Search Results for author: Amir Barati Farimani

Found 67 papers, 33 papers with code

Deep Learning the Physics of Transport Phenomena

no code implementations7 Sep 2017 Amir Barati Farimani, Joseph Gomes, Vijay S. Pande

We have developed a new data-driven paradigm for the rapid inference, modeling and simulation of the physics of transport phenomena by deep learning.

Machine Learning Harnesses Molecular Dynamics to Discover New $μ$ Opioid Chemotypes

no code implementations12 Mar 2018 Evan N. Feinberg, Amir Barati Farimani, Rajendra Uprety, Amanda Hunkele, Gavril W. Pasternak, Susruta Majumdar, Vijay S. Pande

Computational chemists typically assay drug candidates by virtually screening compounds against crystal structures of a protein despite the fact that some targets, like the $\mu$ Opioid Receptor and other members of the GPCR family, traverse many non-crystallographic states.

BIG-bench Machine Learning

Deep Learning Phase Segregation

no code implementations23 Mar 2018 Amir Barati Farimani, Joseph Gomes, Rishi Sharma, Franklin L. Lee, Vijay S. Pande

Phase segregation, the process by which the components of a binary mixture spontaneously separate, is a key process in the evolution and design of many chemical, mechanical, and biological systems.

Weakly-Supervised Deep Learning of Heat Transport via Physics Informed Loss

no code implementations24 Jul 2018 Rishi Sharma, Amir Barati Farimani, Joe Gomes, Peter Eastman, Vijay Pande

In typical machine learning tasks and applications, it is necessary to obtain or create large labeled datasets in order to to achieve high performance.

BIG-bench Machine Learning

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

no code implementations18 Jan 2020 Juan Vargas, Lazar Andjelic, Amir Barati Farimani

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.

valid

Potential Neutralizing Antibodies Discovered for Novel Corona Virus Using Machine Learning

no code implementations18 Mar 2020 Rishikesh Magar, Prakarsh Yadav, Amir Barati Farimani

The fast and untraceable virus mutations take lives of thousands of people before the immune system can produce the inhibitory antibody.

BIG-bench Machine Learning

Deep Learning Convective Flow Using Conditional Generative Adversarial Networks

1 code implementation13 May 2020 Changlin Jiang, Amir Barati Farimani

We developed a general deep learning framework, FluidGAN, capable of learning and predicting time-dependent convective flow coupled with energy transport.

Orbital Graph Convolutional Neural Network for Material Property Prediction

no code implementations14 Aug 2020 Mohammadreza Karamad, Rishikesh Magar, Yuting Shi, Samira Siahrostami, Ian D. Gates, Amir Barati Farimani

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.

BIG-bench Machine Learning Property Prediction

FaultNet: A Deep Convolutional Neural Network for bearing fault classification

1 code implementation5 Oct 2020 Rishikesh Magar, Lalit Ghule, Junhan Li, Yang Zhao, Amir Barati Farimani

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.

Ranked #2 on Classification on CWRU Bearing Dataset (using extra training data)

BIG-bench Machine Learning Classification +2

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

1 code implementation21 Oct 2020 Pranshu Pant, Amir Barati Farimani

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.

Image Super-Resolution Vocal Bursts Intensity Prediction

Graph Convolutional Neural Networks for Body Force Prediction

no code implementations3 Dec 2020 Francis Ogoke, Kazem Meidani, Amirreza Hashemi, Amir Barati Farimani

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.

Learning Lagrangian Fluid Dynamics with Graph Neural Networks

no code implementations1 Jan 2021 Zijie Li, Amir Barati Farimani

We present a data-driven model for fluid simulation under Lagrangian representation.

Airfoil GAN: Encoding and Synthesizing Airfoils for Aerodynamic Shape Optimization

no code implementations12 Jan 2021 Yuyang Wang, Kenji Shimada, Amir Barati Farimani

Our model can (1) encode the existing airfoil into a latent vector and reconstruct the airfoil from that, (2) generate novel airfoils by randomly sampling the latent vectors and mapping the vectors to the airfoil coordinate domain, and (3) synthesize airfoils with desired aerodynamic properties by optimizing learned features via a genetic algorithm.

