arXiv subjects

Amir Barati Farimani

Publications and source records attributed to Amir Barati Farimani.

At least 91 records · Page 5Linked to original sources

arXiv2024

AbGPT: De Novo Antibody Design via Generative Language Modeling

The adaptive immune response, largely mediated by B-cell receptors (BCRs), plays a crucial role for effective pathogen neutralization due to its diversity and antigen specificity. Designing BCRs de novo, or from scratch, has been challenging because of their complex structure and diverse binding requirements. Protein language models (PLMs) have shown remarkable performance in contextualizing and performing various downstream tasks without relying on structural information. However, these models often lack a comprehensive understanding of the entire protein space, which limits their application in antibody design. In this study, we introduce Antibody Generative Pretrained Transformer (AbGPT), a model fine-tuned from a foundational PLM to enable a more informed design of BCR sequences. Using a custom generation and filtering pipeline, AbGPT successfully generated a high-quality library of 15,000 BCR sequences, demonstrating a strong understanding of the intrinsic variability and conserved regions within the antibody repertoire.

q-bio.BM↗

arXiv2024

Zero-Shot Uncertainty Quantification using Diffusion Probabilistic Models

The success of diffusion probabilistic models in generative tasks, such as text-to-image generation, has motivated the exploration of their application to regression problems commonly encountered in scientific computing and various other domains. In this context, the use of diffusion regression models for ensemble prediction is becoming a practice with increasing popularity. Under such background, we conducted a study to quantitatively evaluate the effectiveness of ensemble methods on solving different regression problems using diffusion models. We consider the ensemble prediction of a diffusion model as a means for zero-shot uncertainty quantification, since the diffusion models in our study are not trained with a loss function containing any uncertainty estimation. Through extensive experiments on 1D and 2D data, we demonstrate that ensemble methods consistently improve model prediction accuracy across various regression tasks. Notably, we observed a larger accuracy gain in auto-regressive prediction compared with point-wise prediction, and that enhancements take place in both the mean-square error and the physics-informed loss. Additionally, we reveal a statistical correlation between ensemble prediction error and ensemble variance, offering insights into balancing computational complexity with prediction accuracy and monitoring prediction confidence in practical applications where the ground truth is unknown. Our study provides a comprehensive view of the utility of diffusion ensembles, serving as a useful reference for practitioners employing diffusion models in regression problem-solving.

cs.LG↗

arXiv2024

Multi-Peptide: Multimodality Leveraged Language-Graph Learning of Peptide Properties

Peptides are essential in biological processes and therapeutics. In this study, we introduce Multi-Peptide, an innovative approach that combines transformer-based language models with Graph Neural Networks (GNNs) to predict peptide properties. We combine PeptideBERT, a transformer model tailored for peptide property prediction, with a GNN encoder to capture both sequence-based and structural features. By employing Contrastive Language-Image Pre-training (CLIP), Multi-Peptide aligns embeddings from both modalities into a shared latent space, thereby enhancing the model's predictive accuracy. Evaluations on hemolysis and nonfouling datasets demonstrate Multi-Peptide's robustness, achieving state-of-the-art 86.185% accuracy in hemolysis prediction. This study highlights the potential of multimodal learning in bioinformatics, paving the way for accurate and reliable predictions in peptide-based research and applications.

q-bio.QM↗

arXiv2024

Pretraining Strategy for Neural Potentials

We propose a mask pretraining method for Graph Neural Networks (GNNs) to improve their performance on fitting potential energy surfaces, particularly in water systems. GNNs are pretrained by recovering spatial information related to masked-out atoms from molecules, then transferred and finetuned on atomic forcefields. Through such pretraining, GNNs learn meaningful prior about structural and underlying physical information of molecule systems that are useful for downstream tasks. From comprehensive experiments and ablation studies, we show that the proposed method improves the accuracy and convergence speed compared to GNNs trained from scratch or using other pretraining techniques such as denoising. On the other hand, our pretraining method is suitable for both energy-centric and force-centric GNNs. This approach showcases its potential to enhance the performance and data efficiency of GNNs in fitting molecular force fields.

