arXiv subjects

Amir Barati Farimani

Publications and source records attributed to Amir Barati Farimani.

At least 73 records · Page 4Linked to original sources

arXiv2025

Text2PDE: Latent Diffusion Models for Accessible Physics Simulation

Recent advances in deep learning have inspired numerous works on data-driven solutions to partial differential equation (PDE) problems. These neural PDE solvers can often be much faster than their numerical counterparts; however, each presents its unique limitations and generally balances training cost, numerical accuracy, and ease of applicability to different problem setups. To address these limitations, we introduce several methods to apply latent diffusion models to physics simulation. Firstly, we introduce a mesh autoencoder to compress arbitrarily discretized PDE data, allowing for efficient diffusion training across various physics. Furthermore, we investigate full spatio-temporal solution generation to mitigate autoregressive error accumulation. Lastly, we investigate conditioning on initial physical quantities, as well as conditioning solely on a text prompt to introduce text2PDE generation. We show that language can be a compact, interpretable, and accurate modality for generating physics simulations, paving the way for more usable and accessible PDE solvers. Through experiments on both uniform and structured grids, we show that the proposed approach is competitive with current neural PDE solvers in both accuracy and efficiency, with promising scaling behavior up to $\sim$3 billion parameters. By introducing a scalable, accurate, and usable physics simulator, we hope to bring neural PDE solvers closer to practical use.

cs.LG↗

arXiv2025

Discovery of Spatter Constitutive Models in Additive Manufacturing Using Machine Learning

Additive manufacturing (AM) is a rapidly evolving technology that has attracted applications across a wide range of fields due to its ability to fabricate complex geometries. However, one of the key challenges in AM is achieving consistent print quality. This inconsistency is often attributed to uncontrolled melt pool dynamics, partly caused by spatter which can lead to defects. Therefore, capturing and controlling the evolution of the melt pool is crucial for enhancing process stability and part quality. In this study, we developed a framework to support decision-making towards efficient AM process operations, capable of facilitating quality control and minimizing defects via machine learning (ML) and polynomial symbolic regression models. We implemented experimentally validated computational tools, specifically for laser powder bed fusion (LPBF) processes as a cost-effective approach to collect large datasets. For a dataset consisting of 281 varying process conditions, parameters such as melt pool dimensions (length, width, depth), melt pool geometry (area, volume), and volume indicated as spatter were extracted. Using machine learning (ML) and polynomial symbolic regression models, a high R2 of over 95 % was achieved in predicting the melt pool dimensions and geometry features on both the training and testing datasets, with either process conditions (power and velocity) or melt pool dimensions as the model inputs. In the case of volume indicated as spatter the value of the R2 improved after logarithmic transforming the model inputs, which were either the process conditions or the melt pool dimensions. Among the investigated ML models, the ExtraTree model achieved the highest R2 values of 96.7 % and 87.5 %.

cs.LG↗

arXiv2025

AdditiveLLM: Large Language Models Predict Defects in Additive Manufacturing

In this work we investigate the ability of large language models to predict additive manufacturing defect regimes given a set of process parameter inputs. For this task we utilize a process parameter defect dataset to fine-tune a collection of models, titled AdditiveLLM, for the purpose of predicting potential defect regimes including Keyholing, Lack of Fusion, and Balling. We compare different methods of input formatting in order to gauge the model's performance to correctly predict defect regimes on our sparse Baseline dataset and our natural language Prompt dataset. The model displays robust predictive capability, achieving an accuracy of 93\% when asked to provide the defect regimes associated with a set of process parameters. The incorporation of natural language input further simplifies the task of process parameters selection, enabling users to identify optimal settings specific to their build.

cs.LG↗

arXiv2025

Integrating Multi-Physics Simulations and Machine Learning to Define the Spatter Mechanism and Process Window in Laser Powder Bed Fusion

