scholarly journals De novo Molecular Design with Generative Long Short-term Memory

2019 ◽  
Vol 73 (12) ◽  
pp. 1006-1011 ◽  
Author(s):  
Francesca Grisoni ◽  
Gisbert Schneider
Keyword(s):  
Language Processing ◽  
Short Term Memory ◽  
De Novo ◽  
Molecular Design ◽  
Building Blocks ◽  
Generative Models ◽  
Molecular Structures ◽  
Short Term ◽  
Term Memory ◽  
Long Short Term Memory

Drug discovery benefits from computational models aiding the identification of new chemical matter with bespoke properties. The field of de novo drug design has been particularly revitalized by adaptation of generative machine learning models from the field of natural language processing. These deep neural network models are trained on recognizing molecular structures and generate new molecular entities without relying on pre-determined sets of molecular building blocks and chemical transformations for virtual molecule construction. Implicit representation of chemical knowledge provides an alternative to formulating the molecular design task in terms of the established, explicit chemical vocabulary. Here, we review de novo molecular design approaches from the field of 'artificial intelligence', focusing on instances of deep generative models, and highlight the prospective application of long short-term memory models to hit and lead finding in medicinal chemistry.

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 Chinese Text Classification Model Based on Deep Learning

2018 ◽  
Vol 10 (11) ◽  
pp. 113 ◽  
Author(s):  
Yue Li ◽  
Xutao Wang ◽  
Pengjian Xu
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Language Processing ◽  
Chinese Text ◽  
Text Classification ◽  
Short Term Memory ◽  
Classification Model ◽  
Short Term ◽  
Term Memory ◽  
Long Short Term Memory

Text classification is of importance in natural language processing, as the massive text information containing huge amounts of value needs to be classified into different categories for further use. In order to better classify text, our paper tries to build a deep learning model which achieves better classification results in Chinese text than those of other researchers’ models. After comparing different methods, long short-term memory (LSTM) and convolutional neural network (CNN) methods were selected as deep learning methods to classify Chinese text. LSTM is a special kind of recurrent neural network (RNN), which is capable of processing serialized information through its recurrent structure. By contrast, CNN has shown its ability to extract features from visual imagery. Therefore, two layers of LSTM and one layer of CNN were integrated to our new model: the BLSTM-C model (BLSTM stands for bi-directional long short-term memory while C stands for CNN.) LSTM was responsible for obtaining a sequence output based on past and future contexts, which was then input to the convolutional layer for extracting features. In our experiments, the proposed BLSTM-C model was evaluated in several ways. In the results, the model exhibited remarkable performance in text classification, especially in Chinese texts.

scholarly journals An Optimized Abstractive Text Summarization Model Using Peephole Convolutional LSTM

Symmetry ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 1290 ◽  
Author(s):  
Rahman ◽  
Siddiqui
Keyword(s):  
Language Processing ◽  
Short Term Memory ◽  
State Of The Art ◽  
Text Summarization ◽  
Short Term ◽  
Term Memory ◽  
Semantic Coherence ◽  
Long Short Term Memory ◽  
Central Composite ◽  
Convolutional Lstm

Abstractive text summarization that generates a summary by paraphrasing a long text remains an open significant problem for natural language processing. In this paper, we present an abstractive text summarization model, multi-layered attentional peephole convolutional LSTM (long short-term memory) (MAPCoL) that automatically generates a summary from a long text. We optimize parameters of MAPCoL using central composite design (CCD) in combination with the response surface methodology (RSM), which gives the highest accuracy in terms of summary generation. We record the accuracy of our model (MAPCoL) on a CNN/DailyMail dataset. We perform a comparative analysis of the accuracy of MAPCoL with that of the state-of-the-art models in different experimental settings. The MAPCoL also outperforms the traditional LSTM-based models in respect of semantic coherence in the output summary.

