Deep Reinforcement Learning for Multiparameter Optimization in de novo Drug Design

2019 ◽  
Author(s):  
Niclas Ståhl ◽  
Göran Falkman ◽  
Alexander Karlsson ◽  
Gunnar Mathiason ◽  
Jonas Boström
Keyword(s):  
Reinforcement Learning ◽  
Short Term Memory ◽  
De Novo ◽  
De Novo Drug Design ◽  
Generative Process ◽  
New Methods ◽  
Multiparameter Optimization ◽  
Long Short Term Memory ◽  
New Compounds

<p>In medicinal chemistry programs it is key to design and make compounds that are efficacious and safe. This is a long, complex and difficult multi-parameter optimization process, often including several properties with orthogonal trends. New methods for the automated design of compounds against profiles of multiple properties are thus of great value. Here we present a fragment-based reinforcement learning approach based on an actor-critic model, for the generation of novel molecules with optimal properties. The actor and the critic are both modelled with bidirectional long short-term memory (LSTM) networks. The AI method learns how to generate new compounds with desired properties by starting from an initial set of lead molecules and then improve these by replacing some of their fragments. A balanced binary tree based on the similarity of fragments is used in the generative process to bias the output towards structurally similar molecules. The method is demonstrated by a case study showing that 93% of the generated molecules are chemically valid, and a third satisfy the targeted objectives, while there were none in the initial set.</p>

Deep Reinforcement Learning for Multiparameter Optimization in de novo Drug Design

2019 ◽  
Author(s):  
Niclas Ståhl ◽  
Göran Falkman ◽  
Alexander Karlsson ◽  
Gunnar Mathiason ◽  
Jonas Boström
Keyword(s):  
Reinforcement Learning ◽  
Short Term Memory ◽  
De Novo ◽  
De Novo Drug Design ◽  
Generative Process ◽  
New Methods ◽  
Multiparameter Optimization ◽  
Long Short Term Memory ◽  
New Compounds

<p>In medicinal chemistry programs it is key to design and make compounds that are efficacious and safe. This is a long, complex and difficult multi-parameter optimization process, often including several properties with orthogonal trends. New methods for the automated design of compounds against profiles of multiple properties are thus of great value. Here we present a fragment-based reinforcement learning approach based on an actor-critic model, for the generation of novel molecules with optimal properties. The actor and the critic are both modelled with bidirectional long short-term memory (LSTM) networks. The AI method learns how to generate new compounds with desired properties by starting from an initial set of lead molecules and then improve these by replacing some of their fragments. A balanced binary tree based on the similarity of fragments is used in the generative process to bias the output towards structurally similar molecules. The method is demonstrated by a case study showing that 93% of the generated molecules are chemically valid, and a third satisfy the targeted objectives, while there were none in the initial set.</p>

Deep Reinforcement Learning for Multiparameter Optimization in de novo Drug Design

2019 ◽  
Author(s):  
Niclas Ståhl ◽  
Göran Falkman ◽  
Alexander Karlsson ◽  
Gunnar Mathiason ◽  
Jonas Boström
Keyword(s):  
Reinforcement Learning ◽  
Short Term Memory ◽  
De Novo ◽  
De Novo Drug Design ◽  
Generative Process ◽  
New Methods ◽  
Multiparameter Optimization ◽  
Long Short Term Memory ◽  
New Compounds

<p>In medicinal chemistry programs it is key to design and make compounds that are efficacious and safe. This is a long, complex and difficult multi-parameter optimization process, often including several properties with orthogonal trends. New methods for the automated design of compounds against profiles of multiple properties are thus of great value. Here we present a fragment-based reinforcement learning approach based on an actor-critic model, for the generation of novel molecules with optimal properties. The actor and the critic are both modelled with bidirectional long short-term memory (LSTM) networks. The AI method learns how to generate new compounds with desired properties by starting from an initial set of lead molecules and then improve these by replacing some of their fragments. A balanced binary tree based on the similarity of fragments is used in the generative process to bias the output towards structurally similar molecules. The method is demonstrated by a case study showing that 93% of the generated molecules are chemically valid, and a third satisfy the targeted objectives, while there were none in the initial set.</p>

Deep Reinforcement Learning for Multiparameter Optimization in de novo Drug Design

