scholarly journals Cohort selection for clinical trials using deep learning models

2019 ◽  
Vol 26 (11) ◽  
pp. 1181-1188 ◽  
Author(s):  
Isabel Segura-Bedmar ◽  
Pablo Raez
Keyword(s):  
Neural Network ◽  
Clinical Trials ◽  
Deep Learning ◽  
Statistical Significance ◽  
Hybrid Architecture ◽  
Cohort Selection ◽  
Selection For ◽  
Fully Connected ◽  
The Impact ◽  
Learning Architectures

Abstract Objective The goal of the 2018 n2c2 shared task on cohort selection for clinical trials (track 1) is to identify which patients meet the selection criteria for clinical trials. Cohort selection is a particularly demanding task to which natural language processing and deep learning can make a valuable contribution. Our goal is to evaluate several deep learning architectures to deal with this task. Materials and Methods Cohort selection can be formulated as a multilabeling problem whose goal is to determine which criteria are met for each patient record. We explore several deep learning architectures such as a simple convolutional neural network (CNN), a deep CNN, a recurrent neural network (RNN), and CNN-RNN hybrid architecture. Although our architectures are similar to those proposed in existing deep learning systems for text classification, our research also studies the impact of using a fully connected feedforward layer on the performance of these architectures. Results The RNN and hybrid models provide the best results, though without statistical significance. The use of the fully connected feedforward layer improves the results for all the architectures, except for the hybrid architecture. Conclusions Despite the limited size of the dataset, deep learning methods show promising results in learning useful features for the task of cohort selection. Therefore, they can be used as a previous filter for cohort selection for any clinical trial with a minimum of human intervention, thus reducing the cost and time of clinical trials significantly.

scholarly journals Cohort selection for clinical trials using hierarchical neural network

2019 ◽  
Vol 26 (11) ◽  
pp. 1203-1208 ◽  
Author(s):  
Ying Xiong ◽  
Xue Shi ◽  
Shuai Chen ◽  
Dehuan Jiang ◽  
Buzhou Tang ◽  
...  
Keyword(s):  
Neural Network ◽  
Clinical Trials ◽  
Language Processing ◽  
Short Term Memory ◽  
Imbalanced Data ◽  
Cohort Selection ◽  
Highway Network ◽  
Hierarchical Neural Network ◽  
Selection For ◽  
Fully Connected

Abstract Objective Cohort selection for clinical trials is a key step for clinical research. We proposed a hierarchical neural network to determine whether a patient satisfied selection criteria or not. Materials and Methods We designed a hierarchical neural network (denoted as CNN-Highway-LSTM or LSTM-Highway-LSTM) for the track 1 of the national natural language processing (NLP) clinical challenge (n2c2) on cohort selection for clinical trials in 2018. The neural network is composed of 5 components: (1) sentence representation using convolutional neural network (CNN) or long short-term memory (LSTM) network; (2) a highway network to adjust information flow; (3) a self-attention neural network to reweight sentences; (4) document representation using LSTM, which takes sentence representations in chronological order as input; (5) a fully connected neural network to determine whether each criterion is met or not. We compared the proposed method with its variants, including the methods only using the first component to represent documents directly and the fully connected neural network for classification (denoted as CNN-only or LSTM-only) and the methods without using the highway network (denoted as CNN-LSTM or LSTM-LSTM). The performance of all methods was measured by micro-averaged precision, recall, and F1 score. Results The micro-averaged F1 scores of CNN-only, LSTM-only, CNN-LSTM, LSTM-LSTM, CNN-Highway-LSTM, and LSTM-Highway-LSTM were 85.24%, 84.25%, 87.27%, 88.68%, 88.48%, and 90.21%, respectively. The highest micro-averaged F1 score is higher than our submitted 1 of 88.55%, which is 1 of the top-ranked results in the challenge. The results indicate that the proposed method is effective for cohort selection for clinical trials. Discussion Although the proposed method achieved promising results, some mistakes were caused by word ambiguity, negation, number analysis and incomplete dictionary. Moreover, imbalanced data was another challenge that needs to be tackled in the future. Conclusion In this article, we proposed a hierarchical neural network for cohort selection. Experimental results show that this method is good at selecting cohort.