cs.LG↗

arXiv2024

Query2CAD: Generating CAD models using natural language queries

Computer Aided Design (CAD) engineers typically do not achieve their best prototypes in a single attempt. Instead, they iterate and refine their designs to achieve an optimal solution through multiple revisions. This traditional approach, though effective, is time-consuming and relies heavily on the expertise of skilled engineers. To address these challenges, we introduce Query2CAD, a novel framework to generate CAD designs. The framework uses a large language model to generate executable CAD macros. Additionally, Query2CAD refines the generation of the CAD model with the help of its self-refinement loops. Query2CAD operates without supervised data or additional training, using the LLM as both a generator and a refiner. The refiner leverages feedback generated by the BLIP2 model, and to address false negatives, we have incorporated human-in-the-loop feedback into our system. Additionally, we have developed a dataset that encompasses most operations used in CAD model designing and have evaluated our framework using this dataset. Our findings reveal that when we used GPT-4 Turbo as our language model, the architecture achieved a success rate of 53.6\% on the first attempt. With subsequent refinements, the success rate increased by 23.1\%. In particular, the most significant improvement in the success rate was observed with the first iteration of the refinement. With subsequent refinements, the accuracy of the correct designs did not improve significantly. We have open-sourced our data, model, and code (github.com/akshay140601/Query2CAD).

cs.LG↗

arXiv2024

FaultFormer: Pretraining Transformers for Adaptable Bearing Fault Classification

The growth of global consumption has motivated important applications of deep learning to smart manufacturing and machine health monitoring. In particular, analyzing vibration data offers great potential to extract meaningful insights into predictive maintenance by the detection of bearing faults. Deep learning can be a powerful method to predict these mechanical failures; however, they lack generalizability to new tasks or datasets and require expensive, labeled mechanical data. We address this by presenting a novel self-supervised pretraining and fine-tuning framework based on transformer models. In particular, we investigate different tokenization and data augmentation strategies to reach state-of-the-art accuracies using transformer models. Furthermore, we demonstrate self-supervised masked pretraining for vibration signals and its application to low-data regimes, task adaptation, and dataset adaptation. Pretraining is able to improve performance on scarce, unseen training samples, as well as when fine-tuning on fault classes outside of the pretraining distribution. Furthermore, pretrained transformers are shown to be able to generalize to a different dataset in a few-shot manner. This introduces a new paradigm where models can be pretrained on unlabeled data from different bearings, faults, and machinery and quickly deployed to new, data-scarce applications to suit specific manufacturing needs.

cs.LG↗

arXiv2024

AMGPT: a Large Language Model for Contextual Querying in Additive Manufacturing

Generalized large language models (LLMs) such as GPT-4 may not provide specific answers to queries formulated by materials science researchers. These models may produce a high-level outline but lack the capacity to return detailed instructions on manufacturing and material properties of novel alloys. Enhancing a smaller model with specialized domain knowledge may provide an advantage over large language models which cannot be retrained quickly enough to keep up with the rapid pace of research in metal additive manufacturing (AM). We introduce "AMGPT," a specialized LLM text generator designed for metal AM queries. The goal of AMGPT is to assist researchers and users in navigating the extensive corpus of literature in AM. Instead of training from scratch, we employ a pre-trained Llama2-7B model from Hugging Face in a Retrieval-Augmented Generation (RAG) setup, utilizing it to dynamically incorporate information from $\sim$50 AM papers and textbooks in PDF format. Mathpix is used to convert these PDF documents into TeX format, facilitating their integration into the RAG pipeline managed by LlamaIndex. Expert evaluations of this project highlight that specific embeddings from the RAG setup accelerate response times and maintain coherence in the generated text.

cs.CL↗

arXiv2024

BeadSight: An Inexpensive Tactile Sensor Using Hydro-Gel Beads

In robotic manipulation, tactile sensors are indispensable, especially when dealing with soft objects, objects of varying dimensions, or those out of the robot's direct line of sight. Traditional tactile sensors often grapple with challenges related to cost and durability. To address these issues, our study introduces a novel approach to visuo-tactile sensing with an emphasis on economy and replacablity. Our proposed sensor, BeadSight, uses hydro-gel beads encased in a vinyl bag as an economical, easily replaceable sensing medium. When the sensor makes contact with a surface, the deformation of the hydrogel beads is observed using a rear camera. This observation is then passed through a U-net Neural Network to predict the forces acting on the surface of the bead bag, in the form of a pressure map. Our results show that the sensor can accurately predict these pressure maps, detecting the location and magnitude of forces applied to the surface. These abilities make BeadSight an effective, inexpensive, and easily replaceable tactile sensor, ideal for many robotics applications.

cs.RO↗

arXiv2024

Deep Learning for Melt Pool Depth Contour Prediction From Surface Thermal Images via Vision Transformers

