scholarly journals Coal-Rock Recognition in Top Coal Caving Using Bimodal Deep Learning and Hilbert-Huang Transform

2017 ◽  
Vol 2017 ◽  
pp. 1-13 ◽  
Author(s):  
Guoxin Zhang ◽  
Zengcai Wang ◽  
Lei Zhao ◽  
Yazhou Qi ◽  
Jinshan Wang
Keyword(s):  
Deep Learning ◽  
Transfer Learning ◽  
Acoustic Waves ◽  
Sound Pressure ◽  
Mechanical Vibration ◽  
Training Sample ◽  
Fine Tuning ◽  
Learning Method ◽  
Hilbert Huang Transform ◽  
Coal Rock

This study employs the mechanical vibration and acoustic waves of a hydraulic support tail beam for an accurate and fast coal-rock recognition. The study proposes a diagnosis method based on bimodal deep learning and Hilbert-Huang transform. The bimodal deep neural networks (DNN) adopt bimodal learning and transfer learning. The bimodal learning method attempts to learn joint representation by considering acceleration and sound pressure modalities, which both contribute to coal-rock recognition. The transfer learning method solves the problem regarding DNN, in which a large number of labeled training samples are necessary to optimize the parameters while the labeled training sample is limited. A suitable installation location for sensors is determined in recognizing coal-rock. The extraction features of acceleration and sound pressure signals are combined and effective combination features are selected. Bimodal DNN consists of two deep belief networks (DBN), each DBN model is trained with related samples, and the parameters of the pretrained DBNs are transferred to the final recognition model. Then the parameters of the proposed model are continuously optimized by pretraining and fine-tuning. Finally, the comparison of experimental results demonstrates the superiority of the proposed method in terms of recognition accuracy.

Data augmentation and transfer learning strategies for reaction prediction in low chemical data regimes

2021 ◽  
Author(s):  
Yun Zhang ◽  
Ling Wang ◽  
Xinqiao Wang ◽  
Chengyun Zhang ◽  
Jiamin Ge ◽  
...  
Keyword(s):  
Organic Chemistry ◽  
Deep Learning ◽  
Drug Discovery ◽  
Research And Development ◽  
Learning Strategies ◽  
Transfer Learning ◽  
Chemical Reactions ◽  
Data Augmentation ◽  
Learning Method ◽  
Reaction Prediction

An effective and rapid deep learning method to predict chemical reactions contributes to the research and development of organic chemistry and drug discovery.

scholarly journals Evaluation of Scalability and Degree of Fine-Tuning of Deep Convolutional Neural Networks for COVID-19 Screening on Chest X-ray Images Using Explainable Deep-Learning Algorithm

2020 ◽  
Vol 10 (4) ◽  
pp. 213 ◽  
Author(s):  
Ki-Sun Lee ◽  
Jae Young Kim ◽  
Eun-tae Jeon ◽  
Won Suk Choi ◽  
Nan Hee Kim ◽  
...  
Keyword(s):  
Deep Learning ◽  
Learning Strategies ◽  
Transfer Learning ◽  
Learning Algorithm ◽  
Fine Tuning ◽  
Deep Convolutional Neural Networks ◽  
X Ray ◽  
Backbone Network ◽  
Deep Learning Algorithm ◽  
Chest X Ray

According to recent studies, patients with COVID-19 have different feature characteristics on chest X-ray (CXR) than those with other lung diseases. This study aimed at evaluating the layer depths and degree of fine-tuning on transfer learning with a deep convolutional neural network (CNN)-based COVID-19 screening in CXR to identify efficient transfer learning strategies. The CXR images used in this study were collected from publicly available repositories, and the collected images were classified into three classes: COVID-19, pneumonia, and normal. To evaluate the effect of layer depths of the same CNN architecture, CNNs called VGG-16 and VGG-19 were used as backbone networks. Then, each backbone network was trained with different degrees of fine-tuning and comparatively evaluated. The experimental results showed the highest AUC value to be 0.950 concerning COVID-19 classification in the experimental group of a fine-tuned with only 2/5 blocks of the VGG16 backbone network. In conclusion, in the classification of medical images with a limited number of data, a deeper layer depth may not guarantee better results. In addition, even if the same pre-trained CNN architecture is used, an appropriate degree of fine-tuning can help to build an efficient deep learning model.

scholarly journals Deep Learning Approaches to Automated Video Classification of Upper Limb Tension Test

