arXiv subjects

Amir Barati Farimani

Publications and source records attributed to Amir Barati Farimani.

At least 145 records · Page 8Linked to original sources

arXiv2021

AugLiChem: Data Augmentation Library of Chemical Structures for Machine Learning

Machine learning (ML) has demonstrated the promise for accurate and efficient property prediction of molecules and crystalline materials. To develop highly accurate ML models for chemical structure property prediction, datasets with sufficient samples are required. However, obtaining clean and sufficient data of chemical properties can be expensive and time-consuming, which greatly limits the performance of ML models. Inspired by the success of data augmentations in computer vision and natural language processing, we developed AugLiChem: the data augmentation library for chemical structures. Augmentation methods for both crystalline systems and molecules are introduced, which can be utilized for fingerprint-based ML models and Graph Neural Networks(GNNs). We show that using our augmentation strategies significantly improves the performance of ML models, especially when using GNNs. In addition, the augmentations that we developed can be used as a direct plug-in module during training and have demonstrated the effectiveness when implemented with different GNN models through the AugliChem library. The Python-based package for our implementation of Auglichem: Data augmentation library for chemical structures, is publicly available at: https://github.com/BaratiLab/AugLiChem.

cs.LG↗

arXiv2021

Deep Learning for Reduced Order Modelling and Efficient Temporal Evolution of Fluid Simulations

Reduced Order Modelling (ROM) has been widely used to create lower order, computationally inexpensive representations of higher-order dynamical systems. Using these representations, ROMs can efficiently model flow fields while using significantly lesser parameters. Conventional ROMs accomplish this by linearly projecting higher-order manifolds to lower-dimensional space using dimensionality reduction techniques such as Proper Orthogonal Decomposition (POD). In this work, we develop a novel deep learning framework DL-ROM (Deep Learning - Reduced Order Modelling) to create a neural network capable of non-linear projections to reduced order states. We then use the learned reduced state to efficiently predict future time steps of the simulation using 3D Autoencoder and 3D U-Net based architectures. Our model DL-ROM is able to create highly accurate reconstructions from the learned ROM and is thus able to efficiently predict future time steps by temporally traversing in the learned reduced state. All of this is achieved without ground truth supervision or needing to iteratively solve the expensive Navier-Stokes(NS) equations thereby resulting in massive computational savings. To test the effectiveness and performance of our approach, we evaluate our implementation on five different Computational Fluid Dynamics (CFD) datasets using reconstruction performance and computational runtime metrics. DL-ROM can reduce the computational runtimes of iterative solvers by nearly two orders of magnitude while maintaining an acceptable error threshold.

physics.flu-dyn↗

arXiv2021

Dominant motion identification of multi-particle system using deep learning from video

Identifying underlying governing equations and physical relevant information from high-dimensional observable data has always been a challenge in physical sciences. With the recent advances in sensing technology and available datasets, various machine learning techniques have made it possible to distill underlying mathematical models from sufficiently clean and usable datasets. However, most of these techniques rely on prior knowledge of the system and noise-free data obtained by simulation of physical system or by direct measurements of the signals. Hence, the inference obtained by using these techniques is often unreliable to be used in the real world where observed data is noisy and requires feature engineering to extract relevant features. In this work, we provide a deep-learning framework that extracts relevant information from real-world videos of highly stochastic systems, with no prior knowledge and distills the underlying governing equation representing the system. We demonstrate this approach on videos of confined multi-agent/particle systems of ants, termites, fishes as well as a simulated confined multi-particle system with elastic collision interactions. Furthermore, we explore how these seemingly diverse systems have predictable underlying behavior. In this study, we have used computer vision and motion tracking to extract spatial trajectories of individual agents/particles in a system, and by using LSTM VAE we projected these features on a low-dimensional latent space from which the underlying differential equation representing the data was extracted using SINDy framework.

cs.LG↗

arXiv2021

An Energy-Saving Snake Locomotion Gait Policy Obtained Using Deep Reinforcement Learning

Snake robots, comprised of sequentially connected joint actuators, have recently gained increasing attention in the industrial field, like life detection in narrow space. Such robots can navigate through the complex environment via the cooperation of multiple motors located on the backbone. However, controlling the robots in an unknown environment is challenging, and conventional control strategies can be energy inefficient or even fail to navigate to the destination. In this work, a snake locomotion gait policy is developed via deep reinforcement learning (DRL) for energy-efficient control. We apply proximal policy optimization (PPO) to each joint motor parameterized by angular velocity and the DRL agent learns the standard serpenoid curve at each timestep. The robot simulator and task environment are built upon PyBullet. Comparing to conventional control strategies, the snake robots controlled by the trained PPO agent can achieve faster movement and more energy-efficient locomotion gait. This work demonstrates that DRL provides an energy-efficient solution for robot control.

