arXiv subjects

Amir Barati Farimani

Publications and source records attributed to Amir Barati Farimani.

At least 109 records · Page 6Linked to original sources

arXiv2023

Fluid Viscosity Prediction Leveraging Computer Vision and Robot Interaction

Accurately determining fluid viscosity is crucial for various industrial and scientific applications. Traditional methods of viscosity measurement, though reliable, often require manual intervention and cannot easily adapt to real-time monitoring. With advancements in machine learning and computer vision, this work explores the feasibility of predicting fluid viscosity by analyzing fluid oscillations captured in video data. The pipeline employs a 3D convolutional autoencoder pretrained in a self-supervised manner to extract and learn features from semantic segmentation masks of oscillating fluids. 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. When the latent representations generated by the pretrained autoencoder are used for classification, the system achieves a 97.1% accuracy across a total of 4,140 test datapoints. Similarly, for regression tasks, employing an additional fully-connected network as a regression head allows the pipeline to achieve a mean absolute error of 0.258 over 4,416 test datapoints. This study represents an innovative contribution to both fluid characterization and the evolving landscape of Artificial Intelligence, demonstrating the potential of deep learning in achieving near real-time viscosity estimation and addressing practical challenges in fluid dynamics through the analysis of video data capturing oscillating fluid dynamics.

cs.LG↗

arXiv2023

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

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. For instance, the melt pool can directly contribute to the formation of undesirable porosity, residual stress, and surface roughness in the final part. Experimental in-situ monitoring of the three-dimensional melt pool physical fields is challenging, due to the short length and time scales involved in the process. Multi-physics simulation methods can describe the three-dimensional dynamics of the melt pool, but are computationally expensive at the mesh refinement required for accurate predictions of complex effects, such as the formation of keyhole porosity. Therefore, in this work, we develop a generative deep learning model based on the probabilistic diffusion framework to map low-fidelity, coarse-grained simulation information to the high-fidelity counterpart. By doing so, we bypass the computational expense of conducting multiple high-fidelity simulations for analysis by instead upscaling lightweight coarse mesh simulations. Specifically, we implement a 2-D diffusion model to spatially upscale cross-sections of the coarsely simulated melt pool to their high-fidelity equivalent. We demonstrate the preservation of key metrics of the melting process between the ground truth simulation data and the diffusion model output, such as the temperature field, the melt pool dimensions and the variability of the keyhole vapor cavity. Specifically, we predict the melt pool depth within 3 $μm$ based on low-fidelity input data 4$\times$ coarser than the high-fidelity simulations, reducing analysis time by two orders of magnitude.

cs.LG↗

arXiv2023

Scalable Transformer for PDE Surrogate Modeling

Transformer has shown state-of-the-art performance on various applications and has recently emerged as a promising tool for surrogate modeling of partial differential equations (PDEs). Despite the introduction of linear-complexity attention, applying Transformer to problems with a large number of grid points can be numerically unstable and computationally expensive. In this work, we propose Factorized Transformer (FactFormer), which is based on an axial factorized kernel integral. Concretely, we introduce a learnable projection operator that decomposes the input function into multiple sub-functions with one-dimensional domain. These sub-functions are then evaluated and used to compute the instance-based kernel with an axial factorized scheme. We showcase that the proposed model is able to simulate 2D Kolmogorov flow on a $256\times 256$ grid and 3D smoke buoyancy on a $64\times64\times64$ grid with good accuracy and efficiency. The proposed factorized scheme can serve as a computationally efficient low-rank surrogate for the full attention scheme when dealing with multi-dimensional problems.

cs.LG↗

arXiv2023

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

Developing fast surrogates for Partial Differential Equations (PDEs) will accelerate design and optimization in almost all scientific and engineering applications. Neural networks have been receiving ever-increasing attention and demonstrated remarkable success in computational modeling of PDEs, however; their prediction accuracy is not at the level of full deployment. In this work, we utilize the transformer architecture, the backbone of numerous state-of-the-art AI models, to learn the dynamics of physical systems as the mixing of spatial patterns learned by a convolutional autoencoder. Moreover, we incorporate the idea of multi-scale hierarchical time-stepping to increase the prediction speed and decrease accumulated error over time. Our model achieves similar or better results in predicting the time-evolution of Navier-Stokes equations compared to the powerful Fourier Neural Operator (FNO) and two transformer-based neural operators OFormer and Galerkin Transformer.