scholarly journals COVID-19 detection using cough sound analysis and deep learning algorithms

2021 ◽  
pp. 1-11
Author(s):  
Sunil Rao ◽  
Vivek Narayanaswamy ◽  
Michael Esposito ◽  
Jayaraman J. Thiagarajan ◽  
Andreas Spanias
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Data Augmentation ◽  
Learning Algorithms ◽  
Audio Signal ◽  
Lottery Ticket ◽  
Non Invasive ◽  
Performance Gains ◽  
Fully Connected ◽  
The Impact

Reliable and rapid non-invasive testing has become essential for COVID-19 diagnosis and tracking statistics. Recent studies motivate the use of modern machine learning (ML) and deep learning (DL) tools that utilize features of coughing sounds for COVID-19 diagnosis. In this paper, we describe system designs that we developed for COVID-19 cough detection with the long-term objective of embedding them in a testing device. More specifically, we use log-mel spectrogram features extracted from the coughing audio signal and design a series of customized deep learning algorithms to develop fast and automated diagnosis tools for COVID-19 detection. We first explore the use of a deep neural network with fully connected layers. Additionally, we investigate prospects of efficient implementation by examining the impact on the detection performance by pruning the fully connected neural network based on the Lottery Ticket Hypothesis (LTH) optimization process. In general, pruned neural networks have been shown to provide similar performance gains to that of unpruned networks with reduced computational complexity in a variety of signal processing applications. Finally, we investigate the use of convolutional neural network architectures and in particular the VGG-13 architecture which we tune specifically for this application. Our results show that a unique ensembling of the VGG-13 architecture trained using a combination of binary cross entropy and focal losses with data augmentation significantly outperforms the fully connected networks and other recently proposed baselines on the DiCOVA 2021 COVID-19 cough audio dataset. Our customized VGG-13 model achieves an average validation AUROC of 82.23% and a test AUROC of 78.3% at a sensitivity of 80.49%.

scholarly journals Audio-Based Drone Detection and Identification Using Deep Learning Techniques with Dataset Enhancement through Generative Adversarial Networks

Sensors ◽  
2021 ◽  
Vol 21 (15) ◽  
pp. 4953
Author(s):  
Sara Al-Emadi ◽  
Abdulla Al-Ali ◽  
Abdulaziz Al-Ali
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Recurrent Neural Network ◽  
Learning Algorithms ◽  
Generative Adversarial Networks ◽  
Generative Adversarial Network ◽  
Adversarial Networks ◽  
Detection And Identification ◽  
Learning Techniques ◽  
The Impact

Drones are becoming increasingly popular not only for recreational purposes but in day-to-day applications in engineering, medicine, logistics, security and others. In addition to their useful applications, an alarming concern in regard to the physical infrastructure security, safety and privacy has arisen due to the potential of their use in malicious activities. To address this problem, we propose a novel solution that automates the drone detection and identification processes using a drone’s acoustic features with different deep learning algorithms. However, the lack of acoustic drone datasets hinders the ability to implement an effective solution. In this paper, we aim to fill this gap by introducing a hybrid drone acoustic dataset composed of recorded drone audio clips and artificially generated drone audio samples using a state-of-the-art deep learning technique known as the Generative Adversarial Network. Furthermore, we examine the effectiveness of using drone audio with different deep learning algorithms, namely, the Convolutional Neural Network, the Recurrent Neural Network and the Convolutional Recurrent Neural Network in drone detection and identification. Moreover, we investigate the impact of our proposed hybrid dataset in drone detection. Our findings prove the advantage of using deep learning techniques for drone detection and identification while confirming our hypothesis on the benefits of using the Generative Adversarial Networks to generate real-like drone audio clips with an aim of enhancing the detection of new and unfamiliar drones.

