Learning-based computational MRI reconstruction without big data: from linear interpolation and structured low-rank matrices to recurrent neural networks

2019 ◽  
Author(s):  
Tae Hyung Kim ◽  
Justin P. Haldar
Keyword(s):  
Neural Networks ◽  
Big Data ◽  
Recurrent Neural Networks ◽  
Linear Interpolation ◽  
Low Rank ◽  
Mri Reconstruction

scholarly journals Critical Assessment of Artificial Intelligence Methods for Prediction of hERG Channel Inhibition in the ‘Big Data’ Era

2020 ◽  
Author(s):  
Vishal Babu Siramshetty ◽  
Dac-Trung Nguyen ◽  
Natalia J. Martinez ◽  
Anton Simeonov ◽  
Noel T. Southall ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Neural Networks ◽  
Big Data ◽  
Recurrent Neural Networks ◽  
Deep Neural Networks ◽  
Prediction Models ◽  
Chemical Space ◽  
Superior Performance ◽  
Gradient Boosting ◽  
Artificial Intelligence Methods

The rise of novel artificial intelligence methods necessitates a comparison of this wave of new approaches with classical machine learning for a typical drug discovery project. Inhibition of the potassium ion channel, whose alpha subunit is encoded by human Ether-à-go-go-Related Gene (hERG), leads to prolonged QT interval of the cardiac action potential and is a significant safety pharmacology target for the development of new medicines. Several computational approaches have been employed to develop prediction models for assessment of hERG liabilities of small molecules including recent work using deep learning methods. Here we perform a comprehensive comparison of prediction models based on classical (random forests and gradient boosting) and modern (deep neural networks and recurrent neural networks) artificial intelligence methods. The training set (~9000 compounds) was compiled by integrating hERG bioactivity data from ChEMBL database with experimental data generated from an in-house, high-throughput thallium flux assay. We utilized different molecular descriptors including the latent descriptors, which are real-valued continuous vectors derived from chemical autoencoders trained on a large chemical space (> 1.5 million compounds). The models were prospectively validated on ~840 in-house compounds screened in the same thallium flux assay. The deep neural networks performed significantly better than the classical methods with the latent descriptors. The recurrent neural networks that operate on SMILES provided highest model sensitivity. The best models were merged into a consensus model that offered superior performance compared to reference models from academic and commercial domains. Further, we shed light on the potential of artificial intelligence methods to exploit the chemistry big data and generate novel chemical representations useful in predictive modeling and tailoring new chemical space.<br>

Survey of Applications of Neural Networks and Machine Learning to COVID-19 Predictions

2022 ◽  
pp. 30-57
Author(s):  
Richard S. Segall
Keyword(s):  
Neural Network ◽  
Artificial Intelligence ◽  
Machine Learning ◽  
Neural Networks ◽  
Big Data ◽  
Recurrent Neural Networks ◽  
Big Data Analytics ◽  
Data Sets ◽  
Open Source Data ◽  
Source Data

The purpose of this chapter is to illustrate how artificial intelligence (AI) technologies have been used for COVID-19 detection and analysis. Specifically, the use of neural networks (NN) and machine learning (ML) are described along with which countries are creating these techniques and how these are being used for COVID-19 diagnosis and detection. Illustrations of multi-layer convolutional neural networks (CNN), recurrent neural networks (RNN), and deep neural networks (DNN) are provided to show how these are used for COVID-19 detection and prediction. A summary of big data analytics for COVID-19 and some available COVID-19 open-source data sets and repositories and their characteristics for research and analysis are also provided. An example is also shown for artificial intelligence (AI) and neural network (NN) applications using real-time COVID-19 data.

scholarly journals Compressing Recurrent Neural Networks with Tensor Ring for Action Recognition