Healthcare ◽  
2021 ◽  
Vol 9 (11) ◽  
pp. 1579
Author(s):  
Wansuk Choi ◽  
Seoyoon Heo
Keyword(s):  
Deep Learning ◽  
Transfer Learning ◽  
High Performance ◽  
Model Fit ◽  
Fine Tuning ◽  
Learning Approaches ◽  
Video Classification ◽  
Video Clips ◽  
Performance Computing

The purpose of this study was to classify ULTT videos through transfer learning with pre-trained deep learning models and compare the performance of the models. We conducted transfer learning by combining a pre-trained convolution neural network (CNN) model into a Python-produced deep learning process. Videos were processed on YouTube and 103,116 frames converted from video clips were analyzed. In the modeling implementation, the process of importing the required modules, performing the necessary data preprocessing for training, defining the model, compiling, model creation, and model fit were applied in sequence. Comparative models were Xception, InceptionV3, DenseNet201, NASNetMobile, DenseNet121, VGG16, VGG19, and ResNet101, and fine tuning was performed. They were trained in a high-performance computing environment, and validation and loss were measured as comparative indicators of performance. Relatively low validation loss and high validation accuracy were obtained from Xception, InceptionV3, and DenseNet201 models, which is evaluated as an excellent model compared with other models. On the other hand, from VGG16, VGG19, and ResNet101, relatively high validation loss and low validation accuracy were obtained compared with other models. There was a narrow range of difference between the validation accuracy and the validation loss of the Xception, InceptionV3, and DensNet201 models. This study suggests that training applied with transfer learning can classify ULTT videos, and that there is a difference in performance between models.

scholarly journals Shedding Light on Microbial Dark Matter with A Universal Language of Life

2020 ◽  
Author(s):  
A Hoarfrost ◽  
A Aptekmann ◽  
G Farfañuk ◽  
Y Bromberg
Keyword(s):  
Dark Matter ◽  
Deep Learning ◽  
Open Source ◽  
Transfer Learning ◽  
Dna Sequences ◽  
Biological Data ◽  
Fine Tuning ◽  
Microbial Genomes ◽  
Universal Language ◽  
Reference Databases

AbstractThe majority of microbial genomes have yet to be cultured, and most proteins predicted from microbial genomes or sequenced from the environment cannot be functionally annotated. As a result, current computational approaches to describe microbial systems rely on incomplete reference databases that cannot adequately capture the full functional diversity of the microbial tree of life, limiting our ability to model high-level features of biological sequences. The scientific community needs a means to capture the functionally and evolutionarily relevant features underlying biology, independent of our incomplete reference databases. Such a model can form the basis for transfer learning tasks, enabling downstream applications in environmental microbiology, medicine, and bioengineering. Here we present LookingGlass, a deep learning model capturing a “universal language of life”. LookingGlass encodes contextually-aware, functionally and evolutionarily relevant representations of short DNA reads, distinguishing reads of disparate function, homology, and environmental origin. We demonstrate the ability of LookingGlass to be fine-tuned to perform a range of diverse tasks: to identify novel oxidoreductases, to predict enzyme optimal temperature, and to recognize the reading frames of DNA sequence fragments. LookingGlass is the first contextually-aware, general purpose pre-trained “biological language” representation model for short-read DNA sequences. LookingGlass enables functionally relevant representations of otherwise unknown and unannotated sequences, shedding light on the microbial dark matter that dominates life on Earth.AvailabilityThe pretrained LookingGlass model and the transfer learning-derived models demonstrated in this paper are available in the LookingGlass release v1.01. The open source fastBio Github repository and python package provides classes and functions for training and fine tuning deep learning models with biological data2. Code for reproducing analyses presented in this paper are available as an open source Github repository3.

scholarly journals Transfer learning using AlexNet Convolutional Neural Network for Face Recognition

2020 ◽  
Vol 9 (11) ◽  
pp. 285-294
Keyword(s):  
Neural Network ◽  
Face Recognition ◽  
Transfer Learning ◽  
Data Augmentation ◽  
Recognition System ◽  
Training Data ◽  
Fine Tuning ◽  
Data Sets ◽  
Learning Method ◽  
Face Recognition System

