arXiv subjects

Amir Barati Farimani

Publications and source records attributed to Amir Barati Farimani.

At least 55 records · Page 3Linked to original sources

arXiv2025

Adsorb-Agent: Autonomous Identification of Stable Adsorption Configurations via Large Language Model Agent

Adsorption energy is a key reactivity descriptor in catalysis. Determining adsorption energy requires evaluating numerous adsorbate-catalyst configurations, making it computationally intensive. Current methods rely on exhaustive sampling, which does not guarantee the identification of the global minimum energy. To address this, we introduce Adsorb-Agent, a Large Language Model (LLM) agent designed to efficiently identify stable adsorption configurations corresponding to the global minimum energy. Adsorb-Agent leverages its built-in knowledge and reasoning to strategically explore configurations, significantly reducing the number of initial setups required while improving energy prediction accuracy. In this study, we also evaluated the performance of different LLMs, including GPT-4o, GPT-4o-mini, Claude-3.7-Sonnet, and DeepSeek-Chat, as the reasoning engine for Adsorb-Agent, with GPT-4o showing the strongest overall performance. Tested on twenty diverse systems, Adsorb-Agent identifies comparable adsorption energies for 84% of cases and achieves lower energies for 35%, particularly excelling in complex systems. It identifies lower energies in 47% of intermetallic systems and 67% of systems with large adsorbates. These findings demonstrate Adsorb-Agent's potential to accelerate catalyst discovery by reducing computational costs and enhancing prediction reliability compared to exhaustive search methods.

cs.CL↗

arXiv2025

LLM-Craft: Robotic Crafting of Elasto-Plastic Objects with Large Language Models

When humans create sculptures, we are able to reason about how geometrically we need to alter the clay state to reach our target goal. We are not computing point-wise similarity metrics, or reasoning about low-level positioning of our tools, but instead determining the higher-level changes that need to be made. In this work, we propose LLM-Craft, a novel pipeline that leverages large language models (LLMs) to iteratively reason about and generate deformation-based crafting action sequences. We simplify and couple the state and action representations to further encourage shape-based reasoning. To the best of our knowledge, LLM-Craft is the first system successfully leveraging LLMs for complex deformable object interactions. Through our experiments, we demonstrate that with the LLM-Craft framework, LLMs are able to successfully create a set of simple letter shapes. We explore a variety of rollout strategies, and compare performances of LLM-Craft variants with and without an explicit goal shape images. For videos and prompting details, please visit our project website: https://sites.google.com/andrew.cmu.edu/llmcraft/home

cs.RO↗

arXiv2025

LLM-SRBench: A New Benchmark for Scientific Equation Discovery with Large Language Models

Scientific equation discovery is a fundamental task in the history of scientific progress, enabling the derivation of laws governing natural phenomena. Recently, Large Language Models (LLMs) have gained interest for this task due to their potential to leverage embedded scientific knowledge for hypothesis generation. However, evaluating the true discovery capabilities of these methods remains challenging, as existing benchmarks often rely on common equations that are susceptible to memorization by LLMs, leading to inflated performance metrics that do not reflect discovery. In this paper, we introduce LLM-SRBench, a comprehensive benchmark with 239 challenging problems across four scientific domains specifically designed to evaluate LLM-based scientific equation discovery methods while preventing trivial memorization. Our benchmark comprises two main categories: LSR-Transform, which transforms common physical models into less common mathematical representations to test reasoning beyond memorized forms, and LSR-Synth, which introduces synthetic, discovery-driven problems requiring data-driven reasoning. Through extensive evaluation of several state-of-the-art methods, using both open and closed LLMs, we find that the best-performing system so far achieves only 31.5% symbolic accuracy. These findings highlight the challenges of scientific equation discovery, positioning LLM-SRBench as a valuable resource for future research.

cs.CL↗

arXiv2025

MOFGPT: Generative Design of Metal-Organic Frameworks using Language Models

The discovery of Metal-Organic Frameworks (MOFs) with application-specific properties remains a central challenge in materials chemistry, owing to the immense size and complexity of their structural design space. Conventional computational screening techniques such as molecular simulations and density functional theory (DFT), while accurate, are computationally prohibitive at scale. Machine learning offers an exciting alternative by leveraging data-driven approaches to accelerate materials discovery. The complexity of MOFs, with their extended periodic structures and diverse topologies, creates both opportunities and challenges for generative modeling approaches. To address these challenges, we present a reinforcement learning-enhanced, transformer-based framework for the de novo design of MOFs. Central to our approach is MOFid, a chemically-informed string representation encoding both connectivity and topology, enabling scalable generative modeling. Our pipeline comprises three components: (1) a generative GPT model trained on MOFid sequences, (2) MOFormer, a transformer-based property predictor, and (3) a reinforcement learning (RL) module that optimizes generated candidates via property-guided reward functions. By integrating property feedback into sequence generation, our method drives the model toward synthesizable, topologically valid MOFs with desired functional attributes. This work demonstrates the potential of large language models, when coupled with reinforcement learning, to accelerate inverse design in reticular chemistry and unlock new frontiers in computational MOF discovery.

