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Researcher profile

Amir Barati Farimani

Amir Barati Farimani contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Machine Learningcond-mat.mtrl-sciphysics.chem-phArtificial IntelligenceBiomoleculesComputation and LanguageComputer Visioneess.SPComputational Engineering, Finance, and Scienceeess.IVphysics.app-phphysics.comp-phRobotics

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Published work

20 published item(s)

preprint2026arXiv

Coupled Diffusion-Encoder Models for Reconstruction of Flow Fields

Data-driven flow-field reconstruction typically relies on autoencoder architectures that compress high-dimensional states into low-dimensional latent representations. However, classical approaches such as variational autoencoders (VAEs) often struggle to preserve the higher-order statistical structure of fluid flows when subjected to strong compression. We propose DiffCoder, a coupled framework that integrates a probabilistic diffusion model with a conventional convolutional ResNet encoder and trains both components end-to-end. The encoder compresses the flow field into a latent representation, while the diffusion model learns a generative prior over reconstructions conditioned on the compressed state. This design allows DiffCoder to recover distributional and spectral properties that are not strictly required for minimizing pointwise reconstruction loss but are critical for faithfully representing statistical properties of the flow field. We evaluate DiffCoder and VAE baselines across multiple model sizes and compression ratios on a challenging dataset of Kolmogorov flow fields. Under aggressive compression, DiffCoder significantly improves the spectral accuracy while VAEs exhibit substantial degradation. Although both methods show comparable relative L2 reconstruction error, DiffCoder better preserves the underlying distributional structure of the flow. At moderate compression levels, sufficiently large VAEs remain competitive, suggesting that diffusion-based priors provide the greatest benefit when information bottlenecks are severe. These results demonstrate that the generative decoding by diffusion offers a promising path toward compact, statistically consistent representations of complex flow fields.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

LinkD: AutoRegressive Diffusion Model for Mechanical Linkage Synthesis

Designing mechanical linkages to achieve target end-effector trajectories presents a fundamental challenge due to the intricate coupling between continuous node placements, discrete topological configurations, and nonlinear kinematic constraints. The highly nonlinear motion-to-configuration relationship means small perturbations in joint positions drastically alter trajectories, while the combinatorially expanding design space renders conventional optimization and heuristic methods computationally intractable. We introduce an autoregressive diffusion framework that exploits the dyadic nature of linkage assembly by representing mechanisms as sequentially constructed graphs, where nodes correspond to joints and edges to rigid links. Our approach combines a causal transformer with a Denoising Diffusion Probabilistic Model (DDPM), both conditioned on target trajectories encoded via a transformer encoder. The causal transformer autoregressively predicts discrete topology node-by-node, while the DDPM refines each node's spatial coordinates and edge connectivity to previously generated nodes. This sequential generation enables adaptive trial-and-error synthesis where problematic nodes exhibiting kinematic locking or collisions can be selectively regenerated, allowing autonomous correction of degenerate configurations during design. Our graph-based, data-driven methodology surpasses traditional optimization approaches, enabling scalable inverse design that generalizes to mechanisms with arbitrary node counts. We demonstrate successful synthesis of linkage systems containing up to 20 nodes with extensibility to N-node architectures. This work advances autoregressive graph generation methodologies and computational kinematic synthesis, establishing new paradigms for scalable inverse design of complex mechanical systems.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Material Database Agent: A Multimodal Agentic Framework for Scientific Literature Mining

Materials science workflows rely on structured and unstructured data from the vast body of available scientific literature. However, most of the experimental details remain buried in text, tables, graphs and figures. Thus, constructing databases that incorporate this data is a manual, time-consuming, and hard-to-scale process. Multimodal large language models have made it feasible to extract information from text and scientific figures with high speed and accuracy. This opens the possibility of an AI system that can create production-scale material databases. Material Database Agent (MDA) is a modular, multi-agent system architecture for converting research literature into structured databases. MDA accepts article PDFs as input, which are subsequently processed in parallel into markdown files and figures. Multiple sub-agents read these markdown files and figures in parallel to assemble sub-databases for each paper. These sub-databases are then compiled into a single tabular database by an agent. As opposed to using either a rule-based approach or a single-pass pipeline for extracting information, MDA is a specialized architecture for transforming the literature into a database in the field of materials science. More generally, this study provides a basis for positioning multimodal agentic information extraction as a viable means for constructing next-generation scientific databases from the primary literature.