2019 ◽  
Vol 59 (7) ◽  
pp. 3166-3176 ◽  
Author(s):  
Niclas Ståhl ◽  
Göran Falkman ◽  
Alexander Karlsson ◽  
Gunnar Mathiason ◽  
Jonas Boström
Keyword(s):  
Reinforcement Learning ◽  
Drug Design ◽  
De Novo ◽  
De Novo Drug Design ◽  
Multiparameter Optimization

scholarly journals Discovery of novel chemical reactions by deep generative recurrent neural network

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
William Bort ◽  
Igor I. Baskin ◽  
Timur Gimadiev ◽  
Artem Mukanov ◽  
Ramil Nugmanov ◽  
...  
Keyword(s):  
Chemical Reactions ◽  
Short Term Memory ◽  
De Novo ◽  
Molecular Structures ◽  
Topographic Map ◽  
Short Term ◽  
Suzuki Reactions ◽  
Class A ◽  
Latent Space ◽  
Long Short Term Memory

AbstractThe “creativity” of Artificial Intelligence (AI) in terms of generating de novo molecular structures opened a novel paradigm in compound design, weaknesses (stability & feasibility issues of such structures) notwithstanding. Here we show that “creative” AI may be as successfully taught to enumerate novel chemical reactions that are stoichiometrically coherent. Furthermore, when coupled to reaction space cartography, de novo reaction design may be focused on the desired reaction class. A sequence-to-sequence autoencoder with bidirectional Long Short-Term Memory layers was trained on on-purpose developed “SMILES/CGR” strings, encoding reactions of the USPTO database. The autoencoder latent space was visualized on a generative topographic map. Novel latent space points were sampled around a map area populated by Suzuki reactions and decoded to corresponding reactions. These can be critically analyzed by the expert, cleaned of irrelevant functional groups and eventually experimentally attempted, herewith enlarging the synthetic purpose of popular synthetic pathways.

scholarly journals Arabic dialect sentiment analysis with ZERO effort. \\ Case study: Algerian dialect

2020 ◽  
Vol 23 (65) ◽  
pp. 124-135
Author(s):  
Imane Guellil ◽  
Marcelo Mendoza ◽  
Faical Azouaou
Keyword(s):  
Sentiment Analysis ◽  
Short Term Memory ◽  
State Of The Art ◽  
Short Term ◽  
Term Memory ◽  
Ongoing Work ◽  
Long Short Term Memory ◽  
Large Corpus ◽  
Unique Condition

This paper presents an analytic study showing that it is entirely possible to analyze the sentiment of an Arabic dialect without constructing any resources. The idea of this work is to use the resources dedicated to a given dialect \textit{X} for analyzing the sentiment of another dialect \textit{Y}. The unique condition is to have \textit{X} and \textit{Y} in the same category of dialects. We apply this idea on Algerian dialect, which is a Maghrebi Arabic dialect that suffers from limited available tools and other handling resources required for automatic sentiment analysis. To do this analysis, we rely on Maghrebi dialect resources and two manually annotated sentiment corpus for respectively Tunisian and Moroccan dialect. We also use a large corpus for Maghrebi dialect. We use a state-of-the-art system and propose a new deep learning architecture for automatically classify the sentiment of Arabic dialect (Algerian dialect). Experimental results show that F1-score is up to 83% and it is achieved by Multilayer Perceptron (MLP) with Tunisian corpus and with Long short-term memory (LSTM) with the combination of Tunisian and Moroccan. An improvement of 15% compared to its closest competitor was observed through this study. Ongoing work is aimed at manually constructing an annotated sentiment corpus for Algerian dialect and comparing the results

scholarly journals Prediksi Kunjungan Wisatawan Taman Nasional Gunung Merbabu dengan Time Series Forecasting dan LSTM

2020 ◽  
Vol 11 (2) ◽  
pp. 131
Author(s):  
Josua Manullang ◽  
Albertus Joko Santoso ◽  
Andi Wahju Rahardjo Emanuel
Keyword(s):  
Time Series ◽  
National Park ◽  
Short Term Memory ◽  
Lag Time ◽  
Time Series Forecasting ◽  
Mean Square ◽  
Short Term ◽  
Term Memory ◽  
Long Short Term Memory