cs.LG↗

arXiv2025

BlastOFormer: Attention and Neural Operator Deep Learning Methods for Explosive Blast Prediction

Accurate prediction of blast pressure fields is essential for applications in structural safety, defense planning, and hazard mitigation. Traditional methods such as empirical models and computational fluid dynamics (CFD) simulations offer limited trade offs between speed and accuracy; empirical models fail to capture complex interactions in cluttered environments, while CFD simulations are computationally expensive and time consuming. In this work, we introduce BlastOFormer, a novel Transformer based surrogate model for full field maximum pressure prediction from arbitrary obstacle and charge configurations. BlastOFormer leverages a signed distance function (SDF) encoding and a grid to grid attention based architecture inspired by OFormer and Vision Transformer (ViT) frameworks. Trained on a dataset generated using the open source blastFoam CFD solver, our model outperforms convolutional neural networks (CNNs) and Fourier Neural Operators (FNOs) across both log transformed and unscaled domains. Quantitatively, BlastOFormer achieves the highest R2 score (0.9516) and lowest error metrics, while requiring only 6.4 milliseconds for inference, more than 600,000 times faster than CFD simulations. Qualitative visualizations and error analyses further confirm BlastOFormer's superior spatial coherence and generalization capabilities. These results highlight its potential as a real time alternative to conventional CFD approaches for blast pressure estimation in complex environments.

cs.LG↗

arXiv2025

Semantic Intelligence: Integrating GPT-4 with A Planning in Low-Cost Robotics

Classical robot navigation often relies on hardcoded state machines and purely geometric path planners, limiting a robot's ability to interpret high-level semantic instructions. In this paper, we first assess GPT-4's ability to act as a path planner compared to the A* algorithm, then present a hybrid planning framework that integrates GPT-4's semantic reasoning with A* on a low-cost robot platform operating on ROS2 Humble. Our approach eliminates explicit finite state machine (FSM) coding by using prompt-based GPT-4 reasoning to handle task logic while maintaining the accurate paths computed by A*. The GPT-4 module provides semantic understanding of instructions and environmental cues (e.g., recognizing toxic obstacles or crowded areas to avoid, or understanding low-battery situations requiring alternate route selection), and dynamically adjusts the robot's occupancy grid via obstacle buffering to enforce semantic constraints. We demonstrate multi-step reasoning for sequential tasks, such as first navigating to a resource goal and then reaching a final destination safely. Experiments on a Petoi Bittle robot with an overhead camera and Raspberry Pi Zero 2W compare classical A* against GPT-4-assisted planning. Results show that while A* is faster and more accurate for basic route generation and obstacle avoidance, the GPT-4-integrated system achieves high success rates (96-100%) on semantic tasks that are infeasible for pure geometric planners. This work highlights how affordable robots can exhibit intelligent, context-aware behaviors by leveraging large language model reasoning with minimal hardware and no fine-tuning.

cs.RO↗

arXiv2025

Large Language Model Agent as a Mechanical Designer

Conventional mechanical design follows an iterative process in which initial concepts are refined through cycles of expert assessment and resource-intensive Finite Element Method (FEM) analysis to meet performance goals. While machine learning models have been developed to assist in parts of this process, they typically require large datasets, extensive training, and are often tailored to specific tasks, limiting their generalizability. To address these limitations, we propose a framework that leverages a pretrained Large Language Model (LLM) in conjunction with an FEM module to autonomously generate, evaluate, and refine structural designs based on performance specifications and numerical feedback. The LLM operates without domain-specific fine-tuning, using general reasoning to propose design candidates, interpret FEM-derived performance metrics, and apply structurally sound modifications. Using 2D truss structures as a testbed, we show that the LLM can effectively navigate highly discrete and multi-faceted design spaces, balance competing objectives, and identify convergence when further optimization yields diminishing returns. Compared to Non-dominated Sorting Genetic Algorithm II (NSGA-II), our method achieves faster convergence and fewer FEM evaluations. Experiments with varying temperature settings (0.5, 1.0, 1.2) and model sizes (GPT-4.1 and GPT-4.1-mini) indicate that smaller models yield higher constraint satisfaction with fewer steps, while lower temperatures enhance design consistency. These results establish LLMs as a promising new class of reasoning-based, natural language-driven optimizers for autonomous design and iterative structural refinement.

