scholarly journals RIM-ONE DL: A Unified Retinal Image Database for Assessing Glaucoma Using Deep Learning

2020 ◽  
Vol 39 (3) ◽  
pp. 161-167
Author(s):  
Francisco José Fumero Batista ◽  
Tinguaro Diaz-Aleman ◽  
Jose Sigut ◽  
Silvia Alayon ◽  
Rafael Arnay ◽  
...  
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Optic Nerve ◽  
Retinal Image ◽  
Image Database ◽  
Normal Subjects ◽  
Manual Segmentation ◽  
Learning Models ◽  
Improper Use ◽  
Reference Images

The first version of the Retinal IMage database for Optic Nerve Evaluation (RIM-ONE) was published in 2011. This was followed by two more, turning it into one of the most cited public retinography databases for evaluating glaucoma. Although it was initially intended to be a database with reference images for segmenting the optic disc, in recent years we have observed that its use has been more oriented toward training and testing deep learning models. The recent REFUGE challenge laid out some criteria that a set of images of these characteristics must satisfy to be used as a standard reference for validating deep learning methods that rely on the use of these data. This, combined with the certain confusion and even improper use observed in some cases of the three versions published, led us to consider revising and combining them into a new, publicly available version called RIM-ONE DL (RIM-ONE for Deep Learning). This paper describes this set of images, consisting of 313 retinographies from normal subjects and 172 retinographies from patients with glaucoma. All of these images have been assessed by two experts and include a manual segmentation of the disc and cup. It also describes an evaluation benchmark with different models of well-known convolutional neural networks.

Levenshtein Augmentation Improves Performance of SMILES Based Deep-Learning Synthesis Prediction

2020 ◽  
Author(s):  
Dean Sumner ◽  
Jiazhen He ◽  
Amol Thakkar ◽  
Ola Engkvist ◽  
Esben Jannik Bjerrum
Keyword(s):  
Neural Networks ◽  
Pattern Recognition ◽  
Deep Learning ◽  
Recurrent Neural Networks ◽  
Data Augmentation ◽  
State Of The Art ◽  
Sequence Similarity ◽  
Learning Models ◽  
Underlying Network

<p>SMILES randomization, a form of data augmentation, has previously been shown to increase the performance of deep learning models compared to non-augmented baselines. Here, we propose a novel data augmentation method we call “Levenshtein augmentation” which considers local SMILES sub-sequence similarity between reactants and their respective products when creating training pairs. The performance of Levenshtein augmentation was tested using two state of the art models - transformer and sequence-to-sequence based recurrent neural networks with attention. Levenshtein augmentation demonstrated an increase performance over non-augmented, and conventionally SMILES randomization augmented data when used for training of baseline models. Furthermore, Levenshtein augmentation seemingly results in what we define as <i>attentional gain </i>– an enhancement in the pattern recognition capabilities of the underlying network to molecular motifs.</p>

scholarly journals Fully Automated Colorimetric Analysis of the Optic Nerve Aided by Deep Learning and Its Association with Perimetry and OCT for the Study of Glaucoma

2021 ◽  
Vol 10 (15) ◽  
pp. 3231
Author(s):  
Marta Gonzalez-Hernandez ◽  
Daniel Gonzalez-Hernandez ◽  
Daniel Perez-Barbudo ◽  
Paloma Rodriguez-Esteve ◽  
Nisamar Betancor-Caro ◽  
...  
Keyword(s):  
Distribution Function ◽  
Deep Learning ◽  
Optic Nerve ◽  
Roc Analysis ◽  
Operating Characteristic ◽  
Learning Models ◽  
Colorimetric Analysis ◽  
Cirrus Oct ◽  
And Function ◽  
Usual Pattern

Background: Laguna-ONhE is an application for the colorimetric analysis of optic nerve images, which topographically assesses the cup and the presence of haemoglobin. Its latest version has been fully automated with five deep learning models. In this paper, perimetry in combination with Laguna-ONhE or Cirrus-OCT was evaluated. Methods: The morphology and perfusion estimated by Laguna ONhE were compiled into a “Globin Distribution Function” (GDF). Visual field irregularity was measured with the usual pattern standard deviation (PSD) and the threshold coefficient of variation (TCV), which analyses its harmony without taking into account age-corrected values. In total, 477 normal eyes, 235 confirmed, and 98 suspected glaucoma cases were examined with Cirrus-OCT and different fundus cameras and perimeters. Results: The best Receiver Operating Characteristic (ROC) analysis results for confirmed and suspected glaucoma were obtained with the combination of GDF and TCV (AUC: 0.995 and 0.935, respectively. Sensitivities: 94.5% and 45.9%, respectively, for 99% specificity). The best combination of OCT and perimetry was obtained with the vertical cup/disc ratio and PSD (AUC: 0.988 and 0.847, respectively. Sensitivities: 84.7% and 18.4%, respectively, for 99% specificity). Conclusion: Using Laguna ONhE, morphology, perfusion, and function can be mutually enhanced with the methods described for the purpose of glaucoma assessment, providing early sensitivity.

scholarly journals Deep Malaria Parasite Detection in Thin Blood Smear Microscopic Images