cs.LG↗

arXiv2021

Deep Learning for Efficient Reconstruction of High-Resolution Turbulent DNS Data

Within the domain of Computational Fluid Dynamics, Direct Numerical Simulation (DNS) is used to obtain highly accurate numerical solutions for fluid flows. However, this approach for numerically solving the Navier-Stokes equations is extremely computationally expensive mostly due to the requirement of greatly refined grids. Large Eddy Simulation (LES) presents a more computationally efficient approach for solving fluid flows on lower-resolution (LR) grids but results in an overall reduction in solution fidelity. Through this paper, we introduce a novel deep learning framework SR-DNS Net, which aims to mitigate this inherent trade-off between solution fidelity and computational complexity by leveraging deep learning techniques used in image super-resolution. Using our model, we wish to learn the mapping from a coarser LR solution to a refined high-resolution (HR) DNS solution so as to eliminate the need for performing DNS on highly refined grids. Our model efficiently reconstructs the high-fidelity DNS data from the LES like low-resolution solutions while yielding good reconstruction metrics. Thus our implementation improves the solution accuracy of LR solutions while incurring only a marginal increase in computational cost required for deploying the trained deep learning model.

physics.flu-dyn↗

arXiv2021

Deep learning of material transport in complex neurite networks

Neurons exhibit complex geometry in their branched networks of neurites which is essential to the function of individual neuron but also brings challenges to transport a wide variety of essential materials throughout their neurite networks for their survival and function. While numerical methods like isogeometric analysis (IGA) have been used for modeling the material transport process via solving partial differential equations (PDEs), they require long computation time and huge computation resources to ensure accurate geometry representation and solution, thus limit their biomedical application. Here we present a graph neural network (GNN)-based deep learning model to learn the IGA-based material transport simulation and provide fast material concentration prediction within neurite networks of any topology. Given input boundary conditions and geometry configurations, the well-trained model can predict the dynamical concentration change during the transport process with an average error less than 10% and 120~330 times faster compared to IGA simulations. The effectiveness of the proposed model is demonstrated within several complex neurite networks.

cs.CE↗

arXiv2021

Deep Reinforcement Learning Optimizes Graphene Nanopores for Efficient Desalination

Two-dimensional nanomaterials, such as graphene, have been extensively studied because of their outstanding physical properties. Structure and geometry optimization of nanopores on such materials is beneficial for their performances in real-world engineering applications, like water desalination. However, the optimization process often involves very large number of experiments or simulations which are expensive and time-consuming. In this work, we propose a graphene nanopore optimization framework via the combination of deep reinforcement learning (DRL) and convolutional neural network (CNN) for efficient water desalination. The DRL agent controls the growth of nanopore by determining the atom to be removed at each timestep, while the CNN predicts the performance of nanoporus graphene for water desalination: the water flux and ion rejection at a certain external pressure. With the synchronous feedback from CNN-accelerated desalination performance prediction, our DRL agent can optimize the nanoporous graphene efficiently in an online manner. Molecular dynamics (MD) simulations on promising DRL-designed graphene nanopores show that they have higher water flux while maintaining rival ion rejection rate compared to the normal circular nanopores. Semi-oval shape with rough edges geometry of DRL-designed pores is found to be the key factor for their high water desalination performance. Ultimately, this study shows that DRL can be a powerful tool for material design.

cs.LG↗

arXiv2021

FaultNet: A Deep Convolutional Neural Network for bearing fault classification

The increased presence of advanced sensors on the production floors has led to the collection of datasets that can provide significant insights into machine health. An important and reliable indicator of machine health, vibration signal data can provide us a greater understanding of different faults occurring in mechanical systems. In this work, we analyze vibration signal data of mechanical systems with bearings by combining different signal processing methods and coupling them with machine learning techniques to classify different types of bearing faults. We also highlight the importance of using different signal processing methods and analyze their effect on accuracy for bearing fault detection. Apart from the traditional machine learning algorithms we also propose a convolutional neural network FaultNet which can effectively determine the type of bearing fault with a high degree of accuracy. The distinguishing factor of this work is the idea of channels proposed to extract more information from the signal, we have stacked the Mean and Median channels to raw signal to extract more useful features to classify the signals with greater accuracy.

eess.SP↗

arXiv2021

Thermal Control of Laser Powder Bed Fusion Using Deep Reinforcement Learning

Powder-based additive manufacturing techniques provide tools to construct intricate structures that are difficult to manufacture using conventional methods. In Laser Powder Bed Fusion, components are built by selectively melting specific areas of the powder bed, to form the two-dimensional cross-section of the specific part. However, the high occurrence of defects impacts the adoption of this method for precision applications. Therefore, a control policy for dynamically altering process parameters to avoid phenomena that lead to defect occurrences is necessary. A Deep Reinforcement Learning (DRL) framework that derives a versatile control strategy for minimizing the likelihood of these defects is presented. The generated control policy alters the velocity of the laser during the melting process to ensure the consistency of the melt pool and reduce overheating in the generated product. The control policy is trained and validated on efficient simulations of the continuum temperature distribution of the powder bed layer under various laser trajectories.

