scholarly journals Predicting the Computational Cost of Deep Learning Models

2018 ◽  
Author(s):  
Daniel Justus ◽  
John Brennan ◽  
Stephen Bonner ◽  
Andrew Stephen McGough
Keyword(s):  
Deep Learning ◽  
Computational Cost ◽  
Learning Models

scholarly journals U-Net Model for Brain Extraction on Non-human Primates

2020 ◽  
Author(s):  
Xindi Wang ◽  
Xin-Hui Li ◽  
Jae Wook Cho ◽  
Brian Russ ◽  
Nanditha Rajamani ◽  
...  
Keyword(s):  
Deep Learning ◽  
Transfer Learning ◽  
Data Exchange ◽  
Computational Cost ◽  
Training Sample ◽  
Learning Models ◽  
Model Code ◽  
Minimal Sample ◽  
Brain Extraction ◽  
Skull Stripping

AbstractBrain extraction (a.k.a. skull stripping) is a fundamental step in the neuroimaging pipeline as it can affect the accuracy of downstream preprocess such as image registration, tissue classification, etc. Most brain extraction tools have been mainly orientated for human data and are often challenging for non-human primates (NHP). In recent attempts to improve the performance in NHP, deep learning models appear to outperform the traditional tools. However, given the minimal sample size of most NHP studies and notable variations in data quality, the deep learning models are very rarely applied in multi-site samples in NHP imaging. To overcome this challenge, we propose to use transfer-learning framework that leverages a large human imaging dataset to pretrain a convolutional neural network (i.e. U-Net Model), and then transferred to NHP data using a small NHP training sample. The resulting transfer-learning model converged faster and achieved more accurate performance than a similar U-Net Model trained exclusively on NHP samples. We improved the generalizability of the model by upgrading the transfer-learned model using additional training datasets from multiple research sites in the Primate Data-Exchange (PRIME-DE) consortium. Our final model outperformed brain extraction routines from popular MRI packages (AFNI, FSL, and FreeSurfer) across multiple heterogeneous multiple sites from PRIME-DE with less computational cost (20s~10min). Our model, code, and the skull-stripped mask repository of 136 macaque monkeys are publicly available for unrestricted use by the neuroimaging community at https://github.com/HumanBrainED/NHP-BrainExtraction.

scholarly journals Multi-Modal Evolutionary Deep Learning Model for Ovarian Cancer Diagnosis

Symmetry ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 643
Author(s):  
Rania M. Ghoniem ◽  
Abeer D. Algarni ◽  
Basel Refky ◽  
Ahmed A. Ewees
Keyword(s):  
Ovarian Cancer ◽  
Deep Learning ◽  
Short Term Memory ◽  
Computational Cost ◽  
Learning Model ◽  
Learning Models ◽  
Lung Cancers ◽  
Proposed Model ◽  
Linear Aggregation ◽  
Deep Learning Model

Ovarian cancer (OC) is a common reason for mortality among women. Deep learning has recently proven better performance in predicting OC stages and subtypes. However, most of the state-of-the-art deep learning models employ single modality data, which may afford low-level performance due to insufficient representation of important OC characteristics. Furthermore, these deep learning models still lack to the optimization of the model construction, which requires high computational cost to train and deploy them. In this work, a hybrid evolutionary deep learning model, using multi-modal data, is proposed. The established multi-modal fusion framework amalgamates gene modality alongside with histopathological image modality. Based on the different states and forms of each modality, we set up deep feature extraction network, respectively. This includes a predictive antlion-optimized long-short-term-memory model to process gene longitudinal data. Another predictive antlion-optimized convolutional neural network model is included to process histopathology images. The topology of each customized feature network is automatically set by the antlion optimization algorithm to make it realize better performance. After that the output from the two improved networks is fused based upon weighted linear aggregation. The deep fused features are finally used to predict OC stage. A number of assessment indicators was used to compare the proposed model to other nine multi-modal fusion models constructed using distinct evolutionary algorithms. This was conducted using a benchmark for OC and two benchmarks for breast and lung cancers. The results reveal that the proposed model is more precise and accurate in diagnosing OC and the other cancers.