2019 ◽  
Vol 33 ◽  
pp. 4683-4690 ◽  
Author(s):  
Yu Pan ◽  
Jing Xu ◽  
Maolin Wang ◽  
Jinmian Ye ◽  
Fei Wang ◽  
...  
Keyword(s):  
Neural Networks ◽  
Action Recognition ◽  
Recurrent Neural Networks ◽  
Input Data ◽  
Short Term Memory ◽  
Computational Cost ◽  
Tensor Decomposition ◽  
Decomposition Methods ◽  
Low Rank ◽  
Sequential Data

Recurrent Neural Networks (RNNs) and their variants, such as Long-Short Term Memory (LSTM) networks, and Gated Recurrent Unit (GRU) networks, have achieved promising performance in sequential data modeling. The hidden layers in RNNs can be regarded as the memory units, which are helpful in storing information in sequential contexts. However, when dealing with high dimensional input data, such as video and text, the input-to-hidden linear transformation in RNNs brings high memory usage and huge computational cost. This makes the training of RNNs very difficult. To address this challenge, we propose a novel compact LSTM model, named as TR-LSTM, by utilizing the low-rank tensor ring decomposition (TRD) to reformulate the input-to-hidden transformation. Compared with other tensor decomposition methods, TR-LSTM is more stable. In addition, TR-LSTM can complete an end-to-end training and also provide a fundamental building block for RNNs in handling large input data. Experiments on real-world action recognition datasets have demonstrated the promising performance of the proposed TR-LSTM compared with the tensor-train LSTM and other state-of-the-art competitors.

scholarly journals Linking Connectivity, Dynamics, and Computations in Low-Rank Recurrent Neural Networks

Neuron ◽  
2018 ◽  
Vol 99 (3) ◽  
pp. 609-623.e29 ◽  
Author(s):  
Francesca Mastrogiuseppe ◽  
Srdjan Ostojic
Keyword(s):  
Neural Networks ◽  
Recurrent Neural Networks ◽  
Low Rank

scholarly journals Critical Assessment of Artificial Intelligence Methods for Prediction of hERG Channel Inhibition in the ‘Big Data’ Era

2020 ◽  
Author(s):  
Vishal Babu Siramshetty ◽  
Dac-Trung Nguyen ◽  
Natalia J. Martinez ◽  
Anton Simeonov ◽  
Noel T. Southall ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Neural Networks ◽  
Big Data ◽  
Recurrent Neural Networks ◽  
Deep Neural Networks ◽  
Prediction Models ◽  
Chemical Space ◽  
Superior Performance ◽  
Gradient Boosting ◽  
Artificial Intelligence Methods

The rise of novel artificial intelligence methods necessitates a comparison of this wave of new approaches with classical machine learning for a typical drug discovery project. Inhibition of the potassium ion channel, whose alpha subunit is encoded by human Ether-à-go-go-Related Gene (hERG), leads to prolonged QT interval of the cardiac action potential and is a significant safety pharmacology target for the development of new medicines. Several computational approaches have been employed to develop prediction models for assessment of hERG liabilities of small molecules including recent work using deep learning methods. Here we perform a comprehensive comparison of prediction models based on classical (random forests and gradient boosting) and modern (deep neural networks and recurrent neural networks) artificial intelligence methods. The training set (~9000 compounds) was compiled by integrating hERG bioactivity data from ChEMBL database with experimental data generated from an in-house, high-throughput thallium flux assay. We utilized different molecular descriptors including the latent descriptors, which are real-valued continuous vectors derived from chemical autoencoders trained on a large chemical space (> 1.5 million compounds). The models were prospectively validated on ~840 in-house compounds screened in the same thallium flux assay. The deep neural networks performed significantly better than the classical methods with the latent descriptors. The recurrent neural networks that operate on SMILES provided highest model sensitivity. The best models were merged into a consensus model that offered superior performance compared to reference models from academic and commercial domains. Further, we shed light on the potential of artificial intelligence methods to exploit the chemistry big data and generate novel chemical representations useful in predictive modeling and tailoring new chemical space.<br>

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