0 citations0 reviewsNo code linkedOpen access
preprint2025arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2025arXiv

LLM-3D Print: Large Language Models To Monitor and Control 3D Printing

Industry 4.0 has revolutionized manufacturing by driving digitalization and shifting the paradigm toward additive manufacturing (AM). Fused Deposition Modeling (FDM), a key AM technology, enables the creation of highly customized, cost-effective products with minimal material waste through layer-by-layer extrusion, posing a significant challenge to traditional subtractive methods. However, the susceptibility of material extrusion techniques to errors often requires expert intervention to detect and mitigate defects that can severely compromise product quality. While automated error detection and machine learning models exist, their generalizability across diverse 3D printer setups, firmware, and sensors is limited, and deep learning methods require extensive labeled datasets, hindering scalability and adaptability. To address these challenges, we present a process monitoring and control framework that leverages pre-trained Large Language Models (LLMs) alongside 3D printers to detect and address printing defects. The LLM evaluates print quality by analyzing images captured after each layer or print segment, identifying failure modes and querying the printer for relevant parameters. It then generates and executes a corrective action plan. We validated the effectiveness of the proposed framework in identifying defects by comparing it against a control group of engineers with diverse AM expertise. Our evaluation demonstrated that LLM-based agents not only accurately identify common 3D printing errors, such as inconsistent extrusion, stringing, warping, and layer adhesion, but also effectively determine the parameters causing these failures and autonomously correct them without any need for human intervention.

0 citations0 reviewsNo code linkedOpen access
preprint2024arXiv

ThermoPore: Predicting Part Porosity Based on Thermal Images Using Deep Learning

We present a deep learning approach for quantifying and localizing ex-situ porosity within Laser Powder Bed Fusion fabricated samples utilizing in-situ thermal image monitoring data. Our goal is to build the real time porosity map of parts based on thermal images acquired during the build. The quantification task builds upon the established Convolutional Neural Network model architecture to predict pore count and the localization task leverages the spatial and temporal attention mechanisms of the novel Video Vision Transformer model to indicate areas of expected porosity. Our model for porosity quantification achieved a $R^2$ score of 0.57 and our model for porosity localization produced an average IoU score of 0.32 and a maximum of 1.0. This work is setting the foundations of part porosity "Digital Twins" based on additive manufacturing monitoring data and can be applied downstream to reduce time-intensive post-inspection and testing activities during part qualification and certification. In addition, we seek to accelerate the acquisition of crucial insights normally only available through ex-situ part evaluation by means of machine learning analysis of in-situ process monitoring data.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Crystal Twins: Self-supervised Learning for Crystalline Material Property Prediction

Machine learning (ML) models have been widely successful in the prediction of material properties. However, large labeled datasets required for training accurate ML models are elusive and computationally expensive to generate. Recent advances in Self-Supervised Learning (SSL) frameworks capable of training ML models on unlabeled data have mitigated this problem and demonstrated superior performance in computer vision and natural language processing tasks. Drawing inspiration from the developments in SSL, we introduce Crystal Twins (CT): an SSL method for crystalline materials property prediction. Using a large unlabeled dataset, we pre-train a Graph Neural Network (GNN) by applying the redundancy reduction principle to the graph latent embeddings of augmented instances obtained from the same crystalline system. By sharing the pre-trained weights when fine-tuning the GNN for regression tasks, we significantly improve the performance for 7 challenging material property prediction benchmarks

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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

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. However, AM produced parts can be subject to undesirable porosity, negatively influencing the properties of printed components. Thus, controlling porosity is integral for creating effective parts. A precise understanding of the porosity distribution is crucial for accurately simulating potential fatigue and failure zones. Previous research on generating synthetic porous microstructures have succeeded in generating parts with high density, isotropic porosity distributions but are often inapplicable to cases with sparser, boundary-dependent pore distributions. Our work bridges this gap by providing a method that considers these constraints by deconstructing the generation problem into its constitutive parts. A framework is introduced that combines Generative Adversarial Networks with Mallat Scattering Transform-based autocorrelation methods to construct novel realizations of the individual pore geometries and surface roughness, then stochastically reconstruct them to form realizations of a porous printed part. The generated parts are compared to the existing experimental porosity distributions based on statistical and dimensional metrics, such as nearest neighbor distances, pore volumes, pore anisotropies and scattering transform based auto-correlations.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Graph Neural Networks Accelerated Molecular Dynamics

