Neural network activation similarity: a new measure to assist decision making in chemical toxicology

Deep learning neural networks, constructed for the prediction of chemical binding at 79 pharmacologically important human biological targets, show extremely high performance on test data (accuracy 92.2 ± 4.2%, MCC 0.814 ± 0.093, ROC-AUC 0.96 ± 0.04).

Download Full-text

Optimizing Convolution Neural Network on the TI C6678 multicore DSP

MATEC Web of Conferences ◽

10.1051/matecconf/201824603044 ◽

2018 ◽

Vol 246 ◽

pp. 03044 ◽

Cited By ~ 1

Author(s):

Guozhao Zeng ◽

Xiao Hu ◽

Yueyue Chen

Keyword(s):

Neural Network ◽

Neural Networks ◽

Image Processing ◽

Deep Learning ◽

Digital Signal Processor ◽

High Performance ◽

Digital Signal ◽

Automatic Translation ◽

Convolution Operation ◽

Multicore Dsp

Convolutional Neural Networks (CNNs) have become the most advanced algorithms for deep learning. They are widely used in image processing, object detection and automatic translation. As the demand for CNNs continues to increase, the platforms on which they are deployed continue to expand. As an excellent low-power, high-performance, embedded solution, Digital Signal Processor (DSP) is used frequently in many key areas. This paper attempts to deploy the CNN to Texas Instruments (TI)’s TMS320C6678 multi-core DSP and optimize the main operations (convolution) to accommodate the DSP structure. The efficiency of the improved convolution operation has increased by tens of times.

Download Full-text

Heart Disease Classification Using Artificial Neural Networks

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.781.624 ◽

2015 ◽

Vol 781 ◽

pp. 624-627 ◽

Cited By ~ 1

Author(s):

Rati Wongsathan ◽

Pasit Pothong

Keyword(s):

Neural Network ◽

Neural Networks ◽

Decision Making ◽

Heart Disease ◽

Classification Accuracy ◽

High Performance ◽

Disease Classification ◽

Generalized Regression Neural Network ◽

The Neural Networks ◽

Very High

Neural Networks (NNs) has emerged as an importance tool for classification in the field of decision making. The main objective of this work is to design the structure and select the optimized parameter in the neural networks to implement the heart disease classifier. Three types of neural networks, i.e. Multi-layered Perceptron Neural Network (MLP-NN), Radial Basis Function Neural Networks (RBF-NN), and Generalized Regression Neural Network (GR-NN) have been used to test the performance of heart disease classification. The classification accuracy obtained by RBFNN gave a very high performance than MLP-NN and GR-NN respectively. The performance of accuracy is very promising compared with the previously reported another type of neural networks.

Download Full-text

Deep Learning Neural Networks to Predict Serious Complications After Bariatric Surgery: Analysis of Scandinavian Obesity Surgery Registry Data (Preprint)

10.2196/preprints.15992 ◽

2019 ◽

Author(s):

Yang Cao ◽

Scott Montgomery ◽

Johan Ottosson ◽

Erik Näslund ◽

Erik Stenberg

Keyword(s):

Neural Network ◽

Neural Networks ◽

Bariatric Surgery ◽

Deep Learning ◽

Postoperative Complications ◽

Obesity Surgery ◽

Test Data ◽

Registry Data ◽

Training Data ◽

Complications After Bariatric Surgery

BACKGROUND Obesity is one of today’s most visible public health problems worldwide. Although modern bariatric surgery is ostensibly considered safe, serious complications and mortality still occur in some patients. OBJECTIVE This study aimed to explore whether serious postoperative complications of bariatric surgery recorded in a national quality registry can be predicted preoperatively using deep learning methods. METHODS Patients who were registered in the Scandinavian Obesity Surgery Registry (SOReg) between 2010 and 2015 were included in this study. The patients who underwent a bariatric procedure between 2010 and 2014 were used as training data, and those who underwent a bariatric procedure in 2015 were used as test data. Postoperative complications were graded according to the Clavien-Dindo classification, and complications requiring intervention under general anesthesia or resulting in organ failure or death were considered serious. Three supervised deep learning neural networks were applied and compared in our study: multilayer perceptron (MLP), convolutional neural network (CNN), and recurrent neural network (RNN). The synthetic minority oversampling technique (SMOTE) was used to artificially augment the patients with serious complications. The performances of the neural networks were evaluated using accuracy, sensitivity, specificity, Matthews correlation coefficient, and area under the receiver operating characteristic curve. RESULTS In total, 37,811 and 6250 patients were used as the training data and test data, with incidence rates of serious complication of 3.2% (1220/37,811) and 3.0% (188/6250), respectively. When trained using the SMOTE data, the MLP appeared to have a desirable performance, with an area under curve (AUC) of 0.84 (95% CI 0.83-0.85). However, its performance was low for the test data, with an AUC of 0.54 (95% CI 0.53-0.55). The performance of CNN was similar to that of MLP. It generated AUCs of 0.79 (95% CI 0.78-0.80) and 0.57 (95% CI 0.59-0.61) for the SMOTE data and test data, respectively. Compared with the MLP and CNN, the RNN showed worse performance, with AUCs of 0.65 (95% CI 0.64-0.66) and 0.55 (95% CI 0.53-0.57) for the SMOTE data and test data, respectively. CONCLUSIONS MLP and CNN showed improved, but limited, ability for predicting the postoperative serious complications after bariatric surgery in the Scandinavian Obesity Surgery Registry data. However, the overfitting issue is still apparent and needs to be overcome by incorporating intra- and perioperative information. CLINICALTRIAL