Generative Adversarial Network

Deep Reinforcement Learning Optimizes Graphene Nanopores for Efficient Desalination

no code implementations19 Jan 2021 Yuyang Wang, Zhonglin Cao, Amir Barati Farimani

Structure and geometry optimization of nanopores on such materials is beneficial for their performances in real-world engineering applications, like water desalination.

reinforcement-learning Reinforcement Learning (RL)

Thermal Control of Laser Powder Bed Fusion Using Deep Reinforcement Learning

no code implementations29 Jan 2021 Francis Ogoke, Amir Barati Farimani

Powder-based additive manufacturing techniques provide tools to construct intricate structures that are difficult to manufacture using conventional methods.

reinforcement-learning Reinforcement Learning (RL)

Molecular Contrastive Learning of Representations via Graph Neural Networks

1 code implementation19 Feb 2021 Yuyang Wang, Jianren Wang, Zhonglin Cao, Amir Barati Farimani

In this work, we present MolCLR: Molecular Contrastive Learning of Representations via Graph Neural Networks (GNNs), a self-supervised learning framework that leverages large unlabeled data (~10M unique molecules).

BIG-bench Machine Learning Contrastive Learning +4

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

no code implementations8 Mar 2021 Yilang Liu, Amir Barati Farimani

Comparing to conventional control strategies, the snake robots controlled by the trained PPO agent can achieve faster movement and more energy-efficient locomotion gait.

Navigate reinforcement-learning +1

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

1 code implementation26 Apr 2021 Yayati Jadhav, Amir Barati Farimani

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.

Feature Engineering

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

1 code implementation9 Jul 2021 Pranshu Pant, Ruchit Doshi, Pranav Bahl, Amir Barati Farimani

Reduced Order Modelling (ROM) has been widely used to create lower order, computationally inexpensive representations of higher-order dynamical systems.

Dimensionality Reduction

Prototype memory and attention mechanisms for few shot image generation

no code implementations ICLR 2022 Tianqin Li, Zijie Li, Andrew Luo, Harold Rockwell, Amir Barati Farimani, Tai Sing Lee

To test our proposal, we show in a few-shot image generation task, that having a prototype memory during attention can improve image synthesis quality, learn interpretable visual concept clusters, as well as improve the robustness of the model.

Image Generation Online Clustering

TPU-GAN: Learning temporal coherence from dynamic point cloud sequences

1 code implementation ICLR 2022 Zijie Li, Tianqin Li, Amir Barati Farimani

Our model, Temporal Point cloud Upsampling GAN (TPU-GAN), can implicitly learn the underlying temporal coherence from point cloud sequence, which in turn guides the generator to produce temporally coherent output.

Generative Adversarial Network point cloud upsampling +1

AugLiChem: Data Augmentation Library of Chemical Structures for Machine Learning

1 code implementation30 Nov 2021 Rishikesh Magar, Yuyang Wang, Cooper Lorsung, Chen Liang, Hariharan Ramasubramanian, Peiyuan Li, Amir Barati Farimani

Inspired by the success of data augmentations in computer vision and natural language processing, we developed AugLiChem: the data augmentation library for chemical structures.

BIG-bench Machine Learning Data Augmentation +1

Graph Neural Networks Accelerated Molecular Dynamics

1 code implementation6 Dec 2021 Zijie Li, Kazem Meidani, Prakarsh Yadav, Amir Barati Farimani

Molecular Dynamics (MD) simulation is a powerful tool for understanding the dynamics and structure of matter.

Improving Molecular Contrastive Learning via Faulty Negative Mitigation and Decomposed Fragment Contrast

1 code implementation18 Feb 2022 Yuyang Wang, Rishikesh Magar, Chen Liang, Amir Barati Farimani

On most benchmarks, the generic GNN pre-trained by iMolCLR rivals or even surpasses supervised learning models with sophisticated architecture designs and engineered features.

Contrastive Learning Self-Supervised Learning

Deep-Learned Generators of Porosity Distributions Produced During Metal Additive Manufacturing

no code implementations11 May 2022 Francis Ogoke, Kyle Johnson, Michael Glinsky, Chris Laursen, Sharlotte Kramer, Amir Barati Farimani

Laser Powder Bed Fusion has become a widely adopted method for metal Additive Manufacturing (AM) due to its ability to mass produce complex parts with increased local control.

Transformer for Partial Differential Equations' Operator Learning

1 code implementation26 May 2022 Zijie Li, Kazem Meidani, Amir Barati Farimani

Data-driven learning of partial differential equations' solution operators has recently emerged as a promising paradigm for approximating the underlying solutions.