Abstract. Prediction of tourist visits of Mount Merbabu National Park (TNGMb) needs to be done to control the number of visitors and to preserve the national park. The combination of time series forecasting (TSF) and deep learning methods has become a new alternative for prediction. This case study was conducted to implement several methods combination of TSF and Long-Short Term Memory (LSTM) to predict the visits. In this case study, there are 18 modelling scenarios as research objects to determine the best model by utilizing tourist visits data from 2013 to 2018. The results show that the model applying the lag time method can improve the model's ability to capture patterns on time series data. The error value is measured using the root mean square error (RMSE), with the smallest value of 3.7 in the LSTM architecture, using seven lags as a feature and one lag as a label.Keywords: Tourist Visit, Taman Nasional Gunung Merbabu, Prediction, Recurrent Neural Network, Long-Short Term MemoryAbstrak. Prediksi kunjungan wisatawan Taman Nasional Gunung Merbabu (TNGMb) perlu dilakukan untul pengendalian jumlah pengunjung dan menjaga kelestarian taman nasional. Gabungan metode antara time series forecasting (TSF) dan deep learning telah menjadi alternatif baru untuk melakukan prediksi. Studi kasus ini dilakukan untuk mengimplementasi gabungan dari beberapa macam metode antara TSF dan Long-Short Term Memory (LSTM) untuk memprediksi kunjungan pada TNGMb. Pada studi kasus ini, terdapat 18 skenario pemodelan sebagai objek penelitian untuk menentukan model terbaik, dengan memanfaatkan data jumlah kunjungan wisatawan di TNGMb mulai dari tahun 2013 sampai dengan tahun 2018. Hasil prediksi menunjukkan pemodelan dengan menerapkan metode lag time dapat meningkatakan kemampuan model untuk menangkap pola pada data deret waktu. Besar nilai kesalahan diukur menggunakan root mean square error (RMSE), dengan nilai terkecil sebesar 3,7 pada arsitektur LSTM, menggunakan tujuh lag sebagai feature dan satu lag sebagai label. Kata Kunci: Kunjungan Wisatawan, Taman Nasional Gunung Merbabu, Prediksi, Recurrent Neural Network, Long-Short Term Memory

scholarly journals Pemanfaatan Asynchronous Advantage Actor-Critic Dalam Pembuatan AI Game Bot Pada Game Arcade

2019 ◽  
Vol 1 (2) ◽  
pp. 74-84
Author(s):  
Evan Kusuma Susanto ◽  
Yosi Kristian
Keyword(s):  
Neural Network ◽  
Artificial Intelligence ◽  
Reinforcement Learning ◽  
Convolutional Neural Network ◽  
Short Term Memory ◽  
Trial And Error ◽  
Short Term ◽  
Term Memory ◽  
Memory Network ◽  
Long Short Term Memory

Asynchronous Advantage Actor-Critic (A3C) adalah sebuah algoritma deep reinforcement learning yang dikembangkan oleh Google DeepMind. Algoritma ini dapat digunakan untuk menciptakan sebuah arsitektur artificial intelligence yang dapat menguasai berbagai jenis game yang berbeda melalui trial and error dengan mempelajari tempilan layar game dan skor yang diperoleh dari hasil tindakannya tanpa campur tangan manusia. Sebuah network A3C terdiri dari Convolutional Neural Network (CNN) di bagian depan, Long Short-Term Memory Network (LSTM) di tengah, dan sebuah Actor-Critic network di bagian belakang. CNN berguna sebagai perangkum dari citra output layar dengan mengekstrak fitur-fitur yang penting yang terdapat pada layar. LSTM berguna sebagai pengingat keadaan game sebelumnya. Actor-Critic Network berguna untuk menentukan tindakan terbaik untuk dilakukan ketika dihadapkan dengan suatu kondisi tertentu. Dari hasil percobaan yang dilakukan, metode ini cukup efektif dan dapat mengalahkan pemain pemula dalam memainkan 5 game yang digunakan sebagai bahan uji coba.

Peak Load Forecasting Using Long-Short Term Memory : Case Study of Jawa-Madura-Bali System

2021 ◽  
Author(s):  
Anindita Satria Surya ◽  
Musa Partahi Marbun ◽  
K.G.H. Mangunkusumo ◽  
Muhammad Ridwan
Keyword(s):  
Short Term Memory ◽  
Peak Load ◽  
Load Forecasting ◽  
Short Term ◽  
Term Memory ◽  
Long Short Term Memory
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