scholarly journals A De Novo Molecular Generation Method Using Latent Vector Based Generative Adversarial Network

2019 ◽  
Author(s):  
Oleksii Prykhodko ◽  
Simon Viet Johansson ◽  
Panagiotis-Christos Kotsias ◽  
Esben Jannik Bjerrum ◽  
Ola Engkvist ◽  
...  
Keyword(s):  
Deep Learning ◽  
De Novo ◽  
Chemical Space ◽  
Learning Method ◽  
Training Set ◽  
Generative Adversarial Network ◽  
Structure Generation ◽  
Adversarial Network ◽  
Molecule Design ◽  
Novel Structures

<p>Recently deep learning method has been used for generating novel structures. In the current study, we proposed a new deep learning method, LatentGAN, which combine an autoencoder and a generative adversarial neural network for doing de novo molecule design. We applied the method for structure generation in two scenarios, one is to generate random drug-like compounds and the other is to generate target biased compounds. Our results show that the method works well in both cases, in which sampled compounds from the trained model can largely occupy the same chemical space of the training set and still a substantial fraction of the generated compound are novel. The distribution of drug-likeness score for compounds sampled from LatentGAN is also similar to that of the training set.</p>

scholarly journals A De Novo Molecular Generation Method Using Latent Vector Based Generative Adversarial Network

2019 ◽  
Author(s):  
Oleksii Prykhodko ◽  
Simon Viet Johansson ◽  
Panagiotis-Christos Kotsias ◽  
Esben Jannik Bjerrum ◽  
Ola Engkvist ◽  
...  
Keyword(s):  
Deep Learning ◽  
De Novo ◽  
Chemical Space ◽  
Learning Method ◽  
Training Set ◽  
Generative Adversarial Network ◽  
Structure Generation ◽  
Adversarial Network ◽  
Molecule Design ◽  
Novel Structures

<p>Recently deep learning method has been used for generating novel structures. In the current study, we proposed a new deep learning method, LatentGAN, which combine an autoencoder and a generative adversarial neural network for doing de novo molecule design. We applied the method for structure generation in two scenarios, one is to generate random drug-like compounds and the other is to generate target biased compounds. Our results show that the method works well in both cases, in which sampled compounds from the trained model can largely occupy the same chemical space of the training set and still a substantial fraction of the generated compound are novel. The distribution of drug-likeness score for compounds sampled from LatentGAN is also similar to that of the training set.</p>

scholarly journals A De Novo Molecular Generation Method Using Latent Vector Based Generative Adversarial Network

2019 ◽  
Author(s):  
Oleksii Prykhodko ◽  
Simon Viet Johansson ◽  
Panagiotis-Christos Kotsias ◽  
Josep Arús-Pous ◽  
Esben Jannik Bjerrum ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
De Novo ◽  
Molecular Design ◽  
Chemical Space ◽  
Training Set ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
De Novo Molecular Design ◽  
Novel Structures

<p> </p><p>Deep learning methods applied to drug discovery have been used to generate novel structures. In this study, we propose a new deep learning architecture, LatentGAN, which combines an autoencoder and a generative adversarial neural network for de novo molecular design. We applied the method in two scenarios: one to generate random drug-like compounds and another to generate target-biased compounds. Our results show that the method works well in both cases: sampled compounds from the trained model can largely occupy the same chemical space as the training set and also generate a substantial fraction of novel compounds. Moreover, the drug-likeness score of compounds sampled from LatentGAN is also similar to that of the training set. Lastly, generated compounds differ from those obtained with a Recurrent Neural Network-based generative model approach, indicating that both methods can be used complementarily.</p><p> </p>

scholarly journals A de novo molecular generation method using latent vector based generative adversarial network

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Oleksii Prykhodko ◽  
Simon Viet Johansson ◽  
Panagiotis-Christos Kotsias ◽  
Josep Arús-Pous ◽  
Esben Jannik Bjerrum ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
De Novo ◽  
Molecular Design ◽  
Chemical Space ◽  
Training Set ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
De Novo Molecular Design ◽  
Novel Structures