Operator learning

Surrogate Modeling of Melt Pool Thermal Field using Deep Learning

no code implementations25 Jul 2022 AmirPouya Hemmasian, Francis Ogoke, Parand Akbari, Jonathan Malen, Jack Beuth, Amir Barati Farimani

In this work, we create three datasets of single-trail processes using Flow-3D and use them to train a convolutional neural network capable of predicting the behavior of the three-dimensional thermal field of the melt pool solely by taking three parameters as input: laser power, laser velocity, and time step.

TransPolymer: a Transformer-based language model for polymer property predictions

1 code implementation3 Sep 2022 Changwen Xu, Yuyang Wang, Amir Barati Farimani

Rigorous experiments on ten polymer property prediction benchmarks demonstrate the superior performance of TransPolymer.

Language Modelling Masked Language Modeling +2

Graph Neural Networks for Molecules

no code implementations12 Sep 2022 Yuyang Wang, Zijie Li, Amir Barati Farimani

Graph neural networks (GNNs), which are capable of learning representations from graphical data, are naturally suitable for modeling molecular systems.

Molecular Property Prediction Property Prediction +1

MAN: Multi-Action Networks Learning

1 code implementation19 Sep 2022 Keqin Wang, Alison Bartsch, Amir Barati Farimani

In this work, we introduce a Deep Reinforcement Learning (DRL) algorithm call Multi-Action Networks (MAN) Learning that addresses the challenge of high-dimensional large discrete action spaces.

Atari Games Q-Learning +2

Predicting CO$_2$ Absorption in Ionic Liquids with Molecular Descriptors and Explainable Graph Neural Networks

1 code implementation29 Sep 2022 Yue Jian, Yuyang Wang, Amir Barati Farimani

Fingerprint works on graph structure at the feature extraction stage, while GNNs directly handle molecule structure in both the feature extraction and model prediction stage.

MOFormer: Self-Supervised Transformer model for Metal-Organic Framework Property Prediction

1 code implementation25 Oct 2022 Zhonglin Cao, Rishikesh Magar, Yuyang Wang, Amir Barati Farimani

Furthermore, we revealed that MOFormer can be more data-efficient on quantum-chemical property prediction than structure-based CGCNN when training data is limited.

Property Prediction Self-Supervised Learning

A Physics-informed Diffusion Model for High-fidelity Flow Field Reconstruction

1 code implementation26 Nov 2022 Dule Shu, Zijie Li, Amir Barati Farimani

Machine learning models are gaining increasing popularity in the domain of fluid dynamics for their potential to accelerate the production of high-fidelity computational fluid dynamics data.

Vocal Bursts Intensity Prediction

MeshDQN: A Deep Reinforcement Learning Framework for Improving Meshes in Computational Fluid Dynamics

1 code implementation2 Dec 2022 Cooper Lorsung, Amir Barati Farimani

Current machine learning techniques often require substantial computational cost for training data generation, and are restricted in scope to the training data flow regime.

reinforcement-learning Reinforcement Learning (RL)

Denoise Pretraining on Nonequilibrium Molecules for Accurate and Transferable Neural Potentials

1 code implementation3 Mar 2023 Yuyang Wang, Changwen Xu, Zijie Li, Amir Barati Farimani

These results highlight the potential for leveraging denoise pretraining approaches to build more generalizable neural potentials for complex molecular systems.

Transformer-based Planning for Symbolic Regression

1 code implementation NeurIPS 2023 Parshin Shojaee, Kazem Meidani, Amir Barati Farimani, Chandan K. Reddy

Unlike conventional decoding strategies, TPSR enables the integration of non-differentiable feedback, such as fitting accuracy and complexity, as external sources of knowledge into the transformer-based equation generation process.

regression Symbolic Regression +1

Neural Network Predicts Ion Concentration Profiles under Nanoconfinement

1 code implementation10 Apr 2023 Zhonglin Cao, Yuyang Wang, Cooper Lorsung, Amir Barati Farimani

Overall, our deep learning model is a fast, flexible, and accurate surrogate model to predict ion concentration profiles in nanoconfinement.

