scholarly journals Machine Learning for Molecular Simulation

2020 ◽  
Vol 71 (1) ◽  
pp. 361-390 ◽  
Author(s):  
Frank Noé ◽  
Alexandre Tkatchenko ◽  
Klaus-Robert Müller ◽  
Cecilia Clementi
Keyword(s):  
Machine Learning ◽  
Molecular Simulation ◽  
Deep Neural Networks ◽  
Coarse Grained ◽  
Quantum Mechanical ◽  
Molecular Physics ◽  
Equilibrium Structures ◽  
Methodological Problems ◽  
Network Approaches ◽  
Energy Surfaces

Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for an ML revolution and have already been profoundly affected by the application of existing ML methods. Here we review recent ML methods for molecular simulation, with particular focus on (deep) neural networks for the prediction of quantum-mechanical energies and forces, on coarse-grained molecular dynamics, on the extraction of free energy surfaces and kinetics, and on generative network approaches to sample molecular equilibrium structures and compute thermodynamics. To explain these methods and illustrate open methodological problems, we review some important principles of molecular physics and describe how they can be incorporated into ML structures. Finally, we identify and describe a list of open challenges for the interface between ML and molecular simulation.

Adsorption Isotherm Predictions for Multiple Molecules in MOFs Using the Same Deep Learning Model

2019 ◽  
Author(s):  
Ryther Anderson ◽  
Achay Biong ◽  
Diego Gómez-Gualdrón
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Molecular Simulation ◽  
Large Scale ◽  
Learning Model ◽  
Operating Conditions ◽  
Small Subset ◽  
Screening Methods ◽  
Large Set ◽  
Metal Organic

<div>Tailoring the structure and chemistry of metal-organic frameworks (MOFs) enables the manipulation of their adsorption properties to suit specific energy and environmental applications. As there are millions of possible MOFs (with tens of thousands already synthesized), molecular simulation, such as grand canonical Monte Carlo (GCMC), has frequently been used to rapidly evaluate the adsorption performance of a large set of MOFs. This allows subsequent experiments to focus only on a small subset of the most promising MOFs. In many instances, however, even molecular simulation becomes prohibitively time consuming, underscoring the need for alternative screening methods, such as machine learning, to precede molecular simulation efforts. In this study, as a proof of concept, we trained a neural network as the first example of a machine learning model capable of predicting full adsorption isotherms of different molecules not included in the training of the model. To achieve this, we trained our neural network only on alchemical species, represented only by their geometry and force field parameters, and used this neural network to predict the loadings of real adsorbates. We focused on predicting room temperature adsorption of small (one- and two-atom) molecules relevant to chemical separations. Namely, argon, krypton, xenon, methane, ethane, and nitrogen. However, we also observed surprisingly promising predictions for more complex molecules, whose properties are outside the range spanned by the alchemical adsorbates. Prediction accuracies suitable for large-scale screening were achieved using simple MOF (e.g. geometric properties and chemical moieties), and adsorbate (e.g. forcefield parameters and geometry) descriptors. Our results illustrate a new philosophy of training that opens the path towards development of machine learning models that can predict the adsorption loading of any new adsorbate at any new operating conditions in any new MOF.</div>

BAND NN: A Deep Learning Framework For Energy Prediction and Geometry Optimization of Organic Small Molecules

2019 ◽  
Author(s):  
Siddhartha Laghuvarapu ◽  
Yashaswi Pathak ◽  
U. Deva Priyakumar
Keyword(s):  
Machine Learning ◽  
Density Functional ◽  
Computational Cost ◽  
Geometry Optimization ◽  
Dft Methods ◽  
Energy Prediction ◽  
Machine Learning Model ◽  
Equilibrium Structures ◽  
High Level ◽  
Non Equilibrium

Recent advances in artificial intelligence along with development of large datasets of energies calculated using quantum mechanical (QM)/density functional theory (DFT) methods have enabled prediction of accurate molecular energies at reasonably low computational cost. However, machine learning models that have been reported so far requires the atomic positions obtained from geometry optimizations using high level QM/DFT methods as input in order to predict the energies, and do not allow for geometry optimization. In this paper, a transferable and molecule-size independent machine learning model (BAND NN) based on a chemically intuitive representation inspired by molecular mechanics force fields is presented. The model predicts the atomization energies of equilibrium and non-equilibrium structures as sum of energy contributions from bonds (B), angles (A), nonbonds (N) and dihedrals (D) at remarkable accuracy. The robustness of the proposed model is further validated by calculations that span over the conformational, configurational and reaction space. The transferability of this model on systems larger than the ones in the dataset is demonstrated by performing calculations on select large molecules. Importantly, employing the BAND NN model, it is possible to perform geometry optimizations starting from non-equilibrium structures along with predicting their energies.