cs.LG↗

arXiv2023

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

With the rise of Transformers and Large Language Models (LLMs) in Chemistry and Biology, new avenues for the design and understanding of therapeutics have opened up to the scientific community. Protein sequences can be modeled as language and can take advantage of recent advances in LLMs, specifically with the abundance of our access to the protein sequence datasets. In this paper, we developed the GPCR-BERT model for understanding the sequential design of G Protein-Coupled Receptors (GPCRs). GPCRs are the target of over one-third of FDA-approved pharmaceuticals. However, there is a lack of comprehensive understanding regarding the relationship between amino acid sequence, ligand selectivity, and conformational motifs (such as NPxxY, CWxP, E/DRY). By utilizing the pre-trained protein model (Prot-Bert) and fine-tuning with prediction tasks of variations in the motifs, we were able to shed light on several relationships between residues in the binding pocket and some of the conserved motifs. To achieve this, we took advantage of attention weights, and hidden states of the model that are interpreted to extract the extent of contributions of amino acids in dictating the type of masked ones. The fine-tuned models demonstrated high accuracy in predicting hidden residues within the motifs. In addition, the analysis of embedding was performed over 3D structures to elucidate the higher-order interactions within the conformations of the receptors.

cs.LG↗

arXiv2023

Transformer-based Planning for Symbolic Regression

Symbolic regression (SR) is a challenging task in machine learning that involves finding a mathematical expression for a function based on its values. Recent advancements in SR have demonstrated the effectiveness of pre-trained transformer-based models in generating equations as sequences, leveraging large-scale pre-training on synthetic datasets and offering notable advantages in terms of inference time over classical Genetic Programming (GP) methods. However, these models primarily rely on supervised pre-training goals borrowed from text generation and overlook equation discovery objectives like accuracy and complexity. To address this, we propose TPSR, a Transformer-based Planning strategy for Symbolic Regression that incorporates Monte Carlo Tree Search into the transformer decoding process. 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. Extensive experiments on various datasets show that our approach outperforms state-of-the-art methods, enhancing the model's fitting-complexity trade-off, extrapolation abilities, and robustness to noise.

cs.LG↗

arXiv2023

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

With the emergence of Transformer architectures and their powerful understanding of textual data, a new horizon has opened up to predict the molecular properties based on text description. While SMILES are the most common form of representation, they are lacking robustness, rich information and canonicity, which limit their effectiveness in becoming generalizable representations. Here, we present GPT-MolBERTa, a self-supervised large language model (LLM) which uses detailed textual descriptions of molecules to predict their properties. A text based description of 326000 molecules were collected using ChatGPT and used to train LLM to learn the representation of molecules. To predict the properties for the downstream tasks, both BERT and RoBERTa models were used in the finetuning stage. Experiments show that GPT-MolBERTa performs well on various molecule property benchmarks, and approaching state of the art performance in regression tasks. Additionally, further analysis of the attention mechanisms show that GPT-MolBERTa is able to pick up important information from the input textual data, displaying the interpretability of the model.

physics.chem-ph↗

arXiv2023

Hyena Neural Operator for Partial Differential Equations

Numerically solving partial differential equations typically requires fine discretization to resolve necessary spatiotemporal scales, which can be computationally expensive. Recent advances in deep learning have provided a new approach to solving partial differential equations that involves the use of neural operators. Neural operators are neural network architectures that learn mappings between function spaces and have the capability to solve partial differential equations based on data. This study utilizes a novel neural operator called Hyena, which employs a long convolutional filter that is parameterized by a multilayer perceptron. 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. This mechanism enhances the model's comprehension of the input's context and enables data-dependent weight for different partial differential equations instances. To measure how effective the layers are in solving partial differential equations, we conduct experiments on Diffusion-Reaction equation and Navier Stokes equation. Our findings indicate Hyena Neural operator can serve as an efficient and accurate model for learning partial differential equations solution operator. The data and code used can be found at: https://github.com/Saupatil07/Hyena-Neural-Operator

cs.LG↗

arXiv2023

Pour me a drink: Robotic Precision Pouring Carbonated Beverages into Transparent Containers

With the growing emphasis on the development and integration of service robots within household environments, we will need to endow robots with the ability to reliably pour a variety of liquids. However, liquid handling and pouring is a challenging task due to the complex dynamics and varying properties of different liquids, the exacting precision required to prevent spills and ensure accurate pouring, and the necessity for robots to adapt seamlessly to a multitude of containers in real-world scenarios. In response to these challenges, we propose a novel autonomous robotics pipeline that empowers robots to execute precision pouring tasks, encompassing both carbonated and non-carbonated liquids, as well as opaque and transparent liquids, into a variety of transparent containers. Our proposed approach maximizes the potential of RGB input alone, achieving zero-shot capability by harnessing existing pre-trained vision segmentation models. This eliminates the need for additional data collection, manual image annotations, or extensive training. Furthermore, our work integrates ChatGPT, facilitating seamless interaction between individuals without prior expertise in robotics and our pouring pipeline, this integration enables users to effortlessly request and execute pouring actions. Our experiments demonstrate the pipeline's capability to successfully pour a diverse range of carbonated and non-carbonated beverages into containers of varying sizes, relying solely on visual input.