This research is aimed to achieve high-precision accuracy and for face recognition system. Convolution Neural Network is one of the Deep Learning approaches and has demonstrated excellent performance in many fields, including image recognition of a large amount of training data (such as ImageNet). In fact, hardware limitations and insufficient training data-sets are the challenges of getting high performance. Therefore, in this work the Deep Transfer Learning method using AlexNet pre-trained CNN is proposed to improve the performance of the face-recognition system even for a smaller number of images. The transfer learning method is used to fine-tuning on the last layer of AlexNet CNN model for new classification tasks. The data augmentation (DA) technique also proposed to minimize the over-fitting problem during Deep transfer learning training and to improve accuracy. The results proved the improvement in over-fitting and in performance after using the data augmentation technique. All the experiments were tested on UTeMFD, GTFD, and CASIA-Face V5 small data-sets. As a result, the proposed system achieved a high accuracy as 100% on UTeMFD, 96.67% on GTFD, and 95.60% on CASIA-Face V5 in less than 0.05 seconds of recognition time.

scholarly journals Deep learning prediction of mild cognitive impairment conversion to Alzheimer’s disease at 3 years after diagnosis using longitudinal and whole-brain 3D MRI

2021 ◽  
Vol 7 ◽  
pp. e560
Author(s):  
Ethan Ocasio ◽  
Tim Q. Duong
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Cognitive Impairment ◽  
Mild Cognitive Impairment ◽  
Longitudinal Data ◽  
Convolutional Neural Network ◽  
Transfer Learning ◽  
Fine Tuning ◽  
3D Mri ◽  
Whole Brain

Background While there is no cure for Alzheimer’s disease (AD), early diagnosis and accurate prognosis of AD may enable or encourage lifestyle changes, neurocognitive enrichment, and interventions to slow the rate of cognitive decline. The goal of our study was to develop and evaluate a novel deep learning algorithm to predict mild cognitive impairment (MCI) to AD conversion at three years after diagnosis using longitudinal and whole-brain 3D MRI. Methods This retrospective study consisted of 320 normal cognition (NC), 554 MCI, and 237 AD patients. Longitudinal data include T1-weighted 3D MRI obtained at initial presentation with diagnosis of MCI and at 12-month follow up. Whole-brain 3D MRI volumes were used without a priori segmentation of regional structural volumes or cortical thicknesses. MRIs of the AD and NC cohort were used to train a deep learning classification model to obtain weights to be applied via transfer learning for prediction of MCI patient conversion to AD at three years post-diagnosis. Two (zero-shot and fine tuning) transfer learning methods were evaluated. Three different convolutional neural network (CNN) architectures (sequential, residual bottleneck, and wide residual) were compared. Data were split into 75% and 25% for training and testing, respectively, with 4-fold cross validation. Prediction accuracy was evaluated using balanced accuracy. Heatmaps were generated. Results The sequential convolutional approach yielded slightly better performance than the residual-based architecture, the zero-shot transfer learning approach yielded better performance than fine tuning, and CNN using longitudinal data performed better than CNN using a single timepoint MRI in predicting MCI conversion to AD. The best CNN model for predicting MCI conversion to AD at three years after diagnosis yielded a balanced accuracy of 0.793. Heatmaps of the prediction model showed regions most relevant to the network including the lateral ventricles, periventricular white matter and cortical gray matter. Conclusions This is the first convolutional neural network model using longitudinal and whole-brain 3D MRIs without extracting regional brain volumes or cortical thicknesses to predict future MCI to AD conversion at 3 years after diagnosis. This approach could lead to early prediction of patients who are likely to progress to AD and thus may lead to better management of the disease.

scholarly journals Transfer Learning for Inference of Metastatic Origin from Whole Slide Histology

2021 ◽  
Author(s):  
Geoffrey F. Schau ◽  
Hassan Ghani ◽  
Erik A. Burlingame ◽  
Guillaume Thibault ◽  
Joe W. Gray ◽  
...  
Keyword(s):  
Deep Learning ◽  
Transfer Learning ◽  
Primary Tumor ◽  
Large Scale ◽  
Metastatic Cancer ◽  
Clinical Diagnostics ◽  
Training Data ◽  
Fine Tuning ◽  
Learning Approach ◽  
Whole Slide Images

