scholarly journals Randomized SMILES Strings Improve the Quality of Molecular Generative Models

2019 ◽  
Author(s):  
Josep Arús-Pous ◽  
Simon Johansson ◽  
Oleksii Prykhodko ◽  
Esben Jannik Bjerrum ◽  
Christian Tyrchan ◽  
...  
Keyword(s):  
Neural Networks ◽  
Recurrent Neural Networks ◽  
Chemical Space ◽  
Cell Types ◽  
Generative Models ◽  
The Other ◽  
Probability Models ◽  
String Representation ◽  
Almost All

Recurrent Neural Networks (RNNs) trained with a set of molecules represented as unique (canonical) SMILES strings, have shown the capacity to create large chemical spaces of valid and meaningful structures. Herein we perform an extensive benchmark on models trained with subsets of GDB-13 of different sizes (1 million , 10,000 and 1,000), with different SMILES variants (canonical, randomized and DeepSMILES), with two different recurrent cell types (LSTM and GRU) and with different hyperparameter combinations. To guide the benchmarks new metrics were developed that define the generated chemical space with respect to its uniformity, closedness and completeness. Results show that models that use LSTM cells trained with 1 million randomized SMILES, a non-unique molecular string representation, are able to generate larger chemical spaces than the other approaches and they represent more accurately the target chemical space. Specifically, a model was trained with randomized SMILES that was able to generate almost all molecules from GDB-13 with a quasi-uniform probability. Models trained with smaller samples show an even bigger improvement when trained with randomized SMILES models. Additionally, models were trained on molecules obtained from ChEMBL and illustrate again that training with randomized SMILES lead to models having a better representation of the drug-like chemical space. Namely, the model trained with randomized SMILES was able to generate at least double the amount of unique molecules with the same distribution of properties comparing to one trained with canonical SMILES.

scholarly journals Randomized SMILES Strings Improve the Quality of Molecular Generative Models

2019 ◽  
Author(s):  
Josep Arús-Pous ◽  
Simon Johansson ◽  
Oleksii Ptykhodko ◽  
Esben Jannik Bjerrum ◽  
Christian Tyrchan ◽  
...  
Keyword(s):  
Neural Networks ◽  
Recurrent Neural Networks ◽  
Chemical Space ◽  
Cell Types ◽  
Generative Models ◽  
The Other ◽  
Probability Models ◽  
String Representation ◽  
Almost All

Recurrent Neural Networks (RNNs) trained with a set of molecules represented as unique (canonical) SMILES strings, have shown the capacity to create large chemical spaces of valid and meaningful structures. Herein we perform an extensive benchmark on models trained with subsets of GDB-13 of different sizes (1 million , 10,000 and 1,000), with different SMILES variants (canonical, randomized and DeepSMILES), with two different recurrent cell types (LSTM and GRU) and with different hyperparameter combinations. To guide the benchmarks new metrics were developed that define the generated chemical space with respect to its uniformity, closedness and completeness. Results show that models that use LSTM cells trained with 1 million randomized SMILES, a non-unique molecular string representation, are able to generate larger chemical spaces than the other approaches and they represent more accurately the target chemical space. Specifically, a model was trained with randomized SMILES that was able to generate almost all molecules from GDB-13 with a quasi-uniform probability. Models trained with smaller samples show an even bigger improvement when trained with randomized SMILES models. Additionally, models were trained on molecules obtained from ChEMBL and illustrate again that training with randomized SMILES lead to models having a better representation of the drug-like chemical space. Namely, the model trained with randomized SMILES was able to generate at least double the amount of unique molecules with the same distribution of properties comparing to one trained with canonical SMILES.

scholarly journals Randomized SMILES Strings Improve the Quality of Molecular Generative Models

2019 ◽  
Author(s):  
Josep Arús-Pous ◽  
Simon Johansson ◽  
Oleksii Prykhodko ◽  
Esben Jannik Bjerrum ◽  
Christian Tyrchan ◽  
...  
Keyword(s):  
Neural Networks ◽  
Recurrent Neural Networks ◽  
Chemical Space ◽  
Cell Types ◽  
Generative Models ◽  
The Other ◽  
Probability Models ◽  
String Representation ◽  
Almost All