AbstractDeep learning methods applied to drug discovery have been used to generate novel structures. In this study, we propose a new deep learning architecture, LatentGAN, which combines an autoencoder and a generative adversarial neural network for de novo molecular design. We applied the method in two scenarios: one to generate random drug-like compounds and another to generate target-biased compounds. Our results show that the method works well in both cases. Sampled compounds from the trained model can largely occupy the same chemical space as the training set and also generate a substantial fraction of novel compounds. Moreover, the drug-likeness score of compounds sampled from LatentGAN is also similar to that of the training set. Lastly, generated compounds differ from those obtained with a Recurrent Neural Network-based generative model approach, indicating that both methods can be used complementarily.

scholarly journals A De Novo Molecular Generation Method Using Latent Vector Based Generative Adversarial Network

2019 ◽  
Author(s):  
Oleksii Prykhodko ◽  
Simon Viet Johansson ◽  
Panagiotis-Christos Kotsias ◽  
Josep Arús-Pous ◽  
Esben Jannik Bjerrum ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
De Novo ◽  
Molecular Design ◽  
Chemical Space ◽  
Training Set ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
De Novo Molecular Design ◽  
Novel Structures

<p> </p><p>Deep learning methods applied to drug discovery have been used to generate novel structures. In this study, we propose a new deep learning architecture, LatentGAN, which combines an autoencoder and a generative adversarial neural network for de novo molecular design. We applied the method in two scenarios: one to generate random drug-like compounds and another to generate target-biased compounds. Our results show that the method works well in both cases: sampled compounds from the trained model can largely occupy the same chemical space as the training set and also generate a substantial fraction of novel compounds. Moreover, the drug-likeness score of compounds sampled from LatentGAN is also similar to that of the training set. Lastly, generated compounds differ from those obtained with a Recurrent Neural Network-based generative model approach, indicating that both methods can be used complementarily.</p><p> </p>

scholarly journals A De Novo Molecular Generation Method Using Latent Vector Based Generative Adversarial Network

2019 ◽  
Author(s):  
Oleksii Prykhodko ◽  
Simon Viet Johansson ◽  
Panagiotis-Christos Kotsias ◽  
Josep Arús-Pous ◽  
Esben Jannik Bjerrum ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
De Novo ◽  
Molecular Design ◽  
Chemical Space ◽  
Training Set ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
De Novo Molecular Design ◽  
Novel Structures

<p> </p><p>Deep learning methods applied to drug discovery have been used to generate novel structures. In this study, we propose a new deep learning architecture, LatentGAN, which combines an autoencoder and a generative adversarial neural network for de novo molecular design. We applied the method in two scenarios: one to generate random drug-like compounds and another to generate target-biased compounds. Our results show that the method works well in both cases: sampled compounds from the trained model can largely occupy the same chemical space as the training set and also generate a substantial fraction of novel compounds. Moreover, the drug-likeness score of compounds sampled from LatentGAN is also similar to that of the training set. Lastly, generated compounds differ from those obtained with a Recurrent Neural Network-based generative model approach, indicating that both methods can be used complementarily.</p><p> </p>

scholarly journals HeartNet: Self Multi-Head Attention Mechanism via Convolutional Network with Adversarial Data Synthesis for ECG-based Arrhythmia Classification

2021 ◽  
Author(s):  
Taki Hasan Rafi ◽  
Young Woong-Ko
Keyword(s):  
Deep Learning ◽  
Attention Mechanism ◽  
Classification Systems ◽  
Insufficient Data ◽  
Learning Method ◽  
Generative Adversarial Network ◽  
Convolutional Network ◽  
Data Synthesis ◽  
Adversarial Network ◽  
Main Challenge

Cardiovascular disease is now one of the leading causes of morbidity and mortality in humans. Electrocardiogram (ECG) is a reliable tool for monitoring the health of the cardiovascular system. Currently, there has been a lot of focus on accurately categorizing heartbeats. There is a high demand on automatic ECG classification systems to assist medical professionals. In this paper we proposed a new deep learning method called HeartNet for developing an automatic ECG classifier. The proposed deep learning method is compressed by multi-head attention mechanism on top of CNN model. The main challenge of insufficient data label is solved by adversarial data synthesis adopting generative adversarial network (GAN) with generating additional training samples. It drastically improves the overall performance of the proposed method by 5-10% on each insufficient data label category. We evaluated our proposed method utilizing MIT-BIH dataset. Our proposed method has shown 99.67 ± 0.11 accuracy and 89.24 ± 1.71 MCC trained with adversarial data synthesized dataset. However, we have also utilized two individual datasets such as Atrial Fibrillation Detection Database and PTB Diagnostic Database to see the performance of our proposed model on ECG classification. The effectiveness and robustness of proposed method are validated by extensive experiments, comparison and analysis. Later on, we also highlighted some limitations of this work.