Insufficient overlap between the melt pools produced during Laser Powder Bed Fusion (L-PBF) can lead to lack-of-fusion defects and deteriorated mechanical and fatigue performance. In-situ monitoring of the melt pool subsurface morphology requires specialized equipment that may not be readily accessible or scalable. Therefore, we introduce a machine learning framework to correlate in-situ two-color thermal images observed via high-speed color imaging to the two-dimensional profile of the melt pool cross-section. Specifically, we employ a hybrid CNN-Transformer architecture to establish a correlation between single bead off-axis thermal image sequences and melt pool cross-section contours measured via optical microscopy. In this architecture, a ResNet model embeds the spatial information contained within the thermal images to a latent vector, while a Transformer model correlates the sequence of embedded vectors to extract temporal information. Our framework is able to model the curvature of the subsurface melt pool structure, with improved performance in high energy density regimes compared to analytical melt pool models. The performance of this model is evaluated through dimensional and geometric comparisons to the corresponding experimental melt pool observations.

cs.LG↗

arXiv2024

CaFA: Global Weather Forecasting with Factorized Attention on Sphere

Accurate weather forecasting is crucial in various sectors, impacting decision-making processes and societal events. Data-driven approaches based on machine learning models have recently emerged as a promising alternative to numerical weather prediction models given their potential to capture physics of different scales from historical data and the significantly lower computational cost during the prediction stage. Renowned for its state-of-the-art performance across diverse domains, the Transformer model has also gained popularity in machine learning weather prediction. Yet applying Transformer architectures to weather forecasting, particularly on a global scale is computationally challenging due to the quadratic complexity of attention and the quadratic increase in spatial points as resolution increases. In this work, we propose a factorized-attention-based model tailored for spherical geometries to mitigate this issue. More specifically, it utilizes multi-dimensional factorized kernels that convolve over different axes where the computational complexity of the kernel is only quadratic to the axial resolution instead of overall resolution. The deterministic forecasting accuracy of the proposed model on $1.5^\circ$ and 0-7 days' lead time is on par with state-of-the-art purely data-driven machine learning weather prediction models. We also showcase the proposed model holds great potential to push forward the Pareto front of accuracy-efficiency for Transformer weather models, where it can achieve better accuracy with less computational cost compared to Transformer based models with standard attention.

cs.LG↗

arXiv2024

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.

cs.CV↗

arXiv2024

GradNav: Accelerated Exploration of Potential Energy Surfaces with Gradient-Based Navigation

The exploration of molecular systems' potential energy surface is important for comprehending their complex behaviors, particularly through identifying various metastable states. However, the transition between these states is often hindered by substantial energy barriers, demanding prolonged molecular simulations that consume considerable computational efforts. Our study introduces the GradNav algorithm, which enhances the exploration of the energy surface, accelerating the reconstruction of the potential energy surface (PES). This algorithm employs a strategy of initiating short simulation runs from updated starting points, derived from prior observations, to effectively navigate across potential barriers and explore new regions. To evaluate GradNav's performance, we introduce two metrics: the deepest well escape frame (DWEF) and the search success initialization ratio (SSIR). Through applications on Langevin dynamics within Mueller-type potential energy surfaces and molecular dynamics simulations of the Fs-Peptide protein, these metrics demonstrate GradNav's enhanced ability to escape deep energy wells, as shown by reduced DWEF values, and its reduced reliance on initial conditions, highlighted by increased SSIR values. Consequently, this improved exploration capability enables more precise energy estimations from simulation trajectories.

physics.chem-ph↗

arXiv2024

AlloyBERT: Alloy Property Prediction with Large Language Models

The pursuit of novel alloys tailored to specific requirements poses significant challenges for researchers in the field. This underscores the importance of developing predictive techniques for essential physical properties of alloys based on their chemical composition and processing parameters. This study introduces AlloyBERT, a transformer encoder-based model designed to predict properties such as elastic modulus and yield strength of alloys using textual inputs. Leveraging the pre-trained RoBERTa encoder model as its foundation, AlloyBERT employs self-attention mechanisms to establish meaningful relationships between words, enabling it to interpret human-readable input and predict target alloy properties. By combining a tokenizer trained on our textual data and a RoBERTa encoder pre-trained and fine-tuned for this specific task, we achieved a mean squared error (MSE) of 0.00015 on the Multi Principal Elemental Alloys (MPEA) data set and 0.00611 on the Refractory Alloy Yield Strength (RAYS) dataset. This surpasses the performance of shallow models, which achieved a best-case MSE of 0.00025 and 0.0076 on the MPEA and RAYS datasets respectively. Our results highlight the potential of language models in material science and establish a foundational framework for text-based prediction of alloy properties that does not rely on complex underlying representations, calculations, or simulations.