scholarly journals Long Short-Term Memory with Dynamic Skip Connections

2019 ◽  
Vol 33 ◽  
pp. 6481-6488 ◽  
Author(s):  
Tao Gui ◽  
Qi Zhang ◽  
Lujun Zhao ◽  
Yaosong Lin ◽  
Minlong Peng ◽  
...  
Keyword(s):  
Language Processing ◽  
Short Term Memory ◽  
Training Data ◽  
Sequential Data ◽  
Short Term ◽  
Term Memory ◽  
Transition Functions ◽  
Proposed Model ◽  
Long Short Term Memory

In recent years, long short-term memory (LSTM) has been successfully used to model sequential data of variable length. However, LSTM can still experience difficulty in capturing long-term dependencies. In this work, we tried to alleviate this problem by introducing a dynamic skip connection, which can learn to directly connect two dependent words. Since there is no dependency information in the training data, we propose a novel reinforcement learning-based method to model the dependency relationship and connect dependent words. The proposed model computes the recurrent transition functions based on the skip connections, which provides a dynamic skipping advantage over RNNs that always tackle entire sentences sequentially. Our experimental results on three natural language processing tasks demonstrate that the proposed method can achieve better performance than existing methods. In the number prediction experiment, the proposed model outperformed LSTM with respect to accuracy by nearly 20%.

scholarly journals Behavior recognition for humanoid robots using long short-term memory

2016 ◽  
Vol 13 (6) ◽  
pp. 172988141666336 ◽  
Author(s):  
Dickson Neoh Tze How ◽  
Chu Kiong Loo ◽  
Khairul Salleh Mohamed Sahari
Keyword(s):  
Neural Network ◽  
Recurrent Neural Network ◽  
Short Term Memory ◽  
Building Blocks ◽  
Humanoid Robots ◽  
Learning From Demonstration ◽  
Short Term ◽  
Term Memory ◽  
Complex Tasks ◽  
Long Short Term Memory

Learning from demonstration plays an important role in enabling robot to acquire new behaviors from human teachers. Within learning from demonstration, robots learn new tasks by recognizing a set of preprogrammed behaviors or skills as building blocks for new, potentially more complex tasks. One important aspect in this approach is the recognition of the set of behaviors that comprises the entire task. The ability to recognize a complex task as a sequence of simple behaviors enables the robot to generalize better on more complex tasks. In this article, we propose that primitive behaviors can be taught to a robot via learning from demonstration. In our experiment, we teach the robot new behaviors by demonstrating the behaviors to the robot several times. Following that, a long short-term memory recurrent neural network is trained to recognize the behaviors. In this study, we managed to teach at least six behaviors on a NAO humanoid robot and trained a long short-term memory recurrent neural network to recognize the behaviors using the supervised learning scheme. Our result shows that long short-term memory can recognize all the taught behaviors effectively, and it is able to generalize to recognize similar types of behaviors that have not been demonstrated on the robot before. We also show that the long short-term memory is advantageous compared to other neural network frameworks in recognizing the behaviors in the presence of noise in the behaviors.

scholarly journals COVID-19 ChatBot

2021 ◽  
Vol 9 (11) ◽  
pp. 44-49
Author(s):  
Satish Tirumalapudi
Keyword(s):  
Deep Learning ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Short Term Memory ◽  
Short Term ◽  
Term Memory ◽  
Long Short Term Memory ◽  
And Control ◽  
Prediction Problems

Abstract: Chat bots are software applications that help users to communicate with the machine and get the required result, this is where Natural Language Processing (NLP) comes into the picture. Natural language processing is based on deep learning that enables computers to acquire meaning from inputs given by the users. Natural language processing techniques can make possible the use of natural language to express ideas, thus drastically increasing accessibility. NLP engines rely on the elements of intent, utterance, entity, context, and session. Here in this project, we will be using Deep learning techniques which will be trained on the dataset which contains categories, patterns, and responses. Long Short-Term Memory (LSTM) is a Recurrent Neural Network that is capable of learning order dependence in sequence prediction problems. One of the most popular RNN approaches is LSTM to identify and control a dynamic system. We use an RNN to classify the category user’s message belongs to and then will give a response from the list of responses. Keywords: NLP – Natural Language Processing, LSTM – Long Short Term Memory, RNN – Recurrent Neural Networks.

