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 CReM: chemically reasonable mutations framework for structure generation

2020 ◽  
Author(s):  
Pavel Polishchuk
Keyword(s):  
Deep Learning ◽  
Open Source ◽  
De Novo ◽  
De Novo Design ◽  
Learning Models ◽  
Structure Generation ◽  
Design Studies ◽  
Flexible Control

Abstract Structure generators are widely used in de novo design studies and their performance substantially influences an outcome. Approaches based on deep learning models and conventional atom-based approaches may result in invalid structures and did not address their synthetic feasibility issues. Conventional reaction-based approaches result in synthetically feasible compounds but novelty and diversity of generated compounds may be limited. Fragment-based approaches can provide 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 fragment-based approach which results in chemically valid structures by design and gives flexible control over diversity, novelty, synthetic complexity and chemotypes of generated compounds. The approach was implemented as an open-source Python module.

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 Deep Generative Models for Ligand-based de Novo Design Applied to Multi-parametric Optimization

2021 ◽  
Author(s):  
Quentin Perron ◽  
Olivier Mirguet ◽  
Hamza Tajmouati ◽  
Adam Skiredj ◽  
Anne Rojas ◽  
...  
Keyword(s):  
Deep Learning ◽  
Drug Discovery ◽  
De Novo ◽  
Molecular Design ◽  
Chemical Space ◽  
New Technology ◽  
De Novo Design ◽  
Generative Models ◽  
De Novo Molecular Design

<div> <div> <div> <p>Multi-Parameter Optimization (MPO) is a major challenge in New Chemical Entity (NCE) drug discovery projects, and the inability to identify molecules meeting all the criteria of lead optimization (LO) is an important cause of NCE project failure. Several ligand- and structure-based de novo design methods have been published over the past decades, some of which have proved useful multiobjective optimization. However, there is still need for improvement to better address the chemical feasibility of generated compounds as well as increasing the explored chemical space while tackling the MPO challenge. Recently, promising results have been reported for deep learning generative models applied to de novo molecular design, but until now, to our knowledge, no report has been made of the value of this new technology for addressing MPO in an actual drug discovery project. Our objective in this study was to evaluate the potential of a ligand-based de novo design technology using deep learning generative models to accelerate the discovery of an optimized lead compound meeting all in vitro late stage LO criteria. </p> </div> </div> </div>

scholarly journals Deep Generative Models for Ligand-based de Novo Design Applied to Multi-parametric Optimization

2021 ◽  
Author(s):  
Quentin Perron ◽  
Olivier Mirguet ◽  
Hamza Tajmouati ◽  
Adam Skiredj ◽  
Anne Rojas ◽  
...  
Keyword(s):  
Deep Learning ◽  
Drug Discovery ◽  
De Novo ◽  
Molecular Design ◽  
Chemical Space ◽  
New Technology ◽  
De Novo Design ◽  
Generative Models ◽  
De Novo Molecular Design

<div> <div> <div> <p>Multi-Parameter Optimization (MPO) is a major challenge in New Chemical Entity (NCE) drug discovery projects, and the inability to identify molecules meeting all the criteria of lead optimization (LO) is an important cause of NCE project failure. Several ligand- and structure-based de novo design methods have been published over the past decades, some of which have proved useful multiobjective optimization. However, there is still need for improvement to better address the chemical feasibility of generated compounds as well as increasing the explored chemical space while tackling the MPO challenge. Recently, promising results have been reported for deep learning generative models applied to de novo molecular design, but until now, to our knowledge, no report has been made of the value of this new technology for addressing MPO in an actual drug discovery project. Our objective in this study was to evaluate the potential of a ligand-based de novo design technology using deep learning generative models to accelerate the discovery of an optimized lead compound meeting all in vitro late stage LO criteria. </p> </div> </div> </div>

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 Deep Generative Models for Ligand-based de Novo Design Applied to Multi-parametric Optimization

2021 ◽  
Author(s):  
Quentin Perron ◽  
Olivier Mirguet ◽  
Hamza Tajmouati ◽  
Adam Skiredj ◽  
Anne Rojas ◽  
...  
Keyword(s):  
Deep Learning ◽  
Drug Discovery ◽  
De Novo ◽  
Molecular Design ◽  
Chemical Space ◽  
New Technology ◽  
De Novo Design ◽  
Generative Models ◽  
De Novo Molecular Design

<div> <div> <div> <p>Multi-Parameter Optimization (MPO) is a major challenge in New Chemical Entity (NCE) drug discovery projects, and the inability to identify molecules meeting all the criteria of lead optimization (LO) is an important cause of NCE project failure. Several ligand- and structure-based de novo design methods have been published over the past decades, some of which have proved useful multiobjective optimization. However, there is still need for improvement to better address the chemical feasibility of generated compounds as well as increasing the explored chemical space while tackling the MPO challenge. Recently, promising results have been reported for deep learning generative models applied to de novo molecular design, but until now, to our knowledge, no report has been made of the value of this new technology for addressing MPO in an actual drug discovery project. Our objective in this study was to evaluate the potential of a ligand-based de novo design technology using deep learning generative models to accelerate the discovery of an optimized lead compound meeting all in vitro late stage LO criteria. </p> </div> </div> </div>

scholarly journals Evaluation of Automatic Speech Recognition Systems

2021 ◽  
Author(s):  
Matheus Xavier Sampaio ◽  
Regis Pires Magalhães ◽  
Ticiana Linhares Coelho da Silva ◽  
Lívia Almada Cruz ◽  
Davi Romero de Vasconcelos ◽  
...  
Keyword(s):  
Deep Learning ◽  
Speech Recognition ◽  
Automatic Speech Recognition ◽  
Smart Homes ◽  
The Other ◽  
Learning Models ◽  
Recognition Systems ◽  
Microsoft Azure