scholarly journals Trigonometric Inference Providing Learning in Deep Neural Networks

2021 ◽  
Vol 11 (15) ◽  
pp. 6704
Author(s):  
Jingyong Cai ◽  
Masashi Takemoto ◽  
Yuming Qiu ◽  
Hironori Nakajo
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Neural Networks ◽  
Activation Function ◽  
Trigonometric Approximation ◽  
Model Parameters ◽  
Training Algorithms ◽  
Activation Functions ◽  
Classical Training ◽  
Sum Formula

Despite being heavily used in the training of deep neural networks (DNNs), multipliers are resource-intensive and insufficient in many different scenarios. Previous discoveries have revealed the superiority when activation functions, such as the sigmoid, are calculated by shift-and-add operations, although they fail to remove multiplications in training altogether. In this paper, we propose an innovative approach that can convert all multiplications in the forward and backward inferences of DNNs into shift-and-add operations. Because the model parameters and backpropagated errors of a large DNN model are typically clustered around zero, these values can be approximated by their sine values. Multiplications between the weights and error signals are transferred to multiplications of their sine values, which are replaceable with simpler operations with the help of the product to sum formula. In addition, a rectified sine activation function is utilized for further converting layer inputs into sine values. In this way, the original multiplication-intensive operations can be computed through simple add-and-shift operations. This trigonometric approximation method provides an efficient training and inference alternative for devices with insufficient hardware multipliers. Experimental results demonstrate that this method is able to obtain a performance close to that of classical training algorithms. The approach we propose sheds new light on future hardware customization research for machine learning.

414 Deep Neural Networks: A Survey Tool for Obstructive Sleep Apnea Prediction

SLEEP ◽  
2021 ◽  
Vol 44 (Supplement_2) ◽  
pp. A164-A164
Author(s):  
Pahnwat Taweesedt ◽  
JungYoon Kim ◽  
Jaehyun Park ◽  
Jangwoon Park ◽  
Munish Sharma ◽  
...  
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Obstructive Sleep Apnea ◽  
Sleep Apnea ◽  
Deep Neural Networks ◽  
Support Vector ◽  
Learning Models ◽  
Obstructive Sleep ◽  
Screening Questionnaires ◽  
Machine Learning Models

Abstract Introduction Obstructive sleep apnea (OSA) is a common sleep-related breathing disorder with an estimation of one billion people. Full-night polysomnography is considered the gold standard for OSA diagnosis. However, it is time-consuming, expensive and is not readily available in many parts of the world. Many screening questionnaires and scores have been proposed for OSA prediction with high sensitivity and low specificity. The present study is intended to develop models with various machine learning techniques to predict the severity of OSA by incorporating features from multiple questionnaires. Methods Subjects who underwent full-night polysomnography in Torr sleep center, Texas and completed 5 OSA screening questionnaires/scores were included. OSA was diagnosed by using Apnea-Hypopnea Index ≥ 5. We trained five different machine learning models including Deep Neural Networks with the scaled principal component analysis (DNN-PCA), Random Forest (RF), Adaptive Boosting classifier (ABC), and K-Nearest Neighbors classifier (KNC) and Support Vector Machine Classifier (SVMC). Training:Testing subject ratio of 65:35 was used. All features including demographic data, body measurement, snoring and sleepiness history were obtained from 5 OSA screening questionnaires/scores (STOP-BANG questionnaires, Berlin questionnaires, NoSAS score, NAMES score and No-Apnea score). Performance parametrics were used to compare between machine learning models. Results Of 180 subjects, 51.5 % of subjects were male with mean (SD) age of 53.6 (15.1). One hundred and nineteen subjects were diagnosed with OSA. Area Under the Receiver Operating Characteristic Curve (AUROC) of DNN-PCA, RF, ABC, KNC, SVMC, STOP-BANG questionnaire, Berlin questionnaire, NoSAS score, NAMES score, and No-Apnea score were 0.85, 0.68, 0.52, 0.74, 0.75, 0.61, 0.63, 0,61, 0.58 and 0,58 respectively. DNN-PCA showed the highest AUROC with sensitivity of 0.79, specificity of 0.67, positive-predictivity of 0.93, F1 score of 0.86, and accuracy of 0.77. Conclusion Our result showed that DNN-PCA outperforms OSA screening questionnaires, scores and other machine learning models. Support (if any):

scholarly journals Balanced Sparsity for Efficient DNN Inference on GPU

2019 ◽  
Vol 33 ◽  
pp. 5676-5683 ◽  
Author(s):  
Zhuliang Yao ◽  
Shijie Cao ◽  
Wencong Xiao ◽  
Chen Zhang ◽  
Lanshun Nie
Keyword(s):  
Deep Neural Networks ◽  
General Purpose ◽  
Coarse Grained ◽  
Efficient Computation ◽  
Model Accuracy ◽  
Sparse Model ◽  
Model Inference ◽  
Fine Grained ◽  
Practical Inference ◽  
Speed Up