cs.RO↗

arXiv2023

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

Learning from human demonstrations (behavior cloning) is a cornerstone of robot learning. However, most behavior cloning algorithms require a large number of demonstrations to learn a task, especially for general tasks that have a large variety of initial conditions. Humans, however, can learn to complete tasks, even complex ones, after only seeing one or two demonstrations. Our work seeks to emulate this ability, using behavior cloning to learn a task given only a single human demonstration. 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. With these demonstrations, we are able to train a behavior cloning agent to successfully complete three block manipulation tasks. Additionally, we developed a novel addition to the temporal ensembling method used by action chunking agents during inference. By incorporating the standard deviation of the action predictions into the ensembling method, our approach is more robust to unforeseen changes in the environment, resulting in significant performance improvements.

cs.RO↗

arXiv2023

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

Deformable object manipulation presents a unique set of challenges in robotic manipulation by exhibiting high degrees of freedom and severe self-occlusion. State representation for materials that exhibit plastic behavior, like modeling clay or bread dough, is also difficult because they permanently deform under stress and are constantly changing shape. In this work, we investigate each of these challenges using the task of robotic sculpting with a parallel gripper. We propose a system that uses point clouds as the state representation and leverages pre-trained point cloud reconstruction Transformer to learn a latent dynamics model to predict material deformations given a grasp action. We design a novel action sampling algorithm that reasons about geometrical differences between point clouds to further improve the efficiency of model-based planners. All data and experiments are conducted entirely in the real world. Our experiments show the proposed system is able to successfully capture the dynamics of clay, and is able to create a variety of simple shapes.

cs.RO↗

arXiv2023

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

Recently, the remarkable capabilities of large language models (LLMs) have been illustrated across a variety of research domains such as natural language processing, computer vision, and molecular modeling. We extend this paradigm by utilizing LLMs for material property prediction by introducing our model Materials Informatics Transformer (MatInFormer). Specifically, we introduce a novel approach that involves learning the grammar of crystallography through the tokenization of pertinent space group information. We further illustrate the adaptability of MatInFormer by incorporating task-specific data pertaining to Metal-Organic Frameworks (MOFs). Through attention visualization, we uncover the key features that the model prioritizes during property prediction. The effectiveness of our proposed model is empirically validated across 14 distinct datasets, hereby underscoring its potential for high throughput screening through accurate material property prediction.

cs.LG↗

arXiv2023

Catalyst Property Prediction with CatBERTa: Unveiling Feature Exploration Strategies through Large Language Models

Efficient catalyst screening necessitates predictive models for adsorption energy, a key property of reactivity. However, prevailing methods, notably graph neural networks (GNNs), demand precise atomic coordinates for constructing graph representations, while integrating observable attributes remains challenging. This research introduces CatBERTa, an energy prediction Transformer model using textual inputs. Built on a pretrained Transformer encoder, CatBERTa processes human-interpretable text, incorporating target features. Attention score analysis reveals CatBERTa's focus on tokens related to adsorbates, bulk composition, and their interacting atoms. Moreover, interacting atoms emerge as effective descriptors for adsorption configurations, while factors such as bond length and atomic properties of these atoms offer limited predictive contributions. By predicting adsorption energy from the textual representation of initial structures, CatBERTa achieves a mean absolute error (MAE) of 0.75 eV-comparable to vanilla Graph Neural Networks (GNNs). Furthermore, the subtraction of the CatBERTa-predicted energies effectively cancels out their systematic errors by as much as 19.3% for chemically similar systems, surpassing the error reduction observed in GNNs. This outcome highlights its potential to enhance the accuracy of energy difference predictions. This research establishes a fundamental framework for text-based catalyst property prediction, without relying on graph representations, while also unveiling intricate feature-property relationships.