Laser powder bed fusion (LPBF) has shown promise for wide range of applications due to its ability to fabricate freeform geometries and generate a controlled microstructure. However, components generated by LPBF still possess sub-optimal mechanical properties due to the defects that are created during laser-material interactions. In this work, we investigate mechanism of spatter formation, using a high-fidelity modelling tool that was built to simulate the multi-physics phenomena in LPBF. The modelling tool have the capability to capture the 3D resolution of the meltpool and the spatter behavior. To understand spatter behavior and formation, we reveal its properties at ejection and evaluate its variation from the meltpool, the source where it is formed. The dataset of the spatter and the meltpool collected consist of 50 % spatter and 50 % melt pool samples, with features that include position components, velocity components, velocity magnitude, temperature, density and pressure. The relationship between the spatter and the meltpool were evaluated via correlation analysis and machine learning (ML) algorithms for classification tasks. Upon screening different ML algorithms on the dataset, a high accuracy was observed for all the ML models, with ExtraTrees having the highest at 96 % and KNN having the lowest at 94 %.

cs.LG↗

arXiv2025

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

Neural networks have shown promising potential in accelerating the numerical simulation of systems governed by partial differential equations (PDEs). Different from many existing neural network surrogates operating on high-dimensional discretized fields, we propose to learn the dynamics of the system in the latent space with much coarser discretizations. In our proposed framework - Latent Neural PDE Solver (LNS), a non-linear autoencoder is first trained to project the full-order representation of the system onto the mesh-reduced space, then a temporal model is trained to predict the future state in this mesh-reduced space. This reduction process simplifies the training of the temporal model by greatly reducing the computational cost accompanying a fine discretization. We study the capability of the proposed framework and several other popular neural PDE solvers on various types of systems including single-phase and multi-phase flows along with varying system parameters. We showcase that it has competitive accuracy and efficiency compared to the neural PDE solver that operates on full-order space.

cs.LG↗

arXiv2024

Airfoil Diffusion: Denoising Diffusion Model For Conditional Airfoil Generation

The design of aerodynamic shapes, such as airfoils, has traditionally required significant computational resources and relied on predefined design parameters, which limit the potential for novel shape synthesis. In this work, we introduce a data-driven methodology for airfoil generation using a diffusion model. Trained on a dataset of preexisting airfoils, our model can generate an arbitrary number of new airfoils from random vectors, which can be conditioned on specific aerodynamic performance metrics such as lift and drag, or geometric criteria. Our results demonstrate that the diffusion model effectively produces airfoil shapes with realistic aerodynamic properties, offering substantial improvements in efficiency, flexibility, and the potential for discovering innovative airfoil designs. This approach significantly expands the design space, facilitating the synthesis of high-performance aerodynamic shapes that transcend the limitations of traditional methods.

cs.LG↗

arXiv2024

Masked Autoencoders are PDE Learners

Neural solvers for partial differential equations (PDEs) have great potential to generate fast and accurate physics solutions, yet their practicality is currently limited by their generalizability. PDEs evolve over broad scales and exhibit diverse behaviors; predicting these phenomena will require learning representations across a wide variety of inputs which may encompass different coefficients, boundary conditions, resolutions, or even equations. As a step towards generalizable PDE modeling, we adapt masked pretraining for physics problems. Through self-supervised learning across PDEs, masked autoencoders can consolidate heterogeneous physics to learn rich latent representations. We show that learned representations can generalize to a limited set of unseen equations or parameters and are meaningful enough to regress PDE coefficients or the classify PDE features. Furthermore, conditioning neural solvers on learned latent representations can improve time-stepping and super-resolution performance across a variety of coefficients, discretizations, or boundary conditions, as well as on certain unseen PDEs. We hope that masked pretraining can emerge as a unifying method across large, unlabeled, and heterogeneous datasets to learn latent physics at scale.

