scholarly journals Tensorflow vs R: A Comparative Study of Usability

2017 ◽  
Author(s):  
Luís Dias ◽  
Rosalvo Neto
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Comparative Study ◽  
Scientific Community ◽  
Deep Neural Network ◽  
Network Algorithms ◽  
Learning Framework ◽  
Usability Tests ◽  
Usability Analysis ◽  
Better Than

Google released on November of 2015 Tensorflow, an open source machine learning framework that can be used to implement Deep Neural Network algorithms, a class of algorithms that shows great potential in solving complex problems. Considering the importance of usability in software success, this research aims to perform a usability analysis on Tensorflow and to compare it with another widely used framework, R. The evaluation was performed through usability tests with university students. The study led do indications that Tensorflow usability is equal or better than the usability of traditional frameworks used by the scientific community.

scholarly journals The use of adversaries for optimal neural network training

2019 ◽  
Vol 214 ◽  
pp. 06013
Author(s):  
Anton Hawthorne-Gonzalvez ◽  
Martin Sevior
Keyword(s):  
Neural Network ◽  
Deep Neural Network ◽  
Neural Net ◽  
Network Algorithms ◽  
Network Training ◽  
Commercial Package ◽  
Boosted Decision Tree ◽  
Input Variables ◽  
Hidden Layer ◽  
Better Than

B-decay data from the Belle experiment at the KEKB collider have a substantial background from e+e- -h> qq¯ events. To suppress this we employ deep neural network algorithms. These provide improved signal from background discrimination. However, the deep neural network develops a substantial correlation with the ∆E kinematic variable used to distinguish signal from background in the final fit due to its relationship with input variables. The effect of this correlation is reduced by deploying an adversarial neural network. Over-all the adversarial deep neural network performs better than a Boosted Decision Tree algorithimn and a commercial package, NeuroBayes, which employs a neural net with a single hidden layer.

scholarly journals Privacy-preserving Machine Learning as a Service

2018 ◽  
Vol 2018 (3) ◽  
pp. 123-142 ◽  
Author(s):  
Ehsan Hesamifard ◽  
Hassan Takabi ◽  
Mehdi Ghasemi ◽  
Rebecca N. Wright
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Neural Networks ◽  
Deep Neural Network ◽  
Learning Algorithms ◽  
Privacy Preserving ◽  
Machine Learning Algorithms ◽  
Cloud Services ◽  
Network Algorithms ◽  
Encrypted Data

Abstract Machine learning algorithms based on deep Neural Networks (NN) have achieved remarkable results and are being extensively used in different domains. On the other hand, with increasing growth of cloud services, several Machine Learning as a Service (MLaaS) are offered where training and deploying machine learning models are performed on cloud providers’ infrastructure. However, machine learning algorithms require access to the raw data which is often privacy sensitive and can create potential security and privacy risks. To address this issue, we present CryptoDL, a framework that develops new techniques to provide solutions for applying deep neural network algorithms to encrypted data. In this paper, we provide the theoretical foundation for implementing deep neural network algorithms in encrypted domain and develop techniques to adopt neural networks within practical limitations of current homomorphic encryption schemes. We show that it is feasible and practical to train neural networks using encrypted data and to make encrypted predictions, and also return the predictions in an encrypted form. We demonstrate applicability of the proposed CryptoDL using a large number of datasets and evaluate its performance. The empirical results show that it provides accurate privacy-preserving training and classification.

scholarly journals Burst Pressure Prediction of API 5L X-Grade Dented Pipelines Using Deep Neural Network

2020 ◽  
Vol 8 (10) ◽  
pp. 766
Author(s):  
Dohan Oh ◽  
Julia Race ◽  
Selda Oterkus ◽  
Bonguk Koo
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Artificial Neural Network ◽  
Network Model ◽  
Neural Network Model ◽  
Deep Neural Network ◽  
Machine Learning Techniques ◽  
Burst Pressure ◽  
Comparison Results ◽  
Artificial Neural

