arXiv subjects

Amir Barati Farimani

Publications and source records attributed to Amir Barati Farimani.

At least 37 records · Page 2Linked to original sources

arXiv2026

From Natural Language to Materials Discovery:The Materials Knowledge Navigation Agent

Accelerating the discovery of high-performance materials remains a central challenge across energy, electronics, and aerospace technologies, where traditional workflows depend heavily on expert intuition and computationally expensive simulations. Here we introduce the Materials Knowledge Navigation Agent (MKNA), a language-driven system that translates natural-language scientific intent into executable actions for database retrieval, property prediction, structure generation, and stability evaluation. Beyond automating tool invocation, MKNA autonomously extracts quantitative thresholds and chemically meaningful design motifs from literature and database evidence, enabling data-grounded hypothesis formation. Applied to the search for high-Debye-temperature ceramics, the agent identifies a literature-supported screening criterion (Theta_D > 800 K), rediscovers canonical ultra-stiff materials such as diamond, SiC, SiN, and BeO, and proposes thermodynamically stable, previously unreported Be-C-rich compounds that populate the sparsely explored 1500-1700 K regime. These results demonstrate that MKNA not only finds stable candidates but also reconstructs interpretable design heuristics, establishing a generalizable platform for autonomous, language-guided materials exploration.

cs.LG↗

arXiv2026

Synthesizing the Kill Chain: A Zero-Shot Framework for Target Verification and Tactical Reasoning on the Edge

Deploying autonomous edge robotics in dynamic military environments is constrained by both scarce domain-specific training data and the computational limits of edge hardware. This paper introduces a hierarchical, zero-shot framework that cascades lightweight object detection with compact Vision-Language Models (VLMs) from the Qwen and Gemma families (4B-12B parameters). Grounding DINO serves as a high-recall, text-promptable region proposer, and frames with high detection confidence are passed to edge-class VLMs for semantic verification. We evaluate this pipeline on 55 high-fidelity synthetic videos from Battlefield 6 across three tasks: false-positive filtering (up to 100% accuracy), damage assessment (up to 97.5%), and fine-grained vehicle classification (55-90%). We further extend the pipeline into an agentic Scout-Commander workflow, achieving 100% correct asset deployment and a 9.8/10 reasoning score (graded by GPT-4o) with sub-75-second latency. A novel "Controlled Input" methodology decouples perception from reasoning, revealing distinct failure phenotypes: Gemma3-12B excels at tactical logic but fails in visual perception, while Gemma3-4B exhibits reasoning collapse even with accurate inputs. These findings validate hierarchical zero-shot architectures for edge autonomy and provide a diagnostic framework for certifying VLM suitability in safety-critical applications.

cs.CV↗

arXiv2026

DistMLIP: A Distributed Inference Platform for Machine Learning Interatomic Potentials

Large-scale atomistic simulations are essential to bridge computational materials and chemistry to realistic materials and drug discovery applications. In the past few years, rapid developments of machine learning interatomic potentials (MLIPs) have offered a solution to scale up quantum mechanical calculations. Parallelizing these interatomic potentials across multiple devices poses a challenging, but promising approach to further extending simulation scales to real-world applications. In this work, we present DistMLIP, an efficient distributed inference platform for MLIPs based on zero-redundancy, graph-level parallelization. In contrast to conventional spatial partitioning parallelization, DistMLIP enables efficient MLIP parallelization through graph partitioning, allowing multi-device inference on flexible MLIP model architectures like multi-layer graph neural networks. DistMLIP presents an easy-to-use, flexible, plug-in interface that enables distributed inference of pre-existing MLIPs. We demonstrate DistMLIP on four widely used and state-of-the-art MLIPs: CHGNet, MACE, TensorNet, and eSEN. We show that DistMLIP can simulate atomic systems 3.4x larger and up to 8x faster compared to previous multi-GPU methods. We show that existing foundation potentials can perform near-million-atom calculations at the scale of a few seconds on 8 GPUs with DistMLIP.