Physics Informed Token Transformer for Solving Partial Differential Equations

1 code implementation15 May 2023 Cooper Lorsung, Zijie Li, Amir Barati Farimani

Solving Partial Differential Equations (PDEs) is the core of many fields of science and engineering.

OpenVR: Teleoperation for Manipulation

no code implementations16 May 2023 Abraham George, Alison Bartsch, Amir Barati Farimani

Across the robotics field, quality demonstrations are an integral part of many control pipelines.

Scalable Transformer for PDE Surrogate Modeling

1 code implementation NeurIPS 2023 Zijie Li, Dule Shu, Amir Barati Farimani

These sub-functions are then evaluated and used to compute the instance-based kernel with an axial factorized scheme.

PDE Surrogate Modeling

Hyena Neural Operator for Partial Differential Equations

1 code implementation28 Jun 2023 Saurabh Patil, Zijie Li, Amir Barati Farimani

The Hyena operator is an operation that enjoys sub-quadratic complexity and state space model to parameterize long convolution that enjoys a global receptive field.

Fluid Viscosity Prediction Leveraging Computer Vision and Robot Interaction

1 code implementation4 Aug 2023 Jong Hoon Park, Gauri Pramod Dalwankar, Alison Bartsch, Abraham George, Amir Barati Farimani

Then, the latent representations of the input data, produced from the pretrained autoencoder, is processed with a distinct inference head to infer either the fluid category (classification) or the fluid viscosity (regression) in a time-resolved manner.

Property Prediction regression +1

PeptideBERT: A Language Model based on Transformers for Peptide Property Prediction

1 code implementation28 Aug 2023 Chakradhar Guntuboina, Adrita Das, Parisa Mollaei, Seongwon Kim, Amir Barati Farimani

In this work, inspired by recent progress in Large Language Models (LLMs), we introduce PeptideBERT, a protein language model for predicting three key properties of peptides (hemolysis, solubility, and non-fouling).

Property Prediction Protein Language Model

Materials Informatics Transformer: A Language Model for Interpretable Materials Properties Prediction

1 code implementation30 Aug 2023 Hongshuo Huang, Rishikesh Magar, Changwen Xu, Amir Barati Farimani

We extend this paradigm by utilizing LLMs for material property prediction by introducing our model Materials Informatics Transformer (MatInFormer).

Language Modelling Property Prediction

SculptBot: Pre-Trained Models for 3D Deformable Object Manipulation

no code implementations15 Sep 2023 Alison Bartsch, Charlotte Avra, Amir Barati Farimani

Deformable object manipulation presents a unique set of challenges in robotic manipulation by exhibiting high degrees of freedom and severe self-occlusion.

Deformable Object Manipulation Object +1

One ACT Play: Single Demonstration Behavior Cloning with Action Chunking Transformers

no code implementations18 Sep 2023 Abraham George, Amir Barati Farimani

We achieve this goal by using linear transforms to augment the single demonstration, generating a set of trajectories for a wide range of initial conditions.

Chunking

GPT-MolBERTa: GPT Molecular Features Language Model for molecular property prediction

no code implementations20 Sep 2023 Suryanarayanan Balaji, Rishikesh Magar, Yayati Jadhav, Amir Barati Farimani

A text based description of 326000 molecules were collected using ChatGPT and used to train LLM to learn the representation of molecules.

Language Modelling Large Language Model +2

SNIP: Bridging Mathematical Symbolic and Numeric Realms with Unified Pre-training

2 code implementations3 Oct 2023 Kazem Meidani, Parshin Shojaee, Chandan K. Reddy, Amir Barati Farimani

To bridge the gap, we introduce SNIP, a Symbolic-Numeric Integrated Pre-training model, which employs contrastive learning between symbolic and numeric domains, enhancing their mutual similarities in the embeddings.

Contrastive Learning Few-Shot Learning +4

GPCR-BERT: Interpreting Sequential Design of G Protein Coupled Receptors Using Protein Language Models

no code implementations30 Oct 2023 Seongwon Kim, Parisa Mollaei, Akshay Antony, Rishikesh Magar, Amir Barati Farimani

In this paper, we developed the GPCR-BERT model for understanding the sequential design of G Protein-Coupled Receptors (GPCRs).

Multi-scale Time-stepping of Partial Differential Equations with Transformers

1 code implementation3 Nov 2023 AmirPouya Hemmasian, Amir Barati Farimani

Developing fast surrogates for Partial Differential Equations (PDEs) will accelerate design and optimization in almost all scientific and engineering applications.