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>

Improving the Accuracy of Protein-Ligand Binding Affinity Prediction by Deep Learning Models: Benchmark and Model

2019 ◽  
Author(s):  
Mohammad Rezaei ◽  
Yanjun Li ◽  
Xiaolin Li ◽  
Chenglong Li
Keyword(s):  
Deep Learning ◽  
Drug Design ◽  
Binding Affinity ◽  
Benchmark Dataset ◽  
Rational Drug Design ◽  
Learning Models ◽  
Structure Based Drug Design ◽  
Binding Affinity Prediction ◽  
Affinity Prediction ◽  
Rational Drug

<b>Introduction:</b> The ability to discriminate among ligands binding to the same protein target in terms of their relative binding affinity lies at the heart of structure-based drug design. Any improvement in the accuracy and reliability of binding affinity prediction methods decreases the discrepancy between experimental and computational results.<br><b>Objectives:</b> The primary objectives were to find the most relevant features affecting binding affinity prediction, least use of manual feature engineering, and improving the reliability of binding affinity prediction using efficient deep learning models by tuning the model hyperparameters.<br><b>Methods:</b> The binding site of target proteins was represented as a grid box around their bound ligand. Both binary and distance-dependent occupancies were examined for how an atom affects its neighbor voxels in this grid. A combination of different features including ANOLEA, ligand elements, and Arpeggio atom types were used to represent the input. An efficient convolutional neural network (CNN) architecture, DeepAtom, was developed, trained and tested on the PDBbind v2016 dataset. Additionally an extended benchmark dataset was compiled to train and evaluate the models.<br><b>Results: </b>The best DeepAtom model showed an improved accuracy in the binding affinity prediction on PDBbind core subset (Pearson’s R=0.83) and is better than the recent state-of-the-art models in this field. In addition when the DeepAtom model was trained on our proposed benchmark dataset, it yields higher correlation compared to the baseline which confirms the value of our model.<br><b>Conclusions:</b> The promising results for the predicted binding affinities is expected to pave the way for embedding deep learning models in virtual screening and rational drug design fields.

Data science in economics: comprehensive review of advanced machine learning and deep learning methods

2020 ◽  
Author(s):  
Saeed Nosratabadi ◽  
Amir Mosavi ◽  
Puhong Duan ◽  
Pedram Ghamisi ◽  
Ferdinand Filip ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Data Science ◽  
State Of The Art ◽  
Science Methods ◽  
Learning Models ◽  
Diverse Range ◽  
Hybrid Machine ◽  
Economics Research

This paper provides a state-of-the-art investigation of advances in data science in emerging economic applications. The analysis was performed on novel data science methods in four individual classes of deep learning models, hybrid deep learning models, hybrid machine learning, and ensemble models. Application domains include a wide and diverse range of economics research from the stock market, marketing, and e-commerce to corporate banking and cryptocurrency. Prisma method, a systematic literature review methodology, was used to ensure the quality of the survey. The findings reveal that the trends follow the advancement of hybrid models, which, based on the accuracy metric, outperform other learning algorithms. It is further expected that the trends will converge toward the advancements of sophisticated hybrid deep learning models.

A Study on the Auxiliary Diagnosis of Thyroid Disease Images Based on Multiple Dimensional Deep Learning Algorithms

2020 ◽  
Vol 16 (3) ◽  
pp. 199-205
Author(s):  
Yuejun Liu ◽  
Yifei Xu ◽  
Xiangzheng Meng ◽  
Xuguang Wang ◽  
Tianxu Bai
Keyword(s):  
Deep Learning ◽  
Learning Algorithms ◽  
Region Of Interest ◽  
Classification Performance ◽  
Thyroid Diseases ◽  
Great Success ◽  
Learning Models ◽  
Good Classification Performance ◽  
Spect Images

Background: Medical imaging plays an important role in the diagnosis of thyroid diseases. In the field of machine learning, multiple dimensional deep learning algorithms are widely used in image classification and recognition, and have achieved great success. Objective: The method based on multiple dimensional deep learning is employed for the auxiliary diagnosis of thyroid diseases based on SPECT images. The performances of different deep learning models are evaluated and compared. Methods: Thyroid SPECT images are collected with three types, they are hyperthyroidism, normal and hypothyroidism. In the pre-processing, the region of interest of thyroid is segmented and the amount of data sample is expanded. Four CNN models, including CNN, Inception, VGG16 and RNN, are used to evaluate deep learning methods. Results: Deep learning based methods have good classification performance, the accuracy is 92.9%-96.2%, AUC is 97.8%-99.6%. VGG16 model has the best performance, the accuracy is 96.2% and AUC is 99.6%. Especially, the VGG16 model with a changing learning rate works best. Conclusion: The standard CNN, Inception, VGG16, and RNN four deep learning models are efficient for the classification of thyroid diseases with SPECT images. The accuracy of the assisted diagnostic method based on deep learning is higher than that of other methods reported in the literature.