cs.DC↗

arXiv2026

Smooth Dynamic Cutoffs for Machine Learning Interatomic Potentials

Machine learning interatomic potentials (MLIPs) have proven to be wildly useful for molecular dynamics simulations, powering countless drug and materials discovery applications. However, MLIPs face two primary bottlenecks preventing them from reaching realistic simulation scales: inference time and memory consumption. In this work, we address both issues by challenging the long-held belief that the cutoff radius for the MLIP must be held to a fixed, constant value. For the first time, we introduce a dynamic cutoff formulation that still leads to stable, long timescale molecular dynamics simulation. In introducing the dynamic cutoff, we are able to induce sparsity onto the underlying atom graph by targeting a specific number of neighbors per atom, significantly reducing both memory consumption and inference time. We show the effectiveness of a dynamic cutoff by implementing it onto 4 state of the art MLIPs: MACE, Nequip, Orbv3, and TensorNet, leading to 2.26x less memory consumption and 2.04x faster inference time, depending on the model and atomic system. We also perform an extensive error analysis and find that the dynamic cutoff models exhibit minimal accuracy dropoff compared to their fixed cutoff counterparts on both materials and molecular datasets. All model implementations and training code will be fully open sourced.

cs.LG↗

arXiv2026

TDFlow: Agentic Workflows for Test Driven Development

We introduce TDFlow, a novel test-driven agentic workflow that frames repository-scale software engineering as a test-resolution task, specifically designed to solve human-written tests. Given a set of tests, TDFlow repeatedly proposes, revises, and debugs repository-scale patches using precisely engineered sub-agents and tightly constrained tools. The workflow decomposes software engineering program repair into four components governed by respective sub-agents. This simple, forced decoupling of patch proposing, debugging, patch revision, and optional test generation (1) reduces long-context burden on any individual sub-agent, (2) focuses each sub-agent on specific, pre-defined sub-tasks, and (3) allows for specialized performance improvement on specific sub-tasks. When provided human-written tests, TDFlow attains 88.8% pass rate on SWE-Bench Lite (an absolute improvement of 27.8% over the next best system) and 94.3% on SWE-Bench Verified. Manual inspection of the 800 TDFlow runs within SWE-Bench Lite and Verified uncover only 7 instances of test hacking, which were subsequently counted as failures. Furthermore, we show that the primary obstacle to human-level software engineering performance lies within writing successful reproduction tests. We envision a human-LLM interactive system powered by TDFlow where human developers write tests solved by LLM systems. Together, these results indicate that modern LLMs, when embedded in a narrowly engineered, test-driven workflow, already achieve human-level test resolution -- with the final frontier for fully autonomous repository repair being the accurate generation of valid reproduction tests.

cs.SE↗

arXiv2026

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.

cs.LG↗

arXiv2026

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.

cs.LG↗

arXiv2026

Agentic Additive Manufacturing Alloy Evaluation

Agentic systems enable the intelligent use of research tooling, augmenting a researcher's ability to investigate and propose novel solutions to existing problems. Within Additive Manufacturing (AM), alloy selection and evaluation remains a complex challenge, often requiring expertise in the various domains of materials science, thermodynamic simulations, and experimental analysis. Large Language Model (LLM) enabled agents can facilitate this endeavor by utilizing their extensive knowledge base to dispatch tool calls via Model Context Protocol (MCP) to perform actions such as thermophysical property diagram calculations and lack of fusion process map generation. In addition, the multi-agent system can effectively reason through complex user prompts and provide analysis on the lack of fusion process window of common alloys such as SS316L and IN718 along with proposed composition variants of known alloys. These agents can dynamically adjust their task trajectory to the outcomes of tool call results, effectively enabling autonomous decision-making in practical environments. This work aims to showcase the benefits of adopting a LLM enabled multi-agent system to automate and accelerate the task of evaluating proposed additive manufacturing alloys, both novel and known.