cond-mat.mtrl-sci↗

arXiv2024

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

In an era where symbolic mathematical equations are indispensable for modeling complex natural phenomena, scientific inquiry often involves collecting observations and translating them into mathematical expressions. Recently, deep learning has emerged as a powerful tool for extracting insights from data. However, existing models typically specialize in either numeric or symbolic domains, and are usually trained in a supervised manner tailored to specific tasks. This approach neglects the substantial benefits that could arise from a task-agnostic multi-modal understanding between symbolic equations and their numeric counterparts. 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. By performing latent space analysis, we observe that SNIP provides cross-domain insights into the representations, revealing that symbolic supervision enhances the embeddings of numeric data and vice versa. We evaluate SNIP across diverse tasks, including symbolic-to-numeric mathematical property prediction and numeric-to-symbolic equation discovery, commonly known as symbolic regression. Results show that SNIP effectively transfers to various tasks, consistently outperforming fully supervised baselines and competing strongly with established task-specific methods, especially in the low data regime scenarios where available data is limited. Code and model are available at: https://github.com/deep-symbolic-mathematics/Multimodal-Math-Pretraining

cs.LG↗

arXiv2024

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

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. These challenges are the most pronounced with 3D deformable objects. We propose SculptDiff, a goal-conditioned diffusion-based imitation learning framework that works with point cloud state observations to directly learn clay sculpting policies for a variety of target shapes. To the best of our knowledge this is the first real-world method that successfully learns manipulation policies for 3D deformable objects. For sculpting videos and access to our dataset and hardware CAD models, see the project website: https://sites.google.com/andrew.cmu.edu/imitation-sculpting/home

cs.RO↗

arXiv2024

Inpainting Computational Fluid Dynamics with Deep Learning

Fluid data completion is a research problem with high potential benefit for both experimental and computational fluid dynamics. An effective fluid data completion method reduces the required number of sensors in a fluid dynamics experiment, and allows a coarser and more adaptive mesh for a Computational Fluid Dynamics (CFD) simulation. However, the ill-posed nature of the fluid data completion problem makes it prohibitively difficult to obtain a theoretical solution and presents high numerical uncertainty and instability for a data-driven approach (e.g., a neural network model). To address these challenges, we leverage recent advancements in computer vision, employing the vector quantization technique to map both complete and incomplete fluid data spaces onto discrete-valued lower-dimensional representations via a two-stage learning procedure. We demonstrated the effectiveness of our approach on Kolmogorov flow data (Reynolds number: 1000) occluded by masks of different size and arrangement. Experimental results show that our proposed model consistently outperforms benchmark models under different occlusion settings in terms of point-wise reconstruction accuracy as well as turbulent energy spectrum and vorticity distribution.

cs.LG↗

arXiv2024

Physics Informed Token Transformer for Solving Partial Differential Equations

Solving Partial Differential Equations (PDEs) is the core of many fields of science and engineering. While classical approaches are often prohibitively slow, machine learning models often fail to incorporate complete system information. Over the past few years, transformers have had a significant impact on the field of Artificial Intelligence and have seen increased usage in PDE applications. However, despite their success, transformers currently lack integration with physics and reasoning. This study aims to address this issue by introducing PITT: Physics Informed Token Transformer. The purpose of PITT is to incorporate the knowledge of physics by embedding partial differential equations (PDEs) into the learning process. PITT uses an equation tokenization method to learn an analytically-driven numerical update operator. By tokenizing PDEs and embedding partial derivatives, the transformer models become aware of the underlying knowledge behind physical processes. To demonstrate this, PITT is tested on challenging 1D and 2D PDE neural operator prediction tasks. The results show that PITT outperforms popular neural operator models and has the ability to extract physically relevant information from governing equations.

cs.LG↗

arXiv2023

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

Alzheimer's Disease (AD), a neurodegenerative disorder, is reported as one of the most severe health and socioeconomic problems in current public health. Tau proteins are assumed to be a crucial driving factor of AD that detach from microtubules (MT) and accumulate as neurotoxic aggregates in the brains of AD patients. Extensive experimental and computational research has observed that phosphorylation at specific tau residues enhances aggregation, but the exact mechanisms underlying this phenomenon remain unclear. In this study, we employed molecular dynamics (MD) simulations on pseudo-phosphorylated tau-MT complex (residue 199 ~ 312), incorporating structural data from recent cryo-electron microscopy studies. Simulation results have revealed altered tau conformations after applying pseudo-phosphorylation. Additionally, root-mean-square deviation (RMSD) analyses and dimensionality reduction of dihedral angles revealed key residues responsible for these conformational shifts

q-bio.BM↗