cs.CE↗

arXiv2023

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

Recent advances in Language Models have enabled the protein modeling community with a powerful tool since protein sequences can be represented as text. Specifically, by taking advantage of Transformers, sequence-to-property prediction will be amenable without the need for explicit structural data. 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). The PeptideBert utilizes the ProtBERT pretrained transformer model with 12 attention heads and 12 hidden layers. We then finetuned the pretrained model for the three downstream tasks. Our model has achieved state of the art (SOTA) for predicting Hemolysis, which is a task for determining peptide's potential to induce red blood cell lysis. Our PeptideBert non-fouling model also achieved remarkable accuracy in predicting peptide's capacity to resist non-specific interactions. This model, trained predominantly on shorter sequences, benefits from the dataset where negative examples are largely associated with insoluble peptides. Codes, models, and data used in this study are freely available at: https://github.com/ChakradharG/PeptideBERT

q-bio.BM↗

arXiv2023

RoboChop: Autonomous Framework for Fruit and Vegetable Chopping Leveraging Foundational Models

With the goal of developing fully autonomous cooking robots, developing robust systems that can chop a wide variety of objects is important. Existing approaches focus primarily on the low-level dynamics of the cutting action, which overlooks some of the practical real-world challenges of implementing autonomous cutting systems. In this work we propose an autonomous framework to sequence together action primitives for the purpose of chopping fruits and vegetables on a cluttered cutting board. We present a novel technique to leverage vision foundational models SAM and YOLO to accurately detect, segment, and track fruits and vegetables as they visually change through the sequences of chops, finetuning YOLO on a novel dataset of whole and chopped fruits and vegetables. In our experiments, we demonstrate that our simple pipeline is able to reliably chop a variety of fruits and vegetables ranging in size, appearance, and texture, meeting a variety of chopping specifications, including fruit type, number of slices, and types of slices.

cs.RO↗

arXiv2023

Denoise Pretraining on Nonequilibrium Molecules for Accurate and Transferable Neural Potentials

Recent advances in equivariant graph neural networks (GNNs) have made deep learning amenable to developing fast surrogate models to expensive ab initio quantum mechanics (QM) approaches for molecular potential predictions. However, building accurate and transferable potential models using GNNs remains challenging, as the data is greatly limited by the expensive computational costs and level of theory of QM methods, especially for large and complex molecular systems. In this work, we propose denoise pretraining on nonequilibrium molecular conformations to achieve more accurate and transferable GNN potential predictions. Specifically, atomic coordinates of sampled nonequilibrium conformations are perturbed by random noises and GNNs are pretrained to denoise the perturbed molecular conformations which recovers the original coordinates. Rigorous experiments on multiple benchmarks reveal that pretraining significantly improves the accuracy of neural potentials. Furthermore, we show that the proposed pretraining approach is model-agnostic, as it improves the performance of different invariant and equivariant GNNs. Notably, our models pretrained on small molecules demonstrate remarkable transferability, improving performance when fine-tuned on diverse molecular systems, including different elements, charged molecules, biomolecules, and larger systems. These results highlight the potential for leveraging denoise pretraining approaches to build more generalizable neural potentials for complex molecular systems.

cs.LG↗

arXiv2023

Airfoil GAN: Encoding and Synthesizing Airfoils for Aerodynamic Shape Optimization

The current design of aerodynamic shapes, like airfoils, involves computationally intensive simulations to explore the possible design space. Usually, such design relies on the prior definition of design parameters and places restrictions on synthesizing novel shapes. In this work, we propose a data-driven shape encoding and generating method, which automatically learns representations from existing airfoils and uses the learned representations to generate new airfoils. The representations are then used in the optimization of synthesized airfoil shapes based on their aerodynamic performance. Our model is built upon VAEGAN, a neural network that combines Variational Autoencoder with Generative Adversarial Network and is trained by the gradient-based technique. 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. Our experiments show that the learned features encode shape information thoroughly and comprehensively without predefined design parameters. By interpolating/extrapolating feature vectors or sampling from Gaussian noises, the model can automatically synthesize novel airfoil shapes, some of which possess competitive or even better aerodynamic properties comparing to airfoils used for model training purposes. By optimizing shapes on the learned latent domain via a genetic algorithm, synthesized airfoils can evolve to target aerodynamic properties. This demonstrates an efficient learning-based airfoil design framework, which encodes and optimizes the airfoil on the latent domain and synthesizes promising airfoil candidates for required aerodynamic performance.

cs.CE↗

arXiv2023

Deep Learning Convective Flow Using Conditional Generative Adversarial Networks

We developed a general deep learning framework, FluidGAN, capable of learning and predicting time-dependent convective flow coupled with energy transport. FluidGAN is thoroughly data-driven with high speed and accuracy and satisfies the physics of fluid without any prior knowledge of underlying fluid and energy transport physics. FluidGAN also learns the coupling between velocity, pressure, and temperature fields. Our framework helps understand deterministic multiphysics phenomena where the underlying physical model is complex or unknown.

physics.flu-dyn↗