Recurrent Neural Networks (RNNs) trained with a set of molecules represented as unique (canonical) SMILES strings, have shown the capacity to create large chemical spaces of valid and meaningful structures. Herein we perform an extensive benchmark on models trained with subsets of GDB-13 of different sizes (1 million , 10,000 and 1,000), with different SMILES variants (canonical, randomized and DeepSMILES), with two different recurrent cell types (LSTM and GRU) and with different hyperparameter combinations. To guide the benchmarks new metrics were developed that define the generated chemical space with respect to its uniformity, closedness and completeness. Results show that models that use LSTM cells trained with 1 million randomized SMILES, a non-unique molecular string representation, are able to generate larger chemical spaces than the other approaches and they represent more accurately the target chemical space. Specifically, a model was trained with randomized SMILES that was able to generate almost all molecules from GDB-13 with a quasi-uniform probability. Models trained with smaller samples show an even bigger improvement when trained with randomized SMILES models. Additionally, models were trained on molecules obtained from ChEMBL and illustrate again that training with randomized SMILES lead to models having a better representation of the drug-like chemical space. Namely, the model trained with randomized SMILES was able to generate at least double the amount of unique molecules with the same distribution of properties comparing to one trained with canonical SMILES.

scholarly journals Randomized SMILES strings improve the quality of molecular generative models

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Josep Arús-Pous ◽  
Simon Viet Johansson ◽  
Oleksii Prykhodko ◽  
Esben Jannik Bjerrum ◽  
Christian Tyrchan ◽  
...  
Keyword(s):  
Recurrent Neural Networks ◽  
Chemical Space ◽  
Cell Types ◽  
Generative Models ◽  
The Other ◽  
Probability Models ◽  
Training Set ◽  
String Representation ◽  
Almost All

AbstractRecurrent Neural Networks (RNNs) trained with a set of molecules represented as unique (canonical) SMILES strings, have shown the capacity to create large chemical spaces of valid and meaningful structures. Herein we perform an extensive benchmark on models trained with subsets of GDB-13 of different sizes (1 million, 10,000 and 1000), with different SMILES variants (canonical, randomized and DeepSMILES), with two different recurrent cell types (LSTM and GRU) and with different hyperparameter combinations. To guide the benchmarks new metrics were developed that define how well a model has generalized the training set. The generated chemical space is evaluated with respect to its uniformity, closedness and completeness. Results show that models that use LSTM cells trained with 1 million randomized SMILES, a non-unique molecular string representation, are able to generalize to larger chemical spaces than the other approaches and they represent more accurately the target chemical space. Specifically, a model was trained with randomized SMILES that was able to generate almost all molecules from GDB-13 with a quasi-uniform probability. Models trained with smaller samples show an even bigger improvement when trained with randomized SMILES models. Additionally, models were trained on molecules obtained from ChEMBL and illustrate again that training with randomized SMILES lead to models having a better representation of the drug-like chemical space. Namely, the model trained with randomized SMILES was able to generate at least double the amount of unique molecules with the same distribution of properties comparing to one trained with canonical SMILES.

scholarly journals Exploring the GDB-13 Chemical Space Using Deep Generative Models

2018 ◽  
Author(s):  
Josep Arús-Pous ◽  
Thomas Blaschke ◽  
Jean-Louis Reymond ◽  
Hongming Chen ◽  
Ola Engkvist
Keyword(s):  
Mathematical Model ◽  
Recurrent Neural Networks ◽  
Chemical Space ◽  
Generative Models ◽  
Training Process ◽  
Complex Molecules ◽  
Training Models ◽  
Coupon Collector ◽  
Log Likelihood

Recent applications of Recurrent Neural Networks enable training models that sample the chemical space. In this study we train RNN with molecular string representations (SMILES) with a subset of the enumerated database GDB-13 (975 million molecules). We show that a model trained with 1 million structures (0.1 % of the database) reproduces 68.9 % of the entire database after training, when sampling 2 billion molecules. We also developed a method to assess the quality of the training process using log-likelihood plots. Furthermore, we use a mathematical model based on the “coupon collector problem” that compares the trained model to an upper bound, which shows that complex molecules with many rings and heteroatoms are more difficult to sample. We also suggest that the metrics obtained from this analysis can be used as a tool to benchmark any molecular generative model.<br>

scholarly journals Exploring the GDB-13 Chemical Space Using Deep Generative Models

2018 ◽  
Author(s):  
Josep Arús-Pous ◽  
Thomas Blaschke ◽  
Silas Ulander ◽  
Jean-Louis Reymond ◽  
Hongming Chen ◽  
...  
Keyword(s):  
Mathematical Model ◽  
Recurrent Neural Networks ◽  
Chemical Space ◽  
Generative Models ◽  
Training Process ◽  
Complex Molecules ◽  
Training Models ◽  
Coupon Collector ◽  
Log Likelihood