Deep Learning in Disease Diagnosis: Models and Datasets

2020 ◽  
Vol 15 ◽  
Author(s):  
Deeksha Saxena ◽  
Mohammed Haris Siddiqui ◽  
Rajnish Kumar
Keyword(s):  
Biological Sciences ◽  
Machine Learning ◽  
Deep Learning ◽  
Disease Diagnosis ◽  
Learning Models ◽  
Data Types ◽  
Related Data ◽  
Abstract Level ◽  
Experimental Validations ◽  
Selection Of

Background: Deep learning (DL) is an Artificial neural network-driven framework with multiple levels of representation for which non-linear modules combined in such a way that the levels of representation can be enhanced from lower to a much abstract level. Though DL is used widely in almost every field, it has largely brought a breakthrough in biological sciences as it is used in disease diagnosis and clinical trials. DL can be clubbed with machine learning, but at times both are used individually as well. DL seems to be a better platform than machine learning as the former does not require an intermediate feature extraction and works well with larger datasets. DL is one of the most discussed fields among the scientists and researchers these days for diagnosing and solving various biological problems. However, deep learning models need some improvisation and experimental validations to be more productive. Objective: To review the available DL models and datasets that are used in disease diagnosis. Methods: Available DL models and their applications in disease diagnosis were reviewed discussed and tabulated. Types of datasets and some of the popular disease related data sources for DL were highlighted. Results: We have analyzed the frequently used DL methods, data types and discussed some of the recent deep learning models used for solving different biological problems. Conclusion: The review presents useful insights about DL methods, data types, selection of DL models for the disease diagnosis.

Improving Sentiment Analysis using Hybrid Deep Learning Model

2020 ◽  
Vol 13 (4) ◽  
pp. 627-640 ◽  
Author(s):  
Avinash Chandra Pandey ◽  
Dharmveer Singh Rajpoot
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Sentiment Analysis ◽  
Classification Accuracy ◽  
Short Term Memory ◽  
Computational Cost ◽  
Extraction Process ◽  
Learning Model ◽  
Sentiment Classification ◽  
Deep Learning Model

Background: Sentiment analysis is a contextual mining of text which determines viewpoint of users with respect to some sentimental topics commonly present at social networking websites. Twitter is one of the social sites where people express their opinion about any topic in the form of tweets. These tweets can be examined using various sentiment classification methods to find the opinion of users. Traditional sentiment analysis methods use manually extracted features for opinion classification. The manual feature extraction process is a complicated task since it requires predefined sentiment lexicons. On the other hand, deep learning methods automatically extract relevant features from data hence; they provide better performance and richer representation competency than the traditional methods. Objective: The main aim of this paper is to enhance the sentiment classification accuracy and to reduce the computational cost. Method: To achieve the objective, a hybrid deep learning model, based on convolution neural network and bi-directional long-short term memory neural network has been introduced. Results: The proposed sentiment classification method achieves the highest accuracy for the most of the datasets. Further, from the statistical analysis efficacy of the proposed method has been validated. Conclusion: Sentiment classification accuracy can be improved by creating veracious hybrid models. Moreover, performance can also be enhanced by tuning the hyper parameters of deep leaning models.

scholarly journals Deep Learning Model Comparison for Vision-Based Classification of Full/Empty-Load Trucks in Earthmoving Operations

2019 ◽  
Vol 9 (22) ◽  
pp. 4871 ◽  
Author(s):  
Quan Liu ◽  
Chen Feng ◽  
Zida Song ◽  
Joseph Louis ◽  
Jian Zhou
Keyword(s):  
Deep Learning ◽  
Model Comparison ◽  
Surveillance Systems ◽  
Comparison Study ◽  
Learning Models ◽  
The Core ◽  
Dump Trucks ◽  
Deep Learning Model ◽  
Contact Field

Earthmoving is an integral civil engineering operation of significance, and tracking its productivity requires the statistics of loads moved by dump trucks. Since current truck loads’ statistics methods are laborious, costly, and limited in application, this paper presents the framework of a novel, automated, non-contact field earthmoving quantity statistics (FEQS) for projects with large earthmoving demands that use uniform and uncovered trucks. The proposed FEQS framework utilizes field surveillance systems and adopts vision-based deep learning for full/empty-load truck classification as the core work. Since convolutional neural network (CNN) and its transfer learning (TL) forms are popular vision-based deep learning models and numerous in type, a comparison study is conducted to test the framework’s core work feasibility and evaluate the performance of different deep learning models in implementation. The comparison study involved 12 CNN or CNN-TL models in full/empty-load truck classification, and the results revealed that while several provided satisfactory performance, the VGG16-FineTune provided the optimal performance. This proved the core work feasibility of the proposed FEQS framework. Further discussion provides model choice suggestions that CNN-TL models are more feasible than CNN prototypes, and models that adopt different TL methods have advantages in either working accuracy or speed for different tasks.

scholarly journals Deep Learning Models for Estimation of the SuperDARN Cross Polar Cap Potential

2020 ◽  
Vol 7 (8) ◽  
Author(s):  
Erxiao Liu ◽  
Hongqiao Hu ◽  
Jianjun Liu ◽  
Lei Qiao
Keyword(s):  
Deep Learning ◽  
Learning Models ◽  
Polar Cap ◽  
Cross Polar Cap Potential
Sign in / Sign up

Export Citation Format

Share Document