cs.LG↗

arXiv2025

Predicting Change, Not States: An Alternate Framework for Neural PDE Surrogates

Neural surrogates for partial differential equations (PDEs) have become popular due to their potential to quickly simulate physics. With a few exceptions, neural surrogates generally treat the forward evolution of time-dependent PDEs as a black box by directly predicting the next state. While this is a natural and easy framework for applying neural surrogates, it can be an over-simplified and rigid framework for predicting physics. In this work, we evaluate an alternate framework in which neural solvers predict the temporal derivative and an ODE integrator forwards the solution in time, which has little overhead and is broadly applicable across model architectures and PDEs. We find that by simply changing the training target and introducing numerical integration during inference, neural surrogates can gain accuracy and stability in finely-discretized regimes. Predicting temporal derivatives also allows models to not be constrained to a specific temporal discretization, allowing for flexible time-stepping during inference or training on higher-resolution PDE data. Lastly, we investigate why this framework can be beneficial and in what situations does it work well.

cs.LG↗

arXiv2025

Dual Diffusion for Unified Image Generation and Understanding

Diffusion models have gained tremendous success in text-to-image generation, yet still lag behind with visual understanding tasks, an area dominated by autoregressive vision-language models. We propose a large-scale and fully end-to-end diffusion model for multi-modal understanding and generation that significantly improves on existing diffusion-based multimodal models, and is the first of its kind to support the full suite of vision-language modeling capabilities. Inspired by the multimodal diffusion transformer (MM-DiT) and recent advances in discrete diffusion language modeling, we leverage a cross-modal maximum likelihood estimation framework that simultaneously trains the conditional likelihoods of both images and text jointly under a single loss function, which is back-propagated through both branches of the diffusion transformer. The resulting model is highly flexible and capable of a wide range of tasks including image generation, captioning, and visual question answering. Our model attained competitive performance compared to recent unified image understanding and generation models, demonstrating the potential of multimodal diffusion modeling as a promising alternative to autoregressive next-token prediction models.

cs.CV↗

arXiv2025

Generative Latent Neural PDE Solver using Flow Matching

Autoregressive next-step prediction models have become the de-facto standard for building data-driven neural solvers to forecast time-dependent partial differential equations (PDEs). Denoise training that is closely related to diffusion probabilistic model has been shown to enhance the temporal stability of neural solvers, while its stochastic inference mechanism enables ensemble predictions and uncertainty quantification. In principle, such training involves sampling a series of discretized diffusion timesteps during both training and inference, inevitably increasing computational overhead. In addition, most diffusion models apply isotropic Gaussian noise on structured, uniform grids, limiting their adaptability to irregular domains. We propose a latent diffusion model for PDE simulation that embeds the PDE state in a lower-dimensional latent space, which significantly reduces computational costs. Our framework uses an autoencoder to map different types of meshes onto a unified structured latent grid, capturing complex geometries. By analyzing common diffusion paths, we propose to use a coarsely sampled noise schedule from flow matching for both training and testing. Numerical experiments show that the proposed model outperforms several deterministic baselines in both accuracy and long-term stability, highlighting the potential of diffusion-based approaches for robust data-driven PDE learning.

cs.LG↗

arXiv2025

Protein Structure-Function Relationship: A Kernel-PCA Approach for Reaction Coordinate Identification

In this study, we propose a Kernel-PCA model designed to capture structure-function relationships in a protein. This model also enables ranking of reaction coordinates according to their impact on protein properties. By leveraging machine learning techniques, including Kernel and principal component analysis (PCA), our model uncovers meaningful patterns in high-dimensional protein data obtained from molecular dynamics (MD) simulations. The effectiveness of our model in accurately identifying reaction coordinates has been demonstrated through its application to a G protein-coupled receptor. Furthermore, this model utilizes a network-based approach to uncover correlations in the dynamic behavior of residues associated with a specific protein property. These findings underscore the potential of our model as a powerful tool for protein structure-function analysis and visualization.