Automatic Speech Recognition (ASR) is an essential task for many applications like automatic caption generation for videos, voice search, voice commands for smart homes, and chatbots. Due to the increasing popularity of these applications and the advances in deep learning models for transcribing speech into text, this work aims to evaluate the performance of commercial solutions for ASR that use deep learning models, such as Facebook Wit.ai, Microsoft Azure Speech, and Google Cloud Speech-to-Text. The results demonstrate that the evaluated solutions slightly differ. However, Microsoft Azure Speech outperformed the other analyzed APIs.

scholarly journals A Hybrid Optimized LSTM Models for Human Activity Recognition with IOT Devices

2021 ◽  
pp. 182-189
Author(s):  
S. Arokiaraj ◽  
Dr. N. Viswanathan
Keyword(s):  
Deep Learning ◽  
Internet Of Things ◽  
Short Term Memory ◽  
The Other ◽  
Learning Models ◽  
Computational Overhead ◽  
Temporal Features ◽  
Human Movements ◽  
Proposed Model ◽  
Iot Devices

With the advent of Internet of things(IoT),HA (HA) recognition has contributed the more application in health care in terms of diagnosis and Clinical process. These devices must be aware of human movements to provide better aid in the clinical applications as well as user’s daily activity.Also , In addition to machine and deep learning algorithms, HA recognition systems has significantly improved in terms of high accurate recognition. However, the most of the existing models designed needs improvisation in terms of accuracy and computational overhead. In this research paper, we proposed a BAT optimized Long Short term Memory (BAT-LSTM) for an effective recognition of human activities using real time IoT systems. The data are collected by implanting the Internet of things) devices invasively. Then, proposed BAT-LSTM is deployed to extract the temporal features which are then used for classification to HA. Nearly 10,0000 dataset were collected and used for evaluating the proposed model. For the validation of proposed framework, accuracy, precision, recall, specificity and F1-score parameters are chosen and comparison is done with the other state-of-art deep learning models. The finding shows the proposed model outperforms the other learning models and finds its suitability for the HA recognition.

scholarly journals Beyond Generative Models: Superfast Traversal, Optimization, Novelty, Exploration and Discovery (STONED) Algorithm for Molecules using SELFIES

2021 ◽  
Author(s):  
AkshatKumar Nigam ◽  
Robert Pollice ◽  
Mario Krenn ◽  
Gabriel dos Passos Gomes ◽  
Alan Aspuru-Guzik
Keyword(s):  
Deep Learning ◽  
Virtual Screening ◽  
Chemical Space ◽  
Generative Models ◽  
Inverse Design ◽  
Learning Models ◽  
Structure Modification ◽  
Design Models ◽  
Comparable Performance ◽  
And Training

Inverse design allows the design of molecules with desirable properties using property optimization. Deep generative models have recently been applied to tackle inverse design, as they possess the ability to optimize molecular properties directly through structure modification using gradients. While the ability to carry out direct property optimizations is promising, the use of generative deep learning models to solve practical problems requires large amounts of data and is very time-consuming. In this work, we propose STONED – a simple and efficient algorithm to perform interpolation and exploration in the chemical space, comparable to deep generative models. STONED bypasses the need for large amounts of data and training times by using string modifications in the SELFIES molecular representation. We achieve comparable performance on typical benchmarks without any training. We demonstrate applications in high-throughput virtual screening for the design of drugs, photovoltaics, and the construction of chemical paths, allowing for both property and structure-based interpolation in the chemical space. We anticipate our results to be a stepping stone for developing more sophisticated inverse design models and benchmarking tools, ultimately helping generative models achieve wide adoption.

scholarly journals Stock Price Prediction Using Deep Learning Models

2021 ◽  
Author(s):  
Jaydip Sen ◽  
Sidra Mehtab ◽  
Gourab Nath
Keyword(s):  
Deep Learning ◽  
Stock Prices ◽  
Stock Price ◽  
Regression Models ◽  
Research Work ◽  
The Other ◽  
Learning Models ◽  
Stock Price Prediction ◽  
Price Prediction ◽  
Other Hand

Prediction of future movement of stock prices has been a subject matter of many research work. On one hand, we have proponents of the Efficient Market Hypothesis who claim that stock prices cannot be predicted, on the other hand, there are propositions illustrating that, if appropriately modeled, stock prices can be predicted with a high level of accuracy. There is also a gamut of literature on technical analysis of stock prices where the objective is to identify patterns in stock price movements and profit from it. In this work, we propose a hybrid approach for stock price prediction using five deep learning-based regression models. We select the NIFTY 50 index values of the National Stock Exchange (NSE) of India, over a period of December 29, 2014 to July 31, 2020. Based on the NIFTY data during December 29, 2014 to December 28, 2018, we build two regression models using <i>convolutional neural networks</i> (CNNs), and three regression models using <i>long-and-short-term memory</i> (LSTM) networks for predicting the <i>open</i> values of the NIFTY 50 index records for the period December 31, 2018 to July 31, 2020. We adopted a multi-step prediction technique with <i>walk-forward validation</i>. The parameters of the five deep learning models are optimized using the grid-search technique so that the validation losses of the models stabilize with an increasing number of epochs in the model training, and the training and validation accuracies converge. Extensive results are presented on various metrics for all the proposed regression models. The results indicate that while both CNN and LSTM-based regression models are very accurate in forecasting the NIFTY 50 <i>open</i> values, the CNN model that previous one week’s data as the input is the fastest in its execution. On the other hand, the encoder-decoder convolutional LSTM model uses the previous two weeks’ data as the input is found to be the most accurate in its forecasting results.

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