scholarly journals Deep Learning for Caries Detection and Classification

Diagnostics ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1672
Author(s):  
Luya Lian ◽  
Tianer Zhu ◽  
Fudong Zhu ◽  
Haihua Zhu
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Disease Diagnosis ◽  
Validation Dataset ◽  
Reference Dataset ◽  
Dice Coefficient ◽  
Learning Methods ◽  
Test Dataset ◽  
The Impact ◽  
Caries Lesions

Objectives: Deep learning methods have achieved impressive diagnostic performance in the field of radiology. The current study aimed to use deep learning methods to detect caries lesions, classify different radiographic extensions on panoramic films, and compare the classification results with those of expert dentists. Methods: A total of 1160 dental panoramic films were evaluated by three expert dentists. All caries lesions in the films were marked with circles, whose combination was defined as the reference dataset. A training and validation dataset (1071) and a test dataset (89) were then established from the reference dataset. A convolutional neural network, called nnU-Net, was applied to detect caries lesions, and DenseNet121 was applied to classify the lesions according to their depths (dentin lesions in the outer, middle, or inner third D1/2/3 of dentin). The performance of the test dataset in the trained nnU-Net and DenseNet121 models was compared with the results of six expert dentists in terms of the intersection over union (IoU), Dice coefficient, accuracy, precision, recall, negative predictive value (NPV), and F1-score metrics. Results: nnU-Net yielded caries lesion segmentation IoU and Dice coefficient values of 0.785 and 0.663, respectively, and the accuracy and recall rate of nnU-Net were 0.986 and 0.821, respectively. The results of the expert dentists and the neural network were shown to be no different in terms of accuracy, precision, recall, NPV, and F1-score. For caries depth classification, DenseNet121 showed an overall accuracy of 0.957 for D1 lesions, 0.832 for D2 lesions, and 0.863 for D3 lesions. The recall results of the D1/D2/D3 lesions were 0.765, 0.652, and 0.918, respectively. All metric values, including accuracy, precision, recall, NPV, and F1-score values, were proven to be no different from those of the experienced dentists. Conclusion: In detecting and classifying caries lesions on dental panoramic radiographs, the performance of deep learning methods was similar to that of expert dentists. The impact of applying these well-trained neural networks for disease diagnosis and treatment decision making should be explored.

scholarly journals KLASIFIKASI BATIK RIAU DENGAN MENGGUNAKAN CONVOLUTIONAL NEURAL NETWORKS (CNN)

2020 ◽  
Vol 9 (1) ◽  
pp. 7-10
Author(s):  
Hendry Fonda
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Artificial Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
18Th Century ◽  
The Public ◽  
Artificial Neural ◽  
The Difference ◽  
Fully Connected

ABSTRACT Riau batik is known since the 18th century and is used by royal kings. Riau Batik is made by using a stamp that is mixed with coloring and then printed on fabric. The fabric used is usually silk. As its development, comparing Javanese  batik with riau batik Riau is very slowly accepted by the public. Convolutional Neural Networks (CNN) is a combination of artificial neural networks and deeplearning methods. CNN consists of one or more convolutional layers, often with a subsampling layer followed by one or more fully connected layers as a standard neural network. In the process, CNN will conduct training and testing of Riau batik so that a collection of batik models that have been classified based on the characteristics that exist in Riau batik can be determined so that images are Riau batik and non-Riau batik. Classification using CNN produces Riau batik and not Riau batik with an accuracy of 65%. Accuracy of 65% is due to basically many of the same motifs between batik and other batik with the difference lies in the color of the absorption in the batik riau. Kata kunci: Batik; Batik Riau; CNN; Image; Deep Learning   ABSTRAK   Batik Riau dikenal sejak abad ke 18 dan digunakan oleh bangsawan raja. Batik Riau dibuat dengan menggunakan cap yang dicampur dengan pewarna kemudian dicetak di kain. Kain yang digunakan biasanya sutra. Seiring perkembangannya, dibandingkan batik Jawa maka batik Riau sangat lambat diterima oleh masyarakat. Convolutional Neural Networks (CNN) merupakan kombinasi dari jaringan syaraf tiruan dan metode deeplearning. CNN terdiri dari satu atau lebih lapisan konvolutional, seringnya dengan suatu lapisan subsampling yang diikuti oleh satu atau lebih lapisan yang terhubung penuh sebagai standar jaringan syaraf. Dalam prosesnya CNN akan melakukan training dan testing terhadap batik Riau sehingga didapat kumpulan model batik yang telah terklasi    fikasi berdasarkan ciri khas yang ada pada batik Riau sehingga dapat ditentukan gambar (image) yang merupakan batik Riau dan yang bukan merupakan batik Riau. Klasifikasi menggunakan CNN menghasilkan batik riau dan bukan batik riau dengan akurasi 65%. Akurasi 65% disebabkan pada dasarnya banyak motif yang sama antara batik riau dengan batik lainnya dengan perbedaan terletak pada warna cerap pada batik riau. Kata kunci: Batik; Batik Riau; CNN; Image; Deep Learning