cs.CL↗

arXiv2025

LLM-Drone: Aerial Additive Manufacturing with Drones Planned Using Large Language Models

Additive manufacturing (AM) has transformed the production landscape by enabling the precision creation of complex geometries. However, AM faces limitations when applied to challenging environments, such as elevated surfaces and remote locations. Aerial additive manufacturing, facilitated by drones, presents a solution to these challenges. However, despite advances in methods for the planning, control, and localization of drones, the accuracy of these methods is insufficient to run traditional feedforward extrusion-based additive manufacturing processes (such as Fused Deposition Manufacturing). Recently, the emergence of LLMs has revolutionized various fields by introducing advanced semantic reasoning and real-time planning capabilities. This paper proposes the integration of LLMs with aerial additive manufacturing to assist with the planning and execution of construction tasks, granting greater flexibility and enabling a feed-back based design and construction system. Using the semantic understanding and adaptability of LLMs, we can overcome the limitations of drone based systems by dynamically generating and adapting building plans on site, ensuring efficient and accurate construction even in constrained environments. Our system is able to design and build structures given only a semantic prompt and has shown success in understanding the spatial environment despite tight planning constraints. Our method's feedback system enables replanning using the LLM if the manufacturing process encounters unforeseen errors, without requiring complicated heuristics or evaluation functions. Combining the semantic planning with automatic error correction, our system achieved a 90% build accuracy, converting simple text prompts to build structures.

cs.RO↗

arXiv2025

LLM-SR: Scientific Equation Discovery via Programming with Large Language Models

Mathematical equations have been unreasonably effective in describing complex natural phenomena across various scientific disciplines. However, discovering such insightful equations from data presents significant challenges due to the necessity of navigating extremely large combinatorial hypothesis spaces. Current methods of equation discovery, commonly known as symbolic regression techniques, largely focus on extracting equations from data alone, often neglecting the domain-specific prior knowledge that scientists typically depend on. They also employ limited representations such as expression trees, constraining the search space and expressiveness of equations. To bridge this gap, we introduce LLM-SR, a novel approach that leverages the extensive scientific knowledge and robust code generation capabilities of Large Language Models (LLMs) to discover scientific equations from data. Specifically, LLM-SR treats equations as programs with mathematical operators and combines LLMs' scientific priors with evolutionary search over equation programs. The LLM iteratively proposes new equation skeleton hypotheses, drawing from its domain knowledge, which are then optimized against data to estimate parameters. We evaluate LLM-SR on four benchmark problems across diverse scientific domains (e.g., physics, biology), which we carefully designed to simulate the discovery process and prevent LLM recitation. Our results demonstrate that LLM-SR discovers physically accurate equations that significantly outperform state-of-the-art symbolic regression baselines, particularly in out-of-domain test settings. We also show that LLM-SR's incorporation of scientific priors enables more efficient equation space exploration than the baselines. Code and data are available: https://github.com/deep-symbolic-mathematics/LLM-SR

cs.LG↗

arXiv2025

Low Fidelity Visuo-Tactile Pretraining Improves Vision-Only Manipulation Performance

Tactile perception is essential for real-world manipulation tasks, yet the high cost and fragility of tactile sensors can limit their practicality. In this work, we explore BeadSight (a low-cost, open-source tactile sensor) alongside a tactile pre-training approach, an alternative method to precise, pre-calibrated sensors. By pre-training with the tactile sensor and then disabling it during downstream tasks, we aim to enhance robustness and reduce costs in manipulation systems. We investigate whether tactile pre-training, even with a low-fidelity sensor like BeadSight, can improve the performance of an imitation learning agent on complex manipulation tasks. Through visuo-tactile pre-training on both similar and dissimilar tasks, we analyze its impact on a longer-horizon downstream task. Our experiments show that visuo-tactile pre-training improved performance on a USB cable plugging task by up to 65% with vision-only inference. Additionally, on a longer-horizon drawer pick-and-place task, pre-training--whether on a similar, dissimilar, or identical task--consistently improved performance, highlighting the potential for a large-scale visuo-tactile pre-trained encoder.

cs.RO↗

arXiv2025

Planning and Reasoning with 3D Deformable Objects for Hierarchical Text-to-3D Robotic Shaping