cs.LG↗

arXiv2024

Explainable Data-driven Modeling of Adsorption Energy in Heterogeneous Catalysis

The increasing popularity of machine learning (ML) in catalysis has spurred interest in leveraging these techniques to enhance catalyst design. Our study aims to bridge the gap between physics-based studies and data-driven methodologies by integrating ML techniques with eXplainable AI (XAI). Specifically, we employ two XAI techniques: Post-hoc XAI analysis and Symbolic Regression. These techniques help us unravel the correlation between adsorption energy and the properties of the adsorbate-catalyst system. Leveraging a large dataset such as the Open Catalyst Dataset (OC20), we employ a combination of shallow ML techniques and XAI methodologies. Our investigation involves utilizing multiple shallow machine learning techniques to predict adsorption energy, followed by post-hoc analysis for feature importance, inter-feature correlations, and the influence of various feature values on the prediction of adsorption energy. The post-hoc analysis reveals that adsorbate properties exert a greater influence than catalyst properties in our dataset. The top five features based on higher Shapley values are adsorbate electronegativity, the number of adsorbate atoms, catalyst electronegativity, effective coordination number, and the sum of atomic numbers of the adsorbate molecule. There is a positive correlation between catalyst and adsorbate electronegativity with the prediction of adsorption energy. Additionally, symbolic regression yields results consistent with SHAP analysis. It deduces a mathematical relationship indicating that the square of the catalyst electronegativity is directly proportional to the adsorption energy. These consistent correlations resemble those derived from physics-based equations in previous research. Our work establishes a robust framework that integrates ML techniques with XAI, leveraging large datasets like OC20 to enhance catalyst design through model explainability.

cs.LG↗

arXiv2024

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

Intrinsically Disordered Proteins (IDPs) constitute a large and structure-less class of proteins with significant functions. The existence of IDPs challenges the conventional notion that the biological functions of proteins rely on their three-dimensional structures. Despite lacking well-defined spatial arrangements, they exhibit diverse biological functions, influencing cellular processes and shedding light on the disease mechanisms. However, it is expensive to run experiments or simulations to characterize this class of proteins. Consequently, we designed an ML model that relies solely on amino acid sequences. 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. Our experiments demonstrate accurate predictions of IDPs properties, including Radius of Gyration, end-to-end Decorrelation Time, and Heat Capacity.

q-bio.BM↗

arXiv2024

Pretraining a Neural Operator in Lower Dimensions

There has recently been increasing attention towards developing foundational neural Partial Differential Equation (PDE) solvers and neural operators through large-scale pretraining. However, unlike vision and language models that make use of abundant and inexpensive (unlabeled) data for pretraining, these neural solvers usually rely on simulated PDE data, which can be costly to obtain, especially for high-dimensional PDEs. In this work, we aim to Pretrain neural PDE solvers on Lower Dimensional PDEs (PreLowD) where data collection is the least expensive. We evaluated the effectiveness of this pretraining strategy in similar PDEs in higher dimensions. We use the Factorized Fourier Neural Operator (FFNO) due to having the necessary flexibility to be applied to PDE data of arbitrary spatial dimensions and reuse trained parameters in lower dimensions. In addition, our work sheds light on the effect of the fine-tuning configuration to make the most of this pretraining strategy. Code is available at https://github.com/BaratiLab/PreLowD.

cs.LG↗

arXiv2024

BAPULM: Binding Affinity Prediction using Language Models

Identifying drug-target interactions is essential for developing effective therapeutics. Binding affinity quantifies these interactions, and traditional approaches rely on computationally intensive 3D structural data. In contrast, language models can efficiently process sequential data, offering an alternative approach to molecular representation. In the current study, we introduce BAPULM, an innovative sequence-based framework that leverages the chemical latent representations of proteins via ProtT5-XL-U50 and ligands through MolFormer, eliminating reliance on complex 3D configurations. Our approach was validated extensively on benchmark datasets, achieving scoring power (R) values of 0.925 $\pm$ 0.043, 0.914 $\pm$ 0.004, and 0.8132 $\pm$ 0.001 on benchmark1k2101, Test2016_290, and CSAR-HiQ_36, respectively. These findings indicate the robustness and accuracy of BAPULM across diverse datasets and underscore the potential of sequence-based models in-silico drug discovery, offering a scalable alternative to 3D-centric methods for screening potential ligands.

q-bio.QM↗

arXiv2024

Peptide-GPT: Generative Design of Peptides using Generative Pre-trained Transformers and Bio-informatic Supervision