2021 ◽  
Vol 11 (5) ◽  
pp. 2284
Author(s):  
Asma Maqsood ◽  
Muhammad Shahid Farid ◽  
Muhammad Hassan Khan ◽  
Marcin Grzegorzek
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Red Blood Cells ◽  
Convolutional Neural Networks ◽  
Blood Cells ◽  
Superior Performance ◽  
Learning Models ◽  
Infected Female ◽  
The World ◽  
Augmentation Techniques

Malaria is a disease activated by a type of microscopic parasite transmitted from infected female mosquito bites to humans. Malaria is a fatal disease that is endemic in many regions of the world. Quick diagnosis of this disease will be very valuable for patients, as traditional methods require tedious work for its detection. Recently, some automated methods have been proposed that exploit hand-crafted feature extraction techniques however, their accuracies are not reliable. Deep learning approaches modernize the world with their superior performance. Convolutional Neural Networks (CNN) are vastly scalable for image classification tasks that extract features through hidden layers of the model without any handcrafting. The detection of malaria-infected red blood cells from segmented microscopic blood images using convolutional neural networks can assist in quick diagnosis, and this will be useful for regions with fewer healthcare experts. The contributions of this paper are two-fold. First, we evaluate the performance of different existing deep learning models for efficient malaria detection. Second, we propose a customized CNN model that outperforms all observed deep learning models. It exploits the bilateral filtering and image augmentation techniques for highlighting features of red blood cells before training the model. Due to image augmentation techniques, the customized CNN model is generalized and avoids over-fitting. All experimental evaluations are performed on the benchmark NIH Malaria Dataset, and the results reveal that the proposed algorithm is 96.82% accurate in detecting malaria from the microscopic blood smears.

Train Deep Learning Models using subsurface geological images datasets

2021 ◽  
Author(s):  
Ramy Abdallah ◽  
Clare E. Bond ◽  
Robert W.H. Butler
Keyword(s):  
Artificial Intelligence ◽  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Learning Models ◽  
Structural Interpretation ◽  
Performance Accuracy ◽  
Learning Techniques ◽  
Machine Learning Models

&lt;p&gt;Machine learning is being presented as a new solution for a wide range of geoscience problems. Primarily machine learning has been used for 3D seismic data processing, seismic facies analysis and well log data correlation. The rapid development in technology with open-source artificial intelligence libraries and the accessibility of affordable computer graphics processing units (GPU) makes the application of machine learning in geosciences increasingly tractable. However, the application of artificial intelligence in structural interpretation workflows of subsurface datasets is still ambiguous. This study aims to use machine learning techniques to classify images of folds and fold-thrust structures. Here we show that convolutional neural networks (CNNs) as supervised deep learning techniques provide excellent algorithms to discriminate between geological image datasets. Four different datasets of images have been used to train and test the machine learning models. These four datasets are a seismic character dataset with five classes (faults, folds, salt, flat layers and basement), folds types with three classes (buckle, chevron and conjugate), fault types with three classes (normal, reverse and thrust) and fold-thrust geometries with three classes (fault bend fold, fault propagation fold and detachment fold). These image datasets are used to investigate three machine learning models. One Feedforward linear neural network model and two convolutional neural networks models (Convolution 2d layer transforms sequential model and Residual block model (ResNet with 9, 34, and 50 layers)). Validation and testing datasets forms a critical part of testing the model&amp;#8217;s performance accuracy. The ResNet model records the highest performance accuracy score, of the machine learning models tested. Our CNN image classification model analysis provides a framework for applying machine learning to increase structural interpretation efficiency, and shows that CNN classification models can be applied effectively to geoscience problems. The study provides a starting point to apply unsupervised machine learning approaches to sub-surface structural interpretation workflows.&lt;/p&gt;

A Review of Recent Deep Learning Models in COVID-19 Diagnosis

2021 ◽  
Vol 6 (5) ◽  
pp. 10-15
Author(s):  
Ela Bhattacharya ◽  
D. Bhattacharya
Keyword(s):  
Artificial Intelligence ◽  
Neural Networks ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
Test Results ◽  
Learning Models ◽  
Future Directions ◽  
Human Contact ◽  
The World ◽  
Short Span

COVID-19 has emerged as the latest worrisome pandemic, which is reported to have its outbreak in Wuhan, China. The infection spreads by means of human contact, as a result, it has caused massive infections across 200 countries around the world. Artificial intelligence has likewise contributed to managing the COVID-19 pandemic in various aspects within a short span of time. Deep Neural Networks that are explored in this paper have contributed to the detection of COVID-19 from imaging sources. The datasets, pre-processing, segmentation, feature extraction, classification and test results which can be useful for discovering future directions in the domain of automatic diagnosis of the disease, utilizing artificial intelligence-based frameworks, have been investigated in this paper.

scholarly journals An Investigation of Deep Learning Models for EEG-Based Emotion Recognition

2020 ◽  
Vol 14 ◽  
Author(s):  
Yaqing Zhang ◽  
Jinling Chen ◽  
Jen Hong Tan ◽  
Yuxuan Chen ◽  
Yunyi Chen ◽  
...  
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Emotion Recognition ◽  
Real Life ◽  
Learning Rate ◽  
Learning Models ◽  
Learning Methods ◽  
Time Frequency ◽  
Comparison Results