Deformable object manipulation remains a key challenge in developing autonomous robotic systems that can be successfully deployed in real-world scenarios. In this work, we explore the challenges of deformable object manipulation through the task of sculpting clay into 3D shapes. We propose the first coarse-to-fine autonomous sculpting system in which the sculpting agent first selects how many and where to place discrete chunks of clay into the workspace to create a coarse shape, and then iteratively refines the shape with sequences of deformation actions. We leverage large language models for sub-goal generation, and train a point cloud region-based action model to predict robot actions from the desired point cloud sub-goals. Additionally, our method is the first autonomous sculpting system that is a real-world text-to-3D shaping pipeline without any explicit 3D goals or sub-goals provided to the system. We demonstrate our method is able to successfully create a set of simple shapes solely from text-based prompting. Furthermore, we explore rigorously how to best quantify success for the text-to-3D sculpting task, and compare existing text-image and text-point cloud similarity metrics to human evaluations for this task. For experimental videos, human evaluation details, and full prompts, please see our project website: https://sites.google.com/andrew.cmu.edu/hierarchicalsculpting

cs.RO↗

arXiv2025

NANOGPT: A Query-Driven Large Language Model Retrieval-Augmented Generation System for Nanotechnology Research

This paper presents the development and application of a Large Language Model Retrieval-Augmented Generation (LLM-RAG) system tailored for nanotechnology research. The system leverages the capabilities of a sophisticated language model to serve as an intelligent research assistant, enhancing the efficiency and comprehensiveness of literature reviews in the nanotechnology domain. Central to this LLM-RAG system is its advanced query backend retrieval mechanism, which integrates data from multiple reputable sources. The system retrieves relevant literature by utilizing Google Scholar's advanced search, and scraping open-access papers from Elsevier, Springer Nature, and ACS Publications. This multifaceted approach ensures a broad and diverse collection of up-to-date scholarly articles and papers. The proposed system demonstrates significant potential in aiding researchers by providing a streamlined, accurate, and exhaustive literature retrieval process, thereby accelerating research advancements in nanotechnology. The effectiveness of the LLM-RAG system is validated through rigorous testing, illustrating its capability to significantly reduce the time and effort required for comprehensive literature reviews, while maintaining high accuracy, query relevance and outperforming standard, publicly available LLMS.

cs.CL↗

arXiv2025

Characterizing the Conformational States of G Protein Coupled Receptors Generated with AlphaFold

G-Protein Coupled Receptors (GPCRs) are integral to numerous physiological processes and are the target of approximately one-third of FDA-approved therapeutics. Despite their significance, only a limited subset of GPCRs has been successfully targeted, primarily due to challenges in accurately modeling their structures. AlphaFold, a state-of-the-art deep learning model, has demonstrated remarkable capability in predicting protein structures with high accuracy. This study conducts an evaluation of AlphaFold performance in predicting GPCR structures and their conformational states by comparing its predictions to experimentally determined structures using metrics such as average deformation between alpha carbon atoms and the Helix 3 - Helix 6 (H3-H6) distance. Our analysis reveals that both AlphaFold 2 (AF2) and AlphaFold 3 (AF3) produce more accurate predictions for GPCRs in inactive conformations, with lower activity levels correlating with smaller deformations. Conversely, higher activity levels are associated with increased variability in AlphaFold performance due to difficulties with accurately predicting conformational changes upon GPCR activation and ligand binding. Additionally, AlphaFold performance varies across different GPCR classes, influenced by the availability and quality of training data as well as the structural complexity and diversity of the receptors. These findings demonstrate the potential of AlphaFold in advancing drug discovery efforts, while also highlighting the necessity for continued refinement to enhance predictive accuracy for active conformations.

q-bio.QM↗

arXiv2025

Explain Like I'm Five: Using LLMs to Improve PDE Surrogate Models with Text

Solving Partial Differential Equations (PDEs) is ubiquitous in science and engineering. Computational complexity and difficulty in writing numerical solvers has motivated the development of data-driven machine learning techniques to generate solutions quickly. The recent rise in popularity of Large Language Models (LLMs) has enabled easy integration of text in multimodal machine learning models, allowing easy integration of additional system information such as boundary conditions and governing equations through text. In this work, we explore using pretrained LLMs to integrate various amounts of known system information into PDE learning. Using FactFormer as our testing backbone, we add a multimodal block to fuse numerical and textual information. We compare sentence-level embeddings, word-level embeddings, and a standard tokenizer across 2D Heat, Burgers, Navier-Stokes, and Shallow-Water data sets. These challenging benchmarks show that pretrained LLMs are able to utilize text descriptions of system information and enable accurate prediction using only initial conditions.

cs.LG↗