scholarly journals Penerapan Convolutional Long Short-Term Memory untuk Klasifikasi Teks Berita Bahasa Indonesia

2021 ◽  
Vol 10 (4) ◽  
pp. 354-361
Author(s):  
Yudi Widhiyasana ◽  
Transmissia Semiawan ◽  
Ilham Gibran Achmad Mudzakir ◽  
Muhammad Randi Noor
Keyword(s):  
Deep Learning ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Short Term Memory ◽  
Learning Rate ◽  
Short Term ◽  
Term Memory ◽  
Long Short Term Memory ◽  
Bahasa Indonesia

Klasifikasi teks saat ini telah menjadi sebuah bidang yang banyak diteliti, khususnya terkait Natural Language Processing (NLP). Terdapat banyak metode yang dapat dimanfaatkan untuk melakukan klasifikasi teks, salah satunya adalah metode deep learning. RNN, CNN, dan LSTM merupakan beberapa metode deep learning yang umum digunakan untuk mengklasifikasikan teks. Makalah ini bertujuan menganalisis penerapan kombinasi dua buah metode deep learning, yaitu CNN dan LSTM (C-LSTM). Kombinasi kedua metode tersebut dimanfaatkan untuk melakukan klasifikasi teks berita bahasa Indonesia. Data yang digunakan adalah teks berita bahasa Indonesia yang dikumpulkan dari portal-portal berita berbahasa Indonesia. Data yang dikumpulkan dikelompokkan menjadi tiga kategori berita berdasarkan lingkupnya, yaitu “Nasional”, “Internasional”, dan “Regional”. Dalam makalah ini dilakukan eksperimen pada tiga buah variabel penelitian, yaitu jumlah dokumen, ukuran batch, dan nilai learning rate dari C-LSTM yang dibangun. Hasil eksperimen menunjukkan bahwa nilai F1-score yang diperoleh dari hasil klasifikasi menggunakan metode C-LSTM adalah sebesar 93,27%. Nilai F1-score yang dihasilkan oleh metode C-LSTM lebih besar dibandingkan dengan CNN, dengan nilai 89,85%, dan LSTM, dengan nilai 90,87%. Dengan demikian, dapat disimpulkan bahwa kombinasi dua metode deep learning, yaitu CNN dan LSTM (C-LSTM),memiliki kinerja yang lebih baik dibandingkan dengan CNN dan LSTM.

scholarly journals Learning molecular dynamics with simple language model built upon long short-term memory neural network

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Sun-Ting Tsai ◽  
En-Jui Kuo ◽  
Pratyush Tiwary
Keyword(s):  
Neural Networks ◽  
Language Processing ◽  
Recurrent Neural Networks ◽  
Short Term Memory ◽  
Language Model ◽  
Short Term ◽  
Term Memory ◽  
Molecular Systems ◽  
Simple Language ◽  
Long Short Term Memory

Abstract Recurrent neural networks have led to breakthroughs in natural language processing and speech recognition. Here we show that recurrent networks, specifically long short-term memory networks can also capture the temporal evolution of chemical/biophysical trajectories. Our character-level language model learns a probabilistic model of 1-dimensional stochastic trajectories generated from higher-dimensional dynamics. The model captures Boltzmann statistics and also reproduces kinetics across a spectrum of timescales. We demonstrate how training the long short-term memory network is equivalent to learning a path entropy, and that its embedding layer, instead of representing contextual meaning of characters, here exhibits a nontrivial connectivity between different metastable states in the underlying physical system. We demonstrate our model’s reliability through different benchmark systems and a force spectroscopy trajectory for multi-state riboswitch. We anticipate that our work represents a stepping stone in the understanding and use of recurrent neural networks for understanding the dynamics of complex stochastic molecular systems.

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