eess.SP↗

arXiv2020

Graph Convolutional Neural Networks for Body Force Prediction

Many scientific and engineering processes produce spatially unstructured data. However, most data-driven models require a feature matrix that enforces both a set number and order of features for each sample. They thus cannot be easily constructed for an unstructured dataset. Therefore, a graph based data-driven model to perform inference on fields defined on an unstructured mesh, using a Graph Convolutional Neural Network (GCNN) is presented. The ability of the method to predict global properties from spatially irregular measurements with high accuracy is demonstrated by predicting the drag force associated with laminar flow around airfoils from scattered velocity measurements. The network can infer from field samples at different resolutions, and is invariant to the order in which the measurements within each sample are presented. The GCNN method, using inductive convolutional layers and adaptive pooling, is able to predict this quantity with a validation $R^{2}$ above 0.98, and a Normalized Mean Squared Error below 0.01, without relying on spatial structure.

cs.LG↗

arXiv2020

Data-driven Identification of 2D Partial Differential Equations using extracted physical features

Many scientific phenomena are modeled by Partial Differential Equations (PDEs). The development of data gathering tools along with the advances in machine learning (ML) techniques have raised opportunities for data-driven identification of governing equations from experimentally observed data. We propose an ML method to discover the terms involved in the equation from two-dimensional spatiotemporal data. Robust and useful physical features are extracted from data samples to represent the specific behaviors imposed by each mathematical term in the equation. Compared to the previous models, this idea provides us with the ability to discover 2D equations with time derivatives of different orders, and also to identify new underlying physics on which the model has not been trained. Moreover, the model can work with small sets of low-resolution data while avoiding numerical differentiations. The results indicate robustness of the features extracted based on prior knowledge in comparison to automatically detected features by a Three-dimensional Convolutional Neural Network (3D CNN) given the same amounts of data. Although particular PDEs are studied in this work, the idea of the proposed approach could be extended for reliable identification of various PDEs.

cs.LG↗

arXiv2020

Orbital Graph Convolutional Neural Network for Material Property Prediction

Material representations that are compatible with machine learning models play a key role in developing models that exhibit high accuracy for property prediction. Atomic orbital interactions are one of the important factors that govern the properties of crystalline materials, from which the local chemical environments of atoms is inferred. Therefore, to develop robust machine learningmodels for material properties prediction, it is imperative to include features representing such chemical attributes. Here, we propose the Orbital Graph Convolutional Neural Network (OGCNN), a crystal graph convolutional neural network framework that includes atomic orbital interaction features that learns material properties in a robust way. In addition, we embedded an encoder-decoder network into the OGCNN enabling it to learn important features among basic atomic (elemental features), orbital-orbital interactions, and topological features. We examined the performance of this model on a broad range of crystalline material data to predict different properties. We benchmarked the performance of the OGCNN model with that of: 1) the crystal graph convolutional neural network (CGCNN), 2) other state-of-the-art descriptors for material representations including Many-body Tensor Representation (MBTR) and the Smooth Overlap of Atomic Positions (SOAP), and 3) other conventional regression machine learning algorithms where different crystal featurization methods have been used. We find that OGCNN significantly outperforms them. The OGCNN model with high predictive accuracy can be used to discover new materials among the immense phase and compound spaces of materials

physics.comp-ph↗

arXiv2020

Reduced Thermal Conductivity of Supported and Encased Monolayer and Bilayer MoS$_2$

Electrical and thermal properties of atomically thin two-dimensional (2D) materials are affected by their environment, e.g. through remote phonon scattering or dielectric screening. However, while it is known that mobility and thermal conductivity (TC) of graphene are reduced on a substrate, these effects are much less explored in 2D semiconductors such as MoS$_2$. Here, we use molecular dynamics to understand TC changes in monolayer (1L) and bilayer (2L) MoS$_2$ by comparing suspended, supported, and encased structures. The TC of monolayer MoS$_2$ is reduced from ~117 Wm$^{-1}$K$^{-1}$ when suspended, to ~31 Wm$^{-1}$K$^{-1}$ when supported by SiO$_2$, at 300 K. Encasing 1L MoS$_2$ in SiO$_2$ further reduces its TC down to ~22 Wm$^{-1}$K$^{-1}$. In contrast, the TC of 2L MoS$_2$ is not as drastically reduced, being >50% higher than 1L both when supported and encased. These effects are due to phonon scattering with remote vibrational modes of the substrate, which are partly screened in 2L MoS$_2$. We also examine the TC of 1L MoS$_2$ across a wide range of temperatures (300 to 700 K) and defect densities (up to 5$\times$10$^{13}$ cm$^{-2}$), finding that the substrate reduces the dependence of TC on these factors. Taken together, these are important findings for all applications which will use 2D semiconductors supported or encased by insulators, instead of freely suspended.