Download Full-text

Deep Learning Neural Networks to Predict Serious Complications After Bariatric Surgery: Analysis of Scandinavian Obesity Surgery Registry Data

JMIR Medical Informatics ◽

10.2196/15992 ◽

2020 ◽

Vol 8 (5) ◽

pp. e15992 ◽

Cited By ~ 1

Author(s):

Yang Cao ◽

Scott Montgomery ◽

Johan Ottosson ◽

Erik Näslund ◽

Erik Stenberg

Keyword(s):

Neural Network ◽

Neural Networks ◽

Bariatric Surgery ◽

Deep Learning ◽

Postoperative Complications ◽

Obesity Surgery ◽

Test Data ◽

Registry Data ◽

Training Data ◽

Complications After Bariatric Surgery

Background Obesity is one of today’s most visible public health problems worldwide. Although modern bariatric surgery is ostensibly considered safe, serious complications and mortality still occur in some patients. Objective This study aimed to explore whether serious postoperative complications of bariatric surgery recorded in a national quality registry can be predicted preoperatively using deep learning methods. Methods Patients who were registered in the Scandinavian Obesity Surgery Registry (SOReg) between 2010 and 2015 were included in this study. The patients who underwent a bariatric procedure between 2010 and 2014 were used as training data, and those who underwent a bariatric procedure in 2015 were used as test data. Postoperative complications were graded according to the Clavien-Dindo classification, and complications requiring intervention under general anesthesia or resulting in organ failure or death were considered serious. Three supervised deep learning neural networks were applied and compared in our study: multilayer perceptron (MLP), convolutional neural network (CNN), and recurrent neural network (RNN). The synthetic minority oversampling technique (SMOTE) was used to artificially augment the patients with serious complications. The performances of the neural networks were evaluated using accuracy, sensitivity, specificity, Matthews correlation coefficient, and area under the receiver operating characteristic curve. Results In total, 37,811 and 6250 patients were used as the training data and test data, with incidence rates of serious complication of 3.2% (1220/37,811) and 3.0% (188/6250), respectively. When trained using the SMOTE data, the MLP appeared to have a desirable performance, with an area under curve (AUC) of 0.84 (95% CI 0.83-0.85). However, its performance was low for the test data, with an AUC of 0.54 (95% CI 0.53-0.55). The performance of CNN was similar to that of MLP. It generated AUCs of 0.79 (95% CI 0.78-0.80) and 0.57 (95% CI 0.59-0.61) for the SMOTE data and test data, respectively. Compared with the MLP and CNN, the RNN showed worse performance, with AUCs of 0.65 (95% CI 0.64-0.66) and 0.55 (95% CI 0.53-0.57) for the SMOTE data and test data, respectively. Conclusions MLP and CNN showed improved, but limited, ability for predicting the postoperative serious complications after bariatric surgery in the Scandinavian Obesity Surgery Registry data. However, the overfitting issue is still apparent and needs to be overcome by incorporating intra- and perioperative information.

Download Full-text

A Deep Convolutional Neural Network Architecture for Cancer Diagnosis using Histopathological Images

International Journal of Innovative Technology and Exploring Engineering - Special Issue ◽

10.35940/ijitee.l9524.10101221 ◽

2021 ◽

Vol 10 (12) ◽

pp. 7-12

Author(s):

Karthika Gidijala ◽

◽

Mansa Devi Pappu ◽

Manasa Vavilapalli ◽

Mahesh Kothuru ◽

...