scholarly journals CReM: chemically reasonable mutations framework for structure generation

2020 ◽  
Author(s):  
Pavel Polishchuk
Keyword(s):  
Deep Learning ◽  
De Novo ◽  
Chemical Space ◽  
De Novo Design ◽  
The Other ◽  
Learning Models ◽  
Structure Generation ◽  
Design Studies ◽  
Flexible Control ◽  
New Framework

Abstract Structure generators are widely used in de novo design studies and their performance substantially influences an outcome. Approaches based on the deep learning models and conventional atom-based approaches may result in invalid structures and fail to address their synthetic feasibility issues. On the other hand, conventional reaction-based approaches result in synthetically feasible compounds but novelty and diversity of generated compounds may be limited. Fragment-based approaches can provide both better novelty and diversity of generated compounds but the issue of synthetic complexity of generated structure was not explicitly addressed before. Here we developed a new framework of fragment-based structure generation that, by design, results in the chemically valid structures and provides flexible control over diversity, novelty, synthetic complexity and chemotypes of generated compounds. The framework was implemented as an open-source Python module and can be used to create custom workflows for the exploration of chemical space.

scholarly journals Improving de novo Molecule Generation by Embedding LSTM and Attention Mechanism in CycleGAN

2021 ◽  
Vol 12 ◽  
Author(s):  
Feng Wang ◽  
Xiaochen Feng ◽  
Xiao Guo ◽  
Lei Xu ◽  
Liangxu Xie ◽  
...  
Keyword(s):  
Short Term Memory ◽  
De Novo ◽  
Chemical Space ◽  
Chemical Properties ◽  
Generative Models ◽  
Attention Mechanism ◽  
Generation Model ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
Starting Compound

The application of deep learning in the field of drug discovery brings the development and expansion of molecular generative models along with new challenges in this field. One of challenges in de novo molecular generation is how to produce new reasonable molecules with desired pharmacological, physical, and chemical properties. To improve the similarity between the generated molecule and the starting molecule, we propose a new molecule generation model by embedding Long Short-Term Memory (LSTM) and Attention mechanism in CycleGAN architecture, LA-CycleGAN. The network layer of the generator in CycleGAN is fused head and tail to improve the similarity of the generated structure. The embedded LSTM and Attention mechanism can overcome long-term dependency problems in treating the normally used SMILES input. From our quantitative evaluation, we present that LA-CycleGAN expands the chemical space of the molecules and improves the ability of structure conversion. The generated molecules are highly similar to the starting compound structures while obtaining expected molecular properties during cycle generative adversarial network learning, which comprehensively improves the performance of the generative model.

scholarly journals A Deep-Learning Method for Radar Micro-Doppler Spectrogram Restoration

Sensors ◽  
2020 ◽  
Vol 20 (17) ◽  
pp. 5007
Author(s):  
Yuan He ◽  
Xinyu Li ◽  
Runlong Li ◽  
Jianping Wang ◽  
Xiaojun Jing
Keyword(s):  
Deep Learning ◽  
Motion Capture ◽  
Radio Frequency Interference ◽  
Learning Method ◽  
High Quality ◽  
Generative Adversarial Network ◽  
Qualitative And Quantitative ◽  
Adversarial Network ◽  
Simulated Motion ◽  
Coarse To Fine

Radio frequency interference, which makes it difficult to produce high-quality radar spectrograms, is a major issue for micro-Doppler-based human activity recognition (HAR). In this paper, we propose a deep-learning-based method to detect and cut out the interference in spectrograms. Then, we restore the spectrograms in the cut-out region. First, a fully convolutional neural network (FCN) is employed to detect and remove the interference. Then, a coarse-to-fine generative adversarial network (GAN) is proposed to restore the part of the spectrogram that is affected by the interferences. The simulated motion capture (MOCAP) spectrograms and the measured radar spectrograms with interference are used to verify the proposed method. Experimental results from both qualitative and quantitative perspectives show that the proposed method can mitigate the interference and restore high-quality radar spectrograms. Furthermore, the comparison experiments also demonstrate the efficiency of the proposed approach.

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