Mechanical damage is recognized as a problem that reduces the performance of oil and gas pipelines and has been the subject of continuous research. The artificial neural network in the spotlight recently is expected to be another solution to solve the problems relating to the pipelines. The deep neural network, which is on the basis of artificial neural network algorithm and is a method amongst various machine learning methods, is applied in this study. The applicability of machine learning techniques such as deep neural network for the prediction of burst pressure has been investigated for dented API 5L X-grade pipelines. To this end, supervised learning is employed, and the deep neural network model has four layers with three hidden layers, and the neural network uses the fully connected layer. The burst pressure computed by deep neural network model has been compared with the results of finite element analysis based parametric study, and the burst pressure calculated by the experimental results. According to the comparison results, it showed good agreement. Therefore, it is concluded that deep neural networks can be another solution for predicting the burst pressure of API 5L X-grade dented pipelines.

scholarly journals A deep neural network model for packing density predictions and its application in the study of 1.5 million organic molecules

2019 ◽  
Vol 10 (36) ◽  
pp. 8374-8383 ◽  
Author(s):  
Mohammad Atif Faiz Afzal ◽  
Aditya Sonpal ◽  
Mojtaba Haghighatlari ◽  
Andrew J. Schultz ◽  
Johannes Hachmann
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Refractive Index ◽  
High Throughput ◽  
Neural Network Model ◽  
High Throughput Screening ◽  
Deep Neural Network ◽  
Organic Molecules ◽  
High Refractive Index ◽  
Computational Pipeline

Computational pipeline for the accelerated discovery of organic materials with high refractive index via high-throughput screening and machine learning.

scholarly journals Clinical Context–Aware Biomedical Text Summarization Using Deep Neural Network: Model Development and Validation (Preprint)

2020 ◽  
Author(s):  
Muhammad Afzal ◽  
Fakhare Alam ◽  
Khalid Mahmood Malik ◽  
Ghaus M Malik
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Deep Neural Network ◽  
Text Summarization ◽  
Biomedical Literature ◽  
Biomedical Text ◽  
Context Aware ◽  
Clinical Context ◽  
Jaccard Similarity ◽  
Recognition Model

BACKGROUND Automatic text summarization (ATS) enables users to retrieve meaningful evidence from big data of biomedical repositories to make complex clinical decisions. Deep neural and recurrent networks outperform traditional machine-learning techniques in areas of natural language processing and computer vision; however, they are yet to be explored in the ATS domain, particularly for medical text summarization. OBJECTIVE Traditional approaches in ATS for biomedical text suffer from fundamental issues such as an inability to capture clinical context, quality of evidence, and purpose-driven selection of passages for the summary. We aimed to circumvent these limitations through achieving precise, succinct, and coherent information extraction from credible published biomedical resources, and to construct a simplified summary containing the most informative content that can offer a review particular to clinical needs. METHODS In our proposed approach, we introduce a novel framework, termed Biomed-Summarizer, that provides quality-aware Patient/Problem, Intervention, Comparison, and Outcome (PICO)-based intelligent and context-enabled summarization of biomedical text. Biomed-Summarizer integrates the prognosis quality recognition model with a clinical context–aware model to locate text sequences in the body of a biomedical article for use in the final summary. First, we developed a deep neural network binary classifier for quality recognition to acquire scientifically sound studies and filter out others. Second, we developed a bidirectional long-short term memory recurrent neural network as a clinical context–aware classifier, which was trained on semantically enriched features generated using a word-embedding tokenizer for identification of meaningful sentences representing PICO text sequences. Third, we calculated the similarity between query and PICO text sequences using Jaccard similarity with semantic enrichments, where the semantic enrichments are obtained using medical ontologies. Last, we generated a representative summary from the high-scoring PICO sequences aggregated by study type, publication credibility, and freshness score. RESULTS Evaluation of the prognosis quality recognition model using a large dataset of biomedical literature related to intracranial aneurysm showed an accuracy of 95.41% (2562/2686) in terms of recognizing quality articles. The clinical context–aware multiclass classifier outperformed the traditional machine-learning algorithms, including support vector machine, gradient boosted tree, linear regression, K-nearest neighbor, and naïve Bayes, by achieving 93% (16127/17341) accuracy for classifying five categories: aim, population, intervention, results, and outcome. The semantic similarity algorithm achieved a significant Pearson correlation coefficient of 0.61 (0-1 scale) on a well-known BIOSSES dataset (with 100 pair sentences) after semantic enrichment, representing an improvement of 8.9% over baseline Jaccard similarity. Finally, we found a highly positive correlation among the evaluations performed by three domain experts concerning different metrics, suggesting that the automated summarization is satisfactory. CONCLUSIONS By employing the proposed method Biomed-Summarizer, high accuracy in ATS was achieved, enabling seamless curation of research evidence from the biomedical literature to use for clinical decision-making.