In trained deep neural networks, unstructured pruning can reduce redundant weights to lower storage cost. However, it requires the customization of hardwares to speed up practical inference. Another trend accelerates sparse model inference on general-purpose hardwares by adopting coarse-grained sparsity to prune or regularize consecutive weights for efficient computation. But this method often sacrifices model accuracy. In this paper, we propose a novel fine-grained sparsity approach, Balanced Sparsity, to achieve high model accuracy with commercial hardwares efficiently. Our approach adapts to high parallelism property of GPU, showing incredible potential for sparsity in the widely deployment of deep learning services. Experiment results show that Balanced Sparsity achieves up to 3.1x practical speedup for model inference on GPU, while retains the same high model accuracy as finegrained sparsity.

scholarly journals A Survey on Bias in Deep NLP

2021 ◽  
Vol 11 (7) ◽  
pp. 3184
Author(s):  
Ismael Garrido-Muñoz  ◽  
Arturo Montejo-Ráez  ◽  
Fernando Martínez-Santiago  ◽  
L. Alfonso Ureña-López 
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Natural Language Processing ◽  
Probability Distribution ◽  
Natural Language ◽  
Network Design ◽  
Language Processing ◽  
Deep Neural Networks ◽  
Learning Processes ◽  
Relevant Issue

Deep neural networks are hegemonic approaches to many machine learning areas, including natural language processing (NLP). Thanks to the availability of large corpora collections and the capability of deep architectures to shape internal language mechanisms in self-supervised learning processes (also known as “pre-training”), versatile and performing models are released continuously for every new network design. These networks, somehow, learn a probability distribution of words and relations across the training collection used, inheriting the potential flaws, inconsistencies and biases contained in such a collection. As pre-trained models have been found to be very useful approaches to transfer learning, dealing with bias has become a relevant issue in this new scenario. We introduce bias in a formal way and explore how it has been treated in several networks, in terms of detection and correction. In addition, available resources are identified and a strategy to deal with bias in deep NLP is proposed.

scholarly journals A transferable active-learning strategy for reactive molecular force fields

2021 ◽  
Author(s):  
Tom Young ◽  
Tristan Johnston-Wood ◽  
Volker L. Deringer ◽  
Fernanda Duarte
Keyword(s):  
Machine Learning ◽  
Active Learning ◽  
Learning Strategy ◽  
Force Fields ◽  
Molecular Simulations ◽  
Quantum Mechanical ◽  
Interatomic Potentials ◽  
Molecular Force ◽  
High Level ◽  
Active Learning Strategy

Predictive molecular simulations require fast, accurate and reactive interatomic potentials. Machine learning offers a promising approach to construct such potentials by fitting energies and forces to high-level quantum-mechanical data, but...

scholarly journals Representing Deep Neural Networks Latent Space Geometries with Graphs

Algorithms ◽  
2021 ◽  
Vol 14 (2) ◽  
pp. 39
Author(s):  
Carlos Lassance ◽  
Vincent Gripon ◽  
Antonio Ortega
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Objective Function ◽  
Learning Process ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
The Core ◽  
Learning Tasks ◽  
Latent Space

Deep Learning (DL) has attracted a lot of attention for its ability to reach state-of-the-art performance in many machine learning tasks. The core principle of DL methods consists of training composite architectures in an end-to-end fashion, where inputs are associated with outputs trained to optimize an objective function. Because of their compositional nature, DL architectures naturally exhibit several intermediate representations of the inputs, which belong to so-called latent spaces. When treated individually, these intermediate representations are most of the time unconstrained during the learning process, as it is unclear which properties should be favored. However, when processing a batch of inputs concurrently, the corresponding set of intermediate representations exhibit relations (what we call a geometry) on which desired properties can be sought. In this work, we show that it is possible to introduce constraints on these latent geometries to address various problems. In more detail, we propose to represent geometries by constructing similarity graphs from the intermediate representations obtained when processing a batch of inputs. By constraining these Latent Geometry Graphs (LGGs), we address the three following problems: (i) reproducing the behavior of a teacher architecture is achieved by mimicking its geometry, (ii) designing efficient embeddings for classification is achieved by targeting specific geometries, and (iii) robustness to deviations on inputs is achieved via enforcing smooth variation of geometry between consecutive latent spaces. Using standard vision benchmarks, we demonstrate the ability of the proposed geometry-based methods in solving the considered problems.

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