Recent applications of Recurrent Neural Networks enable training models that sample the chemical space. In this study we train RNN with molecular string representations (SMILES) with a subset of the enumerated database GDB-13 (975 million molecules). We show that a model trained with 1 million structures (0.1 % of the database) reproduces 68.9 % of the entire database after training, when sampling 2 billion molecules. We also developed a method to assess the quality of the training process using log-likelihood plots. Furthermore, we use a mathematical model based on the “coupon collector problem” that compares the trained model to an upper bound, which shows that complex molecules with many rings and heteroatoms are more difficult to sample. We also suggest that the metrics obtained from this analysis can be used as a tool to benchmark any molecular generative model.<br>

scholarly journals Exploring the GDB-13 Chemical Space Using Deep Generative Models

2018 ◽  
Author(s):  
Josep Arús-Pous ◽  
Thomas Blaschke ◽  
Silas Ulander ◽  
Jean-Louis Reymond ◽  
Hongming Chen ◽  
...  
Keyword(s):  
Mathematical Model ◽  
Recurrent Neural Networks ◽  
Chemical Space ◽  
Generative Models ◽  
Training Process ◽  
Complex Molecules ◽  
Training Models ◽  
Coupon Collector ◽  
Log Likelihood

Recent applications of Recurrent Neural Networks enable training models that sample the chemical space. In this study we train RNN with molecular string representations (SMILES) with a subset of the enumerated database GDB-13 (975 million molecules). We show that a model trained with 1 million structures (0.1 % of the database) reproduces 68.9 % of the entire database after training, when sampling 2 billion molecules. We also developed a method to assess the quality of the training process using log-likelihood plots. Furthermore, we use a mathematical model based on the “coupon collector problem” that compares the trained model to an upper bound, which shows that complex molecules with many rings and heteroatoms are more difficult to sample. We also suggest that the metrics obtained from this analysis can be used as a tool to benchmark any molecular generative model.<br>

scholarly journals Improving Web QoE Monitoring for Encrypted Network Traffic through Time Series Modeling

2021 ◽  
Vol 48 (4) ◽  
pp. 37-40
Author(s):  
Nikolas Wehner ◽  
Michael Seufert ◽  
Joshua Schuler ◽  
Sarah Wassermann ◽  
Pedro Casas ◽  
...  
Keyword(s):  
Neural Networks ◽  
Time Series ◽  
Recurrent Neural Networks ◽  
Quality Of Experience ◽  
Unique Feature ◽  
Time Series Modeling ◽  
Web Browsing ◽  
Large Dataset ◽  
Efficient Approximation

This paper addresses the problem of Quality of Experience (QoE) monitoring for web browsing. In particular, the inference of common Web QoE metrics such as Speed Index (SI) is investigated. Based on a large dataset collected with open web-measurement platforms on different device-types, a unique feature set is designed and used to estimate the RUMSI - an efficient approximation to SI, with machinelearning based regression and classification approaches. Results indicate that it is possible to estimate the RUMSI accurately, and that in particular, recurrent neural networks are highly suitable for the task, as they capture the network dynamics more precisely.

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>

scholarly journals ANN analysis in a vision approach for potato inspection

2008 ◽  
Vol 6 (02) ◽  
Author(s):  
R. Rios-Cabrera ◽  
I Lopez-Juarez ◽  
Hsieh Sheng-Jen
Keyword(s):  
Neural Networks ◽  
Image Processing ◽  
Feature Extraction ◽  
Artificial Neural Networks ◽  
Comparative Analysis ◽  
Physical Properties ◽  
Real Time ◽  
The Other ◽  
Stability And Convergence

An image processing methodology for the extraction of potato properties is explained. The objective is to determine their quality evaluating physical properties and using Artificial Neural Networks (ANN’s) to find misshapen potatoes. A comparative analysis for three connectionist models (Backpropagation, Perceptron and FuzzyARTMAP), evaluating speed and stability for classifying extracted properties is presented. The methodology for image processing and pattern feature extraction is presented together with some results. These results showed that FuzzyARTMAP outperformed the other models due to its stability and convergence speed with times as low as 1 ms per pattern which demonstrates its suitability for real-time inspection. Several algorithms to determine potato defects such as greening, scab, cracks are proposed which can be affectively used for grading different quality of potatoes.

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