Inexpensive High Fidelity Melt Pool Models in Additive Manufacturing Using Generative Deep Diffusion

no code implementations15 Nov 2023 Francis Ogoke, Quanliang Liu, Olabode Ajenifujah, Alexander Myers, Guadalupe Quirarte, Jack Beuth, Jonathan Malen, Amir Barati Farimani

Defects in laser powder bed fusion (L-PBF) parts often result from the meso-scale dynamics of the molten alloy near the laser, known as the melt pool.

FaultFormer: Pretraining Transformers for Adaptable Bearing Fault Classification

1 code implementation4 Dec 2023 Anthony Zhou, Amir Barati Farimani

In this work, we present pretraining and fine-tuning frameworks for identifying bearing faults based on transformer models.

Classification Data Augmentation

Characterization of Phosphorylated Tau-Microtubule complex with Molecular Dynamics (MD) simulation

1 code implementation18 Dec 2023 Seongwon Kim, Parisa Mollaei, Amir Barati Farimani, Anne Skaja Robinson

Alzheimer's Disease (AD), a neurodegenerative disorder, is reported as one of the most severe health and socioeconomic problems in current public health.

Dimensionality Reduction

PICL: Physics Informed Contrastive Learning for Partial Differential Equations

1 code implementation29 Jan 2024 Cooper Lorsung, Amir Barati Farimani

A combination of physics-informed system evolution and latent-space model output are anchored to input data and used in our distance function.

Contrastive Learning

Pretraining Strategy for Neural Potentials

1 code implementation24 Feb 2024 Zehua Zhang, Zijie Li, Amir Barati Farimani

We propose a mask pretraining method for Graph Neural Networks (GNNs) to improve their performance on fitting potential energy surfaces, particularly in water systems.

Denoising

Inpainting Computational Fluid Dynamics with Deep Learning

no code implementations27 Feb 2024 Dule Shu, Wilson Zhen, Zijie Li, Amir Barati Farimani

Fluid data completion is a research problem with high potential benefit for both experimental and computational fluid dynamics.

Quantization

Latent Neural PDE Solver: a reduced-order modelling framework for partial differential equations

no code implementations27 Feb 2024 Zijie Li, Saurabh Patil, Francis Ogoke, Dule Shu, Wilson Zhen, Michael Schneier, John R. Buchanan, Jr., Amir Barati Farimani

Neural networks have shown promising potential in accelerating the numerical simulation of systems governed by partial differential equations (PDEs).

SculptDiff: Learning Robotic Clay Sculpting from Humans with Goal Conditioned Diffusion Policy

no code implementations15 Mar 2024 Alison Bartsch, Arvind Car, Charlotte Avra, Amir Barati Farimani

Manipulating deformable objects remains a challenge within robotics due to the difficulties of state estimation, long-horizon planning, and predicting how the object will deform given an interaction.

Imitation Learning

Visuo-Tactile Pretraining for Cable Plugging

no code implementations18 Mar 2024 Abraham George, Selam Gano, Pranav Katragadda, Amir Barati Farimani

Our results show that by pretraining with tactile information, the performance of a non-tactile agent can be significantly improved, reaching a level on par with visuo-tactile agents.

Imitation Learning

Masked Autoencoders are PDE Learners

no code implementations26 Mar 2024 Anthony Zhou, Amir Barati Farimani

We hope that masked pretraining can emerge as a unifying method across large, unlabeled, and heterogeneous datasets to learn latent physics at scale.

Self-Supervised Learning

IDP-Bert: Predicting Properties of Intrinsically Disordered Proteins (IDP) Using Large Language Models

1 code implementation28 Mar 2024 Parisa Mollaei, Chakradhar Guntuboina, Danush Sadasivam, Amir Barati Farimani

In this study, we introduce IDP-Bert model, a deep-learning architecture leveraging Transformers and Protein Language Models (PLMs) to map sequences directly to IDPs properties.

AlloyBERT: Alloy Property Prediction with Large Language Models

no code implementations28 Mar 2024 Akshat Chaudhari, Chakradhar Guntuboina, Hongshuo Huang, Amir Barati Farimani

The pursuit of novel alloys tailored to specific requirements poses significant challenges for researchers in the field.

Property Prediction

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