Keyword(s):

Breast Cancer ◽

Neural Network ◽

Neural Networks ◽

Decision Making ◽

Deep Learning ◽

Cancer Diagnosis ◽

Network Architecture ◽

Neural Network Architecture ◽

Proposed Model ◽

Histopathological Images

Many different models of Convolution Neural Networks exist in the Deep Learning studies. The application and prudence of the algorithms is known only when they are implemented with strong datasets. The histopathological images of breast cancer are considered as to have much number of haphazard structures and textures. Dealing with such images is a challenging issue in deep learning. Working on wet labs and in coherence to the results many research have blogged with novel annotations in the research. In this paper, we are presenting a model that can work efficiently on the raw images with different resolutions and alleviating with the problems of the presence of the structures and textures. The proposed model achieves considerably good results useful for decision making in cancer diagnosis.

Download Full-text

Towards mechanistic models of mutational effects: Deep Learning on Alzheimer's Aβ peptide

10.1101/2021.12.19.473403 ◽

2021 ◽

Author(s):

Bo Wang ◽

Eric R Gamazon

Keyword(s):

Neural Network ◽

Neural Networks ◽

Deep Learning ◽

High Performance ◽

Missing Values ◽

Molecular Mechanisms ◽

Health Care Systems ◽

Structural Features ◽

Design Data ◽

Protein Properties

Alzheimer's Disease (AD) is a debilitating form of dementia with a high prevalence in the global population and a large burden on the community and health care systems. AD's complex pathobiology consists of extracellular β-amyloid deposition and intracellular hyperphosphorylated tau. Comprehensive mutational analyses can generate a wealth of knowledge about protein properties and enable crucial insights into molecular mechanisms of disease. Deep Mutational Scanning (DMS) has enabled multiplexed measurement of mutational effects on protein properties, including kinematics and self-organization, with unprecedented resolution. However, potential bottlenecks of DMS characterization include experimental design, data quality, and the depth of mutational coverage. Here, we apply Deep Learning to comprehensively model the mutational effect of the AD-associated peptide Aβ42 on aggregation-related biochemical traits from DMS measurements. Among tested neural network architectures, Convolutional Neural Networks (ConvNets) and Recurrent Neural Networks (RNN) are found to be the most cost-effective models with robust high performance even under insufficiently-sampled DMS studies. While sequence features are essential for satisfactory prediction from neural networks, geometric-structural features further enhance the prediction performance. Notably, we demonstrate how mechanistic insights into phenotype may be extracted from the neural networks themselves suitably designed. This methodological benefit is particularly relevant for biochemical systems displaying a strong coupling between structure and phenotype such as the conformation of Aβ42 aggregate and nucleation, as shown here using a Graph Convolutional Neural Network (GCN) developed from the protein atomic structure input. In addition to accurate imputation of missing values (which ranged up to 55% of all phenotype values at key residues), the mutationally-defined nucleation phenotype generated from a GCN shows improved resolution for identifying known disease-causing mutations relative to the original DMS phenotype. Our study suggests that neural network derived sequence-phenotype mapping can be exploited not only to provide direct support for protein engineering or genome editing but also to facilitate therapeutic design with the gained perspectives from biological modeling.

Download Full-text

Toward Multi-FPGA Acceleration of the Neural Networks

ACM Journal on Emerging Technologies in Computing Systems ◽

10.1145/3432816 ◽

2021 ◽

Vol 17 (2) ◽

pp. 1-23

Author(s):

Saman Biookaghazadeh ◽

Pravin Kumar Ravi ◽

Ming Zhao

Keyword(s):

Neural Network ◽

Neural Networks ◽

Deep Learning ◽

High Performance ◽

Low Latency ◽

Fpga Design ◽

Area Efficiency ◽

Linear Speedup ◽

The Neural Networks ◽

Fpga Acceleration

High-throughput and low-latency Convolutional Neural Network (CNN) inference is increasingly important for many cloud- and edge-computing applications. FPGA-based acceleration of CNN inference has demonstrated various benefits compared to other high-performance devices such as GPGPUs. Current FPGA CNN-acceleration solutions are based on a single FPGA design, which are limited by the available resources on an FPGA. In addition, they can only accelerate conventional 2D neural networks. To address these limitations, we present a generic multi-FPGA solution, written in OpenCL, which can accelerate more complex CNNs (e.g., C3D CNN) and achieve a near linear speedup with respect to the available single-FPGA solutions. The design is built upon the Intel Deep Learning Accelerator architecture, with three extensions. First, it includes updates for better area efficiency (up to 25%) and higher performance (up to 24%). Second, it supports 3D convolutions for more challenging applications such as video learning. Third, it supports multi-FPGA communication for higher inference throughput. The results show that utilizing multiple FPGAs can linearly increase the overall bandwidth while maintaining the same end-to-end latency. In addition, the design can outperform other FPGA 2D accelerators by up to 8.4 times and 3D accelerators by up to 1.7 times.