scholarly journals Deciphering gene regulation from gene expression dynamics using deep neural network

2018 ◽  
Author(s):  
Jingxiang Shen ◽  
Mariela D. Petkova ◽  
Yuhai Tu ◽  
Feng Liu ◽  
Chao Tang
Keyword(s):  
Neural Network ◽  
Gene Expression ◽  
Machine Learning ◽  
Gene Regulation ◽  
Gene Network ◽  
Deep Neural Network ◽  
Biological Functions ◽  
Gene Regulation Network ◽  
Regulation Network ◽  
Gene Expression Dynamics

AbstractComplex biological functions are carried out by the interaction of genes and proteins. Uncovering the gene regulation network behind a function is one of the central themes in biology. Typically, it involves extensive experiments of genetics, biochemistry and molecular biology. In this paper, we show that much of the inference task can be accomplished by a deep neural network (DNN), a form of machine learning or artificial intelligence. Specifically, the DNN learns from the dynamics of the gene expression. The learnt DNN behaves like an accurate simulator of the system, on which one can perform in-silico experiments to reveal the underlying gene network. We demonstrate the method with two examples: biochemical adaptation and the gap-gene patterning in fruit fly embryogenesis. In the first example, the DNN can successfully find the two basic network motifs for adaptation – the negative feedback and the incoherent feed-forward. In the second and much more complex example, the DNN can accurately predict behaviors of essentially all the mutants. Furthermore, the regulation network it uncovers is strikingly similar to the one inferred from experiments. In doing so, we develop methods for deciphering the gene regulation network hidden in the DNN “black box”. Our interpretable DNN approach should have broad applications in genotype-phenotype mapping.SignificanceComplex biological functions are carried out by gene regulation networks. The mapping between gene network and function is a central theme in biology. The task usually involves extensive experiments with perturbations to the system (e.g. gene deletion). Here, we demonstrate that machine learning, or deep neural network (DNN), can help reveal the underlying gene regulation for a given function or phenotype with minimal perturbation data. Specifically, after training with wild-type gene expression dynamics data and a few mutant snapshots, the DNN learns to behave like an accurate simulator for the genetic system, which can be used to predict other mutants’ behaviors. Furthermore, our DNN approach is biochemically interpretable, which helps uncover possible gene regulatory mechanisms underlying the observed phenotypic behaviors.

scholarly journals A Machine Learning Framework that Integrates Multi-omics Data Predicts Cancer-related LncRNAs

2021 ◽  
Author(s):  
Lin Yuan ◽  
Jing Zhao ◽  
Tao Sun ◽  
Zhen Shen
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Disease Association ◽  
Interaction Matrix ◽  
Omics Data ◽  
Similarity Matrix ◽  
Lncrna Gene ◽  
Neighborhood Information ◽  
Learning Framework ◽  
Association Matrix