cond-mat.mtrl-sci↗

arXiv2020

StressGAN: A Generative Deep Learning Model for 2D Stress Distribution Prediction

Using deep learning to analyze mechanical stress distributions has been gaining interest with the demand for fast stress analysis methods. Deep learning approaches have achieved excellent outcomes when utilized to speed up stress computation and learn the physics without prior knowledge of underlying equations. However, most studies restrict the variation of geometry or boundary conditions, making these methods difficult to be generalized to unseen configurations. We propose a conditional generative adversarial network (cGAN) model for predicting 2D von Mises stress distributions in solid structures. The cGAN learns to generate stress distributions conditioned by geometries, load, and boundary conditions through a two-player minimax game between two neural networks with no prior knowledge. By evaluating the generative network on two stress distribution datasets under multiple metrics, we demonstrate that our model can predict more accurate high-resolution stress distributions than a baseline convolutional neural network model, given various and complex cases of geometry, load and boundary conditions.

cs.CV↗

arXiv2020

Machine learning force fields and coarse-grained variables in molecular dynamics: application to materials and biological systems

Machine learning encompasses a set of tools and algorithms which are now becoming popular in almost all scientific and technological fields. This is true for molecular dynamics as well, where machine learning offers promises of extracting valuable information from the enormous amounts of data generated by simulation of complex systems. We provide here a review of our current understanding of goals, benefits, and limitations of machine learning techniques for computational studies on atomistic systems, focusing on the construction of empirical force fields from ab-initio databases and the determination of reaction coordinates for free energy computation and enhanced sampling.

physics.comp-ph↗

arXiv2020

Potential Neutralizing Antibodies Discovered for Novel Corona Virus Using Machine Learning

The fast and untraceable virus mutations take lives of thousands of people before the immune system can produce the inhibitory antibody. Recent outbreak of novel coronavirus infected and killed thousands of people in the world. Rapid methods in finding peptides or antibody sequences that can inhibit the viral epitopes of COVID-19 will save the life of thousands. In this paper, we devised a machine learning (ML) model to predict the possible inhibitory synthetic antibodies for Corona virus. We collected 1933 virus-antibody sequences and their clinical patient neutralization response and trained an ML model to predict the antibody response. Using graph featurization with variety of ML methods, we screened thousands of hypothetical antibody sequences and found 8 stable antibodies that potentially inhibit COVID-19. We combined bioinformatics, structural biology, and Molecular Dynamics (MD) simulations to verify the stability of the candidate antibodies that can inhibit the Corona virus.

q-bio.BM↗

arXiv2020

Effects of sparse rewards of different magnitudes in the speed of learning of model-based actor critic methods

Actor critic methods with sparse rewards in model-based deep reinforcement learning typically require a deterministic binary reward function that reflects only two possible outcomes: if, for each step, the goal has been achieved or not. Our hypothesis is that we can influence an agent to learn faster by applying an external environmental pressure during training, which adversely impacts its ability to get higher rewards. As such, we deviate from the classical paradigm of sparse rewards and add a uniformly sampled reward value to the baseline reward to show that (1) sample efficiency of the training process can be correlated to the adversity experienced during training, (2) it is possible to achieve higher performance in less time and with less resources, (3) we can reduce the performance variability experienced seed over seed, (4) there is a maximum point after which more pressure will not generate better results, and (5) that random positive incentives have an adverse effect when using a negative reward strategy, making an agent under those conditions learn poorly and more slowly. These results have been shown to be valid for Deep Deterministic Policy Gradients using Hindsight Experience Replay in a well known Mujoco environment, but we argue that they could be generalized to other methods and environments as well.

cs.LG↗

arXiv2019

Creativity in Robot Manipulation with Deep Reinforcement Learning

Deep Reinforcement Learning (DRL) has emerged as a powerful control technique in robotic science. In contrast to control theory, DRL is more robust in the thorough exploration of the environment. This capability of DRL generates more human-like behaviour and intelligence when applied to the robots. To explore this capability, we designed challenging manipulation tasks to observe robots strategy to handle complex scenarios. We observed that robots not only perform tasks successfully, but also transpire a creative and non intuitive solution. We also observed robot's persistence in tasks that are close to success and its striking ability in discerning to continue or give up.

cs.LG↗