scholarly journals Encoding Health Records into Pathway Representations for Deep Learning

2021 ◽  
Author(s):  
Marco Luca Sbodio ◽  
Natasha Mulligan ◽  
Stefanie Speichert ◽  
Vanessa Lopez ◽  
Joao Bettencourt-Silva
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Deep Learning ◽  
Source Code ◽  
Training Dataset ◽  
Health Records ◽  
Learning Tasks ◽  
Patient Pathways ◽  
Computational Resources ◽  
The Impact

There is a growing trend in building deep learning patient representations from health records to obtain a comprehensive view of a patient’s data for machine learning tasks. This paper proposes a reproducible approach to generate patient pathways from health records and to transform them into a machine-processable image-like structure useful for deep learning tasks. Based on this approach, we generated over a million pathways from FAIR synthetic health records and used them to train a convolutional neural network. Our initial experiments show the accuracy of the CNN on a prediction task is comparable or better than other autoencoders trained on the same data, while requiring significantly less computational resources for training. We also assess the impact of the size of the training dataset on autoencoders performances. The source code for generating pathways from health records is provided as open source.

Combination of Recurrent Neural Network and Deep Learning for Robot Navigation Task in Off-Road Environment

Robotica ◽  
2019 ◽  
Vol 38 (8) ◽  
pp. 1450-1462
Author(s):  
Farinaz Alamiyan-Harandi ◽  
Vali Derhami ◽  
Fatemeh Jamshidi
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Recurrent Neural Network ◽  
Robot Navigation ◽  
Recurrent Network ◽  
Navigation Task ◽  
Sensory Data ◽  
Uneven Terrain ◽  
Target Network ◽  
Fully Connected

SUMMARYThis paper tackles the challenge of the necessity of using the sequence of past environment states as the controller’s inputs in a vision-based robot navigation task. In this task, a robot has to follow a given trajectory without falling in pits and missing its balance in uneven terrain, when the only sensory input is the raw image captured by a camera. The robot should distinguish big pits from small holes to decide between avoiding and passing over. In non-Markov processes such as the abovementioned task, the decision is done using past sensory data to ensure admissible performance. Applying images as sensory inputs naturally causes the curse of dimensionality difficulty. On the other hand, using sequences of past images intensifies this difficulty. In this paper, a new framework called recurrent deep learning (RDL) with combination of deep learning (DL) and recurrent neural network is proposed to cope with the above challenge. At first, the proper features are extracted from the raw image using DL. Then, these represented features plus some expert-defined features are used as the inputs of a fully connected recurrent network (as target network) to generate command control of the robot. To evaluate the proposed RDL framework, some experiments are established on WEBOTS and MATLAB co-simulation platform. The simulation results demonstrate the proposed framework outperforms the conventional controller based on DL for the navigation task in the uneven terrains.

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