Abstract Background: LncRNAs (Long non-coding RNAs) are a type of non-coding RNA molecule with transcript length longer than 200 nucleotides. LncRNA has been novel candidate biomarkers in cancer diagnosis and prognosis. However, it is difficult to discover the true association mechanism between lncRNAs and complex diseases. The unprecedented enrichment of multi-omics data and the rapid development of machine learning technology provide us with the opportunity to design a machine learning framework to study the relationship between lncRNAs and complex diseases. Results: In this article, we proposed a new machine learning approach, namely LGDLDA (LncRNA-Gene-Disease association networks based LncRNA-Disease Association prediction), for disease-related lncRNAs association prediction based multi-omics data, machine learning methods and neural network neighborhood information aggregation. Firstly, LGDLDA calculates the similarity matrix of lncRNA, gene and disease respectively. LGDLDA calculates the similarity between lncRNAs through the lncRNA expression profile matrix, lncRNA-miRNA interaction matrix and lncRNA-protein interaction matrix. LGDLDA obtains gene similarity matrix by calculating the lncRNA-gene association matrix and the gene-disease association matrix. LGDLDA obtains disease similarity matrix by calculating the disease ontology, the disease-miRNA association matrix, and Gaussian interaction profile kernel similarity. Secondly, LGDLDA integrates the neighborhood information in similarity matrices by using nonlinear feature learning of neural network. Thirdly, LGDLDA uses embedded node representations to approximate the observed matrices. Finally, LGDLDA ranks candidate lncRNA-disease pairs and then selects potential disease-related lncRNAs. Conclusions: Compared with lncRNA-disease prediction methods, IHI-BMLLR takes into account more critical information and obtains the performance improvement cancer-related lncRNA predictions. Randomly split data experiment results show that the stability of LGDLDA is better than IDHI-MIRW, NCPLDA, LncDisAP and NCPHLDA. The results on different simulation data sets show that LGDLDA can accurately and effectively predict the disease-related lncRNAs. Furthermore, we applied LGDLDA to three real cancer data including gastric cancer, colorectal cancer and breast cancer to predict potential cancer-related lncRNAs.

First-Break Picking Classification Models Using Recurrent Neural Network

2021 ◽  
Author(s):  
Mohammed Ayub ◽  
SanLinn Kaka
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Deep Neural Network ◽  
Contextual Information ◽  
Classification Model ◽  
Superior Performance ◽  
Learning Models ◽  
Neural Network Models ◽  
Minimum Number ◽  
Machine Learning Models

Abstract Manual first-break picking from a large volume of seismic data is extremely tedious and costly. Deployment of machine learning models makes the process fast and cost effective. However, these machine learning models require high representative and effective features for accurate automatic picking. Therefore, First- Break (FB) picking classification model that uses effective minimum number of features and promises performance efficiency is proposed. The variants of Recurrent Neural Networks (RNNs) such as Long ShortTerm Memory (LSTM) and Gated Recurrent Unit (GRU) can retain contextual information from long previous time steps. We deploy this advantage for FB picking as seismic traces are amplitude values of vibration along the time-axis. We use behavioral fluctuation of amplitude as input features for LSTM and GRU. The models are trained on noisy data and tested for generalization on original traces not seen during the training and validation process. In order to analyze the real-time suitability, the performance is benchmarked using accuracy, F1-measure and three other established metrics. We have trained two RNN models and two deep Neural Network models for FB classification using only amplitude values as features. Both LSTM and GRU have the accuracy and F1-measure with a score of 94.20%. With the same features, Convolutional Neural Network (CNN) has an accuracy of 93.58% and F1-score of 93.63%. Again, Deep Neural Network (DNN) model has scores of 92.83% and 92.59% as accuracy and F1-measure, respectively. From the pexperiment results, we see significant superior performance of LSTM and GRU to CNN and DNN when used the same features. For robustness of LSTM and GRU models, the performance is compared with DNN model that is trained using nine features derived from seismic traces and observed that the performance superiority of RNN models. Therefore, it is safe to conclude that RNN models (LSTM and GRU) are capable of classifying the FB events efficiently even by using a minimum number of features that are not computationally expensive. The novelty of our work is the capability of automatic FB classification with the RNN models that incorporate contextual behavioral information without the need for sophisticated feature extraction or engineering techniques that in turn can help in reducing the cost and fostering classification model robust and faster.

Sign in / Sign up

Export Citation Format

Share Document