Download Full-text

Aspects of programming for implementation of convolutional neural networks on multisystem HPC architectures

Journal of Physics Conference Series ◽

10.1088/1742-6596/2062/1/012016 ◽

2021 ◽

Vol 2062 (1) ◽

pp. 012016

Author(s):

Sunil Pandey ◽

Naresh Kumar Nagwani ◽

Shrish Verma

Keyword(s):

Neural Network ◽

Neural Networks ◽

Deep Learning ◽

Convolutional Neural Network ◽

High Performance Computing ◽

Convolutional Neural Networks ◽

High Performance ◽

Processing Unit ◽

Computational Performance ◽

Performance Computing

Abstract The training of deep learning convolutional neural networks is extremely compute intensive and takes long times for completion, on all except small datasets. This is a major limitation inhibiting the widespread adoption of convolutional neural networks in real world applications despite their better image classification performance in comparison with other techniques. Multidirectional research and development efforts are therefore being pursued with the objective of boosting the computational performance of convolutional neural networks. Development of parallel and scalable deep learning convolutional neural network implementations for multisystem high performance computing architectures is important in this background. Prior analysis based on computational experiments indicates that a combination of pipeline and task parallelism results in significant convolutional neural network performance gains of up to 18 times. This paper discusses the aspects which are important from the perspective of implementation of parallel and scalable convolutional neural networks on central processing unit based multisystem high performance computing architectures including computational pipelines, convolutional neural networks, convolutional neural network pipelines, multisystem high performance computing architectures and parallel programming models.

Download Full-text

Computational Complexity Reduction of Neural Networks of Brain Tumor Image Segmentation by Introducing Fermi–Dirac Correction Functions

Entropy ◽

10.3390/e23020223 ◽

2021 ◽

Vol 23 (2) ◽

pp. 223

Author(s):

Yen-Ling Tai ◽

Shin-Jhe Huang ◽

Chien-Chang Chen ◽

Henry Horng-Shing Lu

Keyword(s):

Neural Networks ◽

Deep Learning ◽

Computational Complexity ◽

High Performance ◽

Low Cost ◽

Structural Complexity ◽

Correction Function ◽

Computational Time ◽

Learning Methods ◽

Band Theory

Nowadays, deep learning methods with high structural complexity and flexibility inevitably lean on the computational capability of the hardware. A platform with high-performance GPUs and large amounts of memory could support neural networks having large numbers of layers and kernels. However, naively pursuing high-cost hardware would probably drag the technical development of deep learning methods. In the article, we thus establish a new preprocessing method to reduce the computational complexity of the neural networks. Inspired by the band theory of solids in physics, we map the image space into a noninteraction physical system isomorphically and then treat image voxels as particle-like clusters. Then, we reconstruct the Fermi–Dirac distribution to be a correction function for the normalization of the voxel intensity and as a filter of insignificant cluster components. The filtered clusters at the circumstance can delineate the morphological heterogeneity of the image voxels. We used the BraTS 2019 datasets and the dimensional fusion U-net for the algorithmic validation, and the proposed Fermi–Dirac correction function exhibited comparable performance to other employed preprocessing methods. By comparing to the conventional z-score normalization function and the Gamma correction function, the proposed algorithm can save at least 38% of computational time cost under a low-cost hardware architecture. Even though the correction function of global histogram equalization has the lowest computational time among the employed correction functions, the proposed Fermi–Dirac correction function exhibits better capabilities of image augmentation and segmentation.

Download Full-text

Convolutional Neural Network for the Semantic Segmentation of Remote Sensing Images

Mobile Networks and Applications ◽

10.1007/s11036-020-01703-3 ◽

2021 ◽

Vol 26 (1) ◽

pp. 200-215

Author(s):

Muhammad Alam ◽

Jian-Feng Wang ◽

Cong Guangpei ◽

LV Yunrong ◽

Yuanfang Chen

Keyword(s):

Neural Network ◽

Remote Sensing ◽

Neural Networks ◽

Image Processing ◽

Deep Learning ◽

Semantic Segmentation ◽

Natural Scene ◽

Remote Sensing Images ◽

Advantages And Disadvantages ◽

Target Segmentation

AbstractIn recent years, the success of deep learning in natural scene image processing boosted its application in the analysis of remote sensing images. In this paper, we applied Convolutional Neural Networks (CNN) on the semantic segmentation of remote sensing images. We improve the Encoder- Decoder CNN structure SegNet with index pooling and U-net to make them suitable for multi-targets semantic segmentation of remote sensing images. The results show that these two models have their own advantages and disadvantages on the segmentation of different objects. In addition, we propose an integrated algorithm that integrates these two models. Experimental results show that the presented integrated algorithm can exploite the advantages of both the models for multi-target segmentation and achieve a better segmentation compared to these two models.

Download Full-text