In recent years, natural language processing (NLP) models have demonstrated remarkable capabilities in various domains beyond traditional text generation. In this work, we introduce PeptideGPT, a protein language model tailored to generate protein sequences with distinct properties: hemolytic activity, solubility, and non-fouling characteristics. To facilitate a rigorous evaluation of these generated sequences, we established a comprehensive evaluation pipeline consisting of ideas from bioinformatics to retain valid proteins with ordered structures. First, we rank the generated sequences based on their perplexity scores, then we filter out those lying outside the permissible convex hull of proteins. Finally, we predict the structure using ESMFold and select the proteins with pLDDT values greater than 70 to ensure ordered structure. The properties of generated sequences are evaluated using task-specific classifiers - PeptideBERT and HAPPENN. We achieved an accuracy of 76.26% in hemolytic, 72.46% in non-hemolytic, 78.84% in non-fouling, and 68.06% in solubility protein generation. Our experimental results demonstrate the effectiveness of PeptideGPT in de novo protein design and underscore the potential of leveraging NLP-based approaches for paving the way for future innovations and breakthroughs in synthetic biology and bioinformatics. Codes, models, and data used in this study are freely available at: https://github.com/aayush-shah14/PeptideGPT.

cs.LG↗

arXiv2024

Multimodal Language and Graph Learning of Adsorption Configuration in Catalysis

Adsorption energy is a reactivity descriptor that must be accurately predicted for effective machine learning (ML) application in catalyst screening. This process involves determining the lowest energy across various adsorption configurations on a catalytic surface, which can exhibit very similar energy values. While graph neural networks (GNNs) have shown great success in computing the energy of catalyst systems, they rely heavily on atomic spatial coordinates. In contrast, transformer-based language models can directly use human-readable text inputs, potentially bypassing the need for detailed atomic positions. However, these language models often struggle with accurately predicting the energy of adsorption configurations. Our study addresses this limitation by introducing a self-supervised multi-modal learning approach called graph-assisted pretraining, which connects well-established GNNs with emerging language model applications. This method reduces the MAE of energy prediction for adsorption configurations by about 10%. Furthermore, our findings demonstrate that graph-assisted pretraining enhances fine-tuning with different datasets, indicating the transferability of this approach. This method also redirects the model's attention toward adsorption configuration, rather than individual adsorbate and catalyst information, similar to common domain knowledge. Building on this, we propose using generative large language models to create text inputs for the predictive model, based solely on chemical composition and surface orientation, without relying on exact atomic positions. This demonstrates a potential use case of language models in energy prediction without geometric information.

cs.CE↗

arXiv2024

Strategies for Pretraining Neural Operators

Pretraining for partial differential equation (PDE) modeling has recently shown promise in scaling neural operators across datasets to improve generalizability and performance. Despite these advances, our understanding of how pretraining affects neural operators is still limited; studies generally propose tailored architectures and datasets that make it challenging to compare or examine different pretraining frameworks. To address this, we compare various pretraining methods without optimizing architecture choices to characterize pretraining dynamics on different models and datasets as well as to understand its scaling and generalization behavior. We find that pretraining is highly dependent on model and dataset choices, but in general transfer learning or physics-based pretraining strategies work best. In addition, pretraining performance can be further improved by using data augmentations. Lastly, pretraining can be additionally beneficial when fine-tuning in scarce data regimes or when generalizing to downstream data similar to the pretraining distribution. Through providing insights into pretraining neural operators for physics prediction, we hope to motivate future work in developing and evaluating pretraining methods for PDEs.

cs.LG↗

arXiv2024

VITaL Pretraining: Visuo-Tactile Pretraining for Tactile and Non-Tactile Manipulation Policies