Molecular Dynamics (MD) simulation is a powerful tool for understanding the dynamics and structure of matter. Since the resolution of MD is atomic-scale, achieving long time-scale simulations with femtosecond integration is very expensive. In each MD step, numerous iterative computations are performed to calculate energy based on different types of interaction and their corresponding spatial gradients. These repetitive computations can be learned and surrogated by a deep learning model like a Graph Neural Network (GNN). In this work, we developed a GNN Accelerated Molecular Dynamics (GAMD) model that directly predicts forces given the state of the system (atom positions, atom types), bypassing the evaluation of potential energy. By training the GNN on a variety of data sources (simulation data derived from classical MD and density functional theory), we show that GAMD can predict the dynamics of two typical molecular systems, Lennard-Jones system and Water system, in the NVT ensemble with velocities regulated by a thermostat. We further show that GAMD's learning and inference are agnostic to the scale, where it can scale to much larger systems at test time. We also perform a comprehensive benchmark test comparing our implementation of GAMD to production-level MD softwares, showing GAMD's competitive performance on the large-scale simulation.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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

Deep learning has been a prevalence in computational chemistry and widely implemented in molecule property predictions. Recently, self-supervised learning (SSL), especially contrastive learning (CL), gathers growing attention for the potential to learn molecular representations that generalize to the gigantic chemical space. Unlike supervised learning, SSL can directly leverage large unlabeled data, which greatly reduces the effort to acquire molecular property labels through costly and time-consuming simulations or experiments. However, most molecular SSL methods borrow the insights from the machine learning community but neglect the unique cheminformatics (e.g., molecular fingerprints) and multi-level graphical structures (e.g., functional groups) of molecules. In this work, we propose iMolCLR: improvement of Molecular Contrastive Learning of Representations with graph neural networks (GNNs) in two aspects, (1) mitigating faulty negative contrastive instances via considering cheminformatics similarities between molecule pairs; (2) fragment-level contrasting between intra- and inter-molecule substructures decomposed from molecules. Experiments have shown that the proposed strategies significantly improve the performance of GNN models on various challenging molecular property predictions. In comparison to the previous CL framework, iMolCLR demonstrates an averaged 1.3% improvement of ROC-AUC on 7 classification benchmarks and an averaged 4.8% decrease of the error on 5 regression benchmarks. On most benchmarks, the generic GNN pre-trained by iMolCLR rivals or even surpasses supervised learning models with sophisticated architecture designs and engineered features. Further investigations demonstrate that representations learned through iMolCLR intrinsically embed scaffolds and functional groups that can reason molecule similarities.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

MeltpoolNet: Melt pool Characteristic Prediction in Metal Additive Manufacturing Using Machine Learning

Characterizing meltpool shape and geometry is essential in metal Additive Manufacturing (MAM) to control the printing process and avoid defects. Predicting meltpool flaws based on process parameters and powder material is difficult due to the complex nature of MAM process. Machine learning (ML) techniques can be useful in connecting process parameters to the type of flaws in the meltpool. In this work, we introduced a comprehensive framework for benchmarking ML for melt pool characterization. An extensive experimental dataset has been collected from more than 80 MAM articles containing MAM processing conditions, materials, meltpool dimensions, meltpool modes and flaw types. We introduced physics-aware MAM featurization, versatile ML models, and evaluation metrics to create a comprehensive learning framework for meltpool defect and geometry prediction. This benchmark can serve as a basis for melt pool control and process optimization. In addition, data-driven explicit models have been identified to estimate meltpool geometry from process parameters and material properties which outperform Rosenthal estimation for meltpool geometry while maintaining interpretability.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Molecular Contrastive Learning of Representations via Graph Neural Networks

Molecular Machine Learning (ML) bears promise for efficient molecule property prediction and drug discovery. However, labeled molecule data can be expensive and time-consuming to acquire. Due to the limited labeled data, it is a great challenge for supervised-learning ML models to generalize to the giant chemical space. 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). In MolCLR pre-training, we build molecule graphs and develop GNN encoders to learn differentiable representations. Three molecule graph augmentations are proposed: atom masking, bond deletion, and subgraph removal. A contrastive estimator maximizes the agreement of augmentations from the same molecule while minimizing the agreement of different molecules. Experiments show that our contrastive learning framework significantly improves the performance of GNNs on various molecular property benchmarks including both classification and regression tasks. Benefiting from pre-training on the large unlabeled database, MolCLR even achieves state-of-the-art on several challenging benchmarks after fine-tuning. Additionally, further investigations demonstrate that MolCLR learns to embed molecules into representations that can distinguish chemically reasonable molecular similarities.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

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.

0 citations0 reviewsNo code linkedOpen access