽  
Condro Kartiko ◽  
Apri Junaidi ◽  
Tri Ginanjar Laksana ◽  
...  
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Convolutional Neural Network ◽  
Computer Science ◽  
No Value ◽  
Convolutional Neural Networks ◽  
Training Process ◽  
Indonesian Government ◽  
Speed Up ◽  
Model Training

Waste is goods / materials that have no value in the scope of production, where in some cases the waste is disposed of carelessly and can damage the environment. The Indonesian government in 2019 recorded waste reaching 66-67 million tons, which is higher than the previous year, which was 64 million tons. Waste is differentiated based on its type, namely organic and anorganic waste. In the field of computer science, the process of sensing the type waste can be done using a camera and the Convolutional Neural Networks (CNN) method, which is a type of neural network that works by receiving input in the form of images. The input will be trained using CNN architecture so that it will produce output that can recognize the object being inputted. This study optimizes the use of the CNN method to obtain accurate results in identifying types of waste. Optimization is done by adding several hyperparameters to the CNN architecture. By adding hyperparameters, the accuracy value is 91.2%. Meanwhile, if the hyperparameter is not used, the accuracy value is only 67.6%. There are three hyperparameters used to increase the accuracy value of the model. They are dropout, padding, and stride. 20% increase in dropout to increase training overfit. Whereas padding and stride are used to speed up the model training process.

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