Tactile information is a critical tool for dexterous manipulation. As humans, we rely heavily on tactile information to understand objects in our environments and how to interact with them. We use touch not only to perform manipulation tasks but also to learn how to perform these tasks. Therefore, to create robotic agents that can learn to complete manipulation tasks at a human or super-human level of performance, we need to properly incorporate tactile information into both skill execution and skill learning. In this paper, we investigate how we can incorporate tactile information into imitation learning platforms to improve performance on manipulation tasks. We show that incorporating visuo-tactile pretraining improves imitation learning performance, not only for tactile agents (policies that use tactile information at inference), but also for non-tactile agents (policies that do not use tactile information at inference). For these non-tactile agents, pretraining with tactile information significantly improved performance (for example, improving the accuracy on USB plugging from 20% to 85%), reaching a level on par with visuo-tactile agents, and even surpassing them in some cases. For demonstration videos and access to our codebase, see the project website: https://sites.google.com/andrew.cmu.edu/visuo-tactile-pretraining

cs.RO↗

arXiv2024

PICL: Physics Informed Contrastive Learning for Partial Differential Equations

Neural operators have recently grown in popularity as Partial Differential Equation (PDE) surrogate models. Learning solution functionals, rather than functions, has proven to be a powerful approach to calculate fast, accurate solutions to complex PDEs. While much work has been done evaluating neural operator performance on a wide variety of surrogate modeling tasks, these works normally evaluate performance on a single equation at a time. In this work, we develop a novel contrastive pretraining framework utilizing Generalized Contrastive Loss that improves neural operator generalization across multiple governing equations simultaneously. Governing equation coefficients are used to measure ground-truth similarity between systems. A combination of physics-informed system evolution and latent-space model output are anchored to input data and used in our distance function. We find that physics-informed contrastive pretraining improves accuracy for the Fourier Neural Operator in fixed-future and autoregressive rollout tasks for the 1D and 2D Heat, Burgers', and linear advection equations.

cs.LG↗

arXiv2024

Deep Learning based Optical Image Super-Resolution via Generative Diffusion Models for Layerwise in-situ LPBF Monitoring

The stochastic formation of defects during Laser Powder Bed Fusion (L-PBF) negatively impacts its adoption for high-precision use cases. Optical monitoring techniques can be used to identify defects based on layer-wise imaging, but these methods are difficult to scale to high resolutions due to cost and memory constraints. Therefore, we implement generative deep learning models to link low-cost, low-resolution images of the build plate to detailed high-resolution optical images of the build plate, enabling cost-efficient process monitoring. To do so, a conditional latent probabilistic diffusion model is trained to produce realistic high-resolution images of the build plate from low-resolution webcam images, recovering the distribution of small-scale features and surface roughness. We first evaluate the performance of the model by analyzing the reconstruction quality of the generated images using peak-signal-to-noise-ratio (PSNR), structural similarity index measure (SSIM) and wavelet covariance metrics that describe the preservation of high-frequency information. Additionally, we design a framework based upon the Segment Anything foundation model to recreate the 3D morphology of the printed part and analyze the surface roughness of the reconstructed samples. Finally, we explore the zero-shot generalization capabilities of the implemented framework to other part geometries by creating synthetic low-resolution data.

eess.IV↗

arXiv2024

PLATO: Planning with LLMs and Affordances for Tool Manipulation

As robotic systems become increasingly integrated into complex real-world environments, there is a growing need for approaches that enable robots to understand and act upon natural language instructions without relying on extensive pre-programmed knowledge of their surroundings. This paper presents PLATO, an innovative system that addresses this challenge by leveraging specialized large language model agents to process natural language inputs, understand the environment, predict tool affordances, and generate executable actions for robotic systems. Unlike traditional systems that depend on hard-coded environmental information, PLATO employs a modular architecture of specialized agents to operate without any initial knowledge of the environment. These agents identify objects and their locations within the scene, generate a comprehensive high-level plan, translate this plan into a series of low-level actions, and verify the completion of each step. The system is particularly tested on challenging tool-use tasks, which involve handling diverse objects and require long-horizon planning. PLATO's design allows it to adapt to dynamic and unstructured settings, significantly enhancing its flexibility and robustness. By evaluating the system across various complex scenarios, we demonstrate its capability to tackle a diverse range of tasks and offer a novel solution to integrate LLMs with robotic platforms, advancing the state-of-the-art in autonomous robotic task execution. For videos and prompt details, please see our project website: https://sites.google.com/andrew.cmu.edu/plato

cs.RO↗