AbstractAccurate diagnosis of metastatic cancer is essential for prescribing optimal control strategies to halt further spread of metastasizing disease. While pathological inspection aided by immunohistochemistry staining provides a valuable gold standard for clinical diagnostics, deep learning methods have emerged as powerful tools for identifying clinically relevant features of whole slide histology relevant to a tumor’s metastatic origin. Although deep learning models require significant training data to learn effectively, transfer learning paradigms provide mechanisms to circumvent limited training data by first training a model on related data prior to fine-tuning on smaller data sets of interest. In this work we propose a transfer learning approach that trains a convolutional neural network to infer the metastatic origin of tumor tissue from whole slide images of hematoxylin and eosin (H&E) stained tissue sections and illustrate the advantages of pre-training network on whole slide images of primary tumor morphology. We further characterize statistical dissimilarity between primary and metastatic tumors of various indications on patch-level images to highlight limitations of our indication-specific transfer learning approach. Using a primary-to-metastatic transfer learning approach, we achieved mean class-specific areas under receiver operator characteristics curve (AUROC) of 0.779, which outperformed comparable models trained on only images of primary tumor (mean AUROC of 0.691) or trained on only images of metastatic tumor (mean AUROC of 0.675), supporting the use of large scale primary tumor imaging data in developing computer vision models to characterize metastatic origin of tumor lesions.

scholarly journals Biologically-relevant transfer learning improves transcription factor binding prediction

2020 ◽  
Author(s):  
Gherman Novakovsky ◽  
Manu Saraswat ◽  
Oriol Fornes ◽  
Sara Mostafavi ◽  
Wyeth W. Wasserman
Keyword(s):  
Transcription Factor ◽  
Deep Learning ◽  
Transfer Learning ◽  
Model Performance ◽  
Fine Tuning ◽  
Binding Prediction ◽  
Single Task ◽  
Biologically Relevant ◽  
Powerful Technique ◽  
Task Model

AbstractBackgroundDeep learning has proven to be a powerful technique for transcription factor (TF) binding prediction, but requires large training datasets. Transfer learning can reduce the amount of data required for deep learning, while improving overall model performance, compared to training a separate model for each new task.ResultsWe assess a transfer learning strategy for TF binding prediction consisting of a pre-training step, wherein we train a multi-task model with multiple TFs, and a fine-tuning step, wherein we initialize single-task models for individual TFs with the weights learned by the multi-task model, after which the single-task models are trained at a lower learning rate. We corroborate that transfer learning improves model performance, especially if in the pre-training step the multi-task model is trained with biologically-relevant TFs. We show the effectiveness of transfer learning for TFs with ∼500 ChIP-seq peak regions. Using model interpretation techniques, we demonstrate that the features learned in the pre-training step are refined in the fine-tuning step to resemble the binding motif of the target TF (i.e. the recipient of transfer learning in the fine-tuning step). Moreover, pre-training with biologically-relevant TFs allows single-task models in the fine-tuning step to learn features other than the motif of the target TF.ConclusionsOur results confirm that transfer learning is a powerful technique for TF binding prediction.

TISSUE CLASSIFICATION FOR COLORECTAL CANCER UTILIZING TECHNIQUES OF DEEP LEARNING AND MACHINE LEARNING

2021 ◽  
pp. 2150022
Author(s):  
Kasikrit Damkliang ◽  
Thakerng Wongsirichot ◽  
Paramee Thongsuksai
Keyword(s):  
Colorectal Cancer ◽  
Machine Learning ◽  
Deep Learning ◽  
Transfer Learning ◽  
Texture Classification ◽  
False Positive Rate ◽  
Fine Tuning ◽  
Machine Learning Techniques ◽  
Cancer Tissues

Since the introduction of image pattern recognition and computer vision processing, the classification of cancer tissues has been a challenge at pixel-level, slide-level, and patient-level. Conventional machine learning techniques have given way to Deep Learning (DL), a contemporary, state-of-the-art approach to texture classification and localization of cancer tissues. Colorectal Cancer (CRC) is the third ranked cause of death from cancer worldwide. This paper proposes image-level texture classification of a CRC dataset by deep convolutional neural networks (CNN). Simple DL techniques consisting of transfer learning and fine-tuning were exploited. VGG-16, a Keras pre-trained model with initial weights by ImageNet, was applied. The transfer learning architecture and methods responding to VGG-16 are proposed. The training, validation, and testing sets included 5000 images of 150 × 150 pixels. The application set for detection and localization contained 10 large original images of 5000 × 5000 pixels. The model achieved F1-score and accuracy of 0.96 and 0.99, respectively, and produced a false positive rate of 0.01. AUC-based evaluation was also measured. The model classified ten large previously unseen images from the application set represented in false color maps. The reported results show the satisfactory performance of the model. The simplicity of the architecture, configuration, and implementation also contributes to the outcome this work.

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