Emotion is the human brain reacting to objective things. In real life, human emotions are complex and changeable, so research into emotion recognition is of great significance in real life applications. Recently, many deep learning and machine learning methods have been widely applied in emotion recognition based on EEG signals. However, the traditional machine learning method has a major disadvantage in that the feature extraction process is usually cumbersome, which relies heavily on human experts. Then, end-to-end deep learning methods emerged as an effective method to address this disadvantage with the help of raw signal features and time-frequency spectrums. Here, we investigated the application of several deep learning models to the research field of EEG-based emotion recognition, including deep neural networks (DNN), convolutional neural networks (CNN), long short-term memory (LSTM), and a hybrid model of CNN and LSTM (CNN-LSTM). The experiments were carried on the well-known DEAP dataset. Experimental results show that the CNN and CNN-LSTM models had high classification performance in EEG-based emotion recognition, and their accurate extraction rate of RAW data reached 90.12 and 94.17%, respectively. The performance of the DNN model was not as accurate as other models, but the training speed was fast. The LSTM model was not as stable as the CNN and CNN-LSTM models. Moreover, with the same number of parameters, the training speed of the LSTM was much slower and it was difficult to achieve convergence. Additional parameter comparison experiments with other models, including epoch, learning rate, and dropout probability, were also conducted in the paper. Comparison results prove that the DNN model converged to optimal with fewer epochs and a higher learning rate. In contrast, the CNN model needed more epochs to learn. As for dropout probability, reducing the parameters by ~50% each time was appropriate.

scholarly journals Winter Wheat Yield Prediction Using Convolutional Neural Networks from Environmental and Phenological Data

2021 ◽  
Author(s):  
Amit Kumar Srivast ◽  
Nima Safaei ◽  
Saeed Khaki ◽  
Gina Lopez ◽  
Wenzhi Zeng ◽  
...  
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Winter Wheat ◽  
Crop Yield ◽  
Wheat Yield ◽  
Yield Prediction ◽  
Learning Models ◽  
Winter Wheat Yield ◽  
Machine Learning Models

Abstract Crop yield forecasting depends on many interactive factors including crop genotype, weather, soil, and management practices. This study analyzes the performance of machine learning and deep learning methods for winter wheat yield prediction using extensive datasets of weather, soil, and crop phenology. We propose a convolutional neural network (CNN) which uses the 1-dimentional convolution operation to capture the time dependencies of environmental variables. The proposed CNN, evaluated along with other machine learning models for winter wheat yield prediction in Germany, outperformed all other models tested. To address the seasonality, weekly features were used that explicitly take soil moisture and meteorological events into account. Our results indicated that nonlinear models such as deep learning models and XGboost are more effective in finding the functional relationship between the crop yield and input data compared to linear models and deep neural networks had a higher prediction accuracy than XGboost. One of the main limitations of machine learning models is their black box property. Therefore, we moved beyond prediction and performed feature selection, as it provides key results towards explaining yield prediction (variable importance by time). As such, our study indicates which variables have the most significant effect on winter wheat yield.

scholarly journals Inference of Brain States under Anesthesia with Meta Learning Based Deep Learning Models

2021 ◽  
Author(s):  
Qihang Wang ◽  
Feng Liu ◽  
Guihong Wan ◽  
Ying Chen
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Short Term Memory ◽  
Signal To Noise Ratio ◽  
General Anesthetics ◽  
Learning Models ◽  
Multi Stage ◽  
Meta Learning ◽  
Brain States ◽  
High Level

AbstractMonitoring the depth of unconsciousness during anesthesia is useful in both clinical settings and neuroscience investigations to understand brain mechanisms. Electroencephalogram (EEG) has been used as an objective means of characterizing brain altered arousal and/or cognition states induced by anesthetics in real-time. Different general anesthetics affect cerebral electrical activities in different ways. However, the performance of conventional machine learning models on EEG data is unsatisfactory due to the low Signal to Noise Ratio (SNR) in the EEG signals, especially in the office-based anesthesia EEG setting. Deep learning models have been used widely in the field of Brain Computer Interface (BCI) to perform classification and pattern recognition tasks due to their capability of good generalization and handling noises. Compared to other BCI applications, where deep learning has demonstrated encouraging results, the deep learning approach for classifying different brain consciousness states under anesthesia has been much less investigated. In this paper, we propose a new framework based on meta-learning using deep neural networks, named Anes-MetaNet, to classify brain states under anesthetics. The Anes-MetaNet is composed of Convolutional Neural Networks (CNN) to extract power spectrum features, and a time consequence model based on Long Short-Term Memory (LSTM) Networks to capture the temporal dependencies, and a meta-learning framework to handle large cross-subject variability. We used a multi-stage training paradigm to improve the performance, which is justified by visualizing the high-level feature mapping. Experiments on the office-based anesthesia EEG dataset demonstrate the effectiveness of our proposed Anes-MetaNet by comparison of existing methods.

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