cs.AI↗

arXiv2025

Beyond Force Metrics: Pre-Training MLFFs for Stable MD Simulations

Machine-learning force fields (MLFFs) have emerged as a promising solution for speeding up ab initio molecular dynamics (MD) simulations, where accurate force predictions are critical but often computationally expensive. In this work, we employ GemNet-T, a graph neural network model, as an MLFF and investigate two training strategies: (1) direct training on MD17 (10K samples) without pre-training, and (2) pre-training on the large-scale OC20 dataset followed by fine-tuning on MD17 (10K). While both approaches achieve low force mean absolute errors (MAEs), reaching 5 meV/A per atom, we find that lower force errors do not necessarily guarantee stable MD simulations. Notably, the pre-trained GemNet-T model yields significantly improved simulation stability, sustaining trajectories up to three times longer than the model trained from scratch. By analyzing local properties of the learned force fields, we find that pre-training produces more structured latent representations, smoother force responses to local geometric changes, and more consistent force differences between nearby configurations, all of which contribute to more stable and reliable MD simulations. These findings underscore the value of pre-training on large, diverse datasets to capture complex molecular interactions and highlight that force MAE alone is not always a sufficient metric of MD simulation stability.

physics.chem-ph↗

arXiv2025

Large Language Model Agent for Modular Task Execution in Drug Discovery

We present a modular framework powered by large language models (LLMs) that automates and streamlines key tasks across the early-stage computational drug discovery pipeline. By combining LLM reasoning with domain-specific tools, the framework performs biomedical data retrieval, literature-grounded question answering via retrieval-augmented generation, molecular generation, multi-property prediction, property-aware molecular refinement, and 3D protein-ligand structure generation. The agent autonomously retrieved relevant biomolecular information, including FASTA sequences, SMILES representations, and literature, and answered mechanistic questions with improved contextual accuracy compared to standard LLMs. It then generated chemically diverse seed molecules and predicted 75 properties, including ADMET-related and general physicochemical descriptors, which guided iterative molecular refinement. Across two refinement rounds, the number of molecules with QED > 0.6 increased from 34 to 55. The number of molecules satisfying empirical drug-likeness filters also rose; for example, compliance with the Ghose filter increased from 32 to 55 within a pool of 100 molecules. The framework also employed Boltz-2 to generate 3D protein-ligand complexes and provide rapid binding affinity estimates for candidate compounds. These results demonstrate that the approach effectively supports molecular screening, prioritization, and structure evaluation. Its modular design enables flexible integration of evolving tools and models, providing a scalable foundation for AI-assisted therapeutic discovery.

cs.LG↗

arXiv2025

Text to Band Gap: Pre-trained Language Models as Encoders for Semiconductor Band Gap Prediction

We investigate transformer-based language models, including RoBERTa, T5, Llama-3, and MatSciBERT, for predicting the band gaps of semiconductor materials directly from textual descriptions. The inputs encode key material features, such as chemical composition, crystal system, space group, and other structural and electronic properties. Unlike shallow machine learning models, which require extensive feature engineering, or Graph Neural Networks, which rely on graph representations derived from atomic coordinates, pretrained language models can process textual inputs directly, eliminating the need for manual feature preprocessing or structure-based encoding. Material descriptions were constructed in two formats: structured strings with a consistent template and natural language narratives generated via the ChatGPT API. Each model was augmented with a custom regression head and finetuned for band gap prediction task. Language models of different architectures and parameter sizes were all able to predict band gaps from human-readable text with strong accuracy, achieving MAEs in the range of 0.25-0.33 eV, highlighting the success of this approach for scientific regression tasks. Finetuned Llama-3, with 1.2 billion parameters, achieved the highest accuracy (MAE 0.248 eV, R2 0.891). MatSciBERT, pretrained on materials science literature, reached comparable performance (MAE 0.288 eV, R2 0.871) with significantly fewer parameters (110 million), emphasizing the importance of domain-specific pretraining. Attention analysis shows that both models selectively focus on compositional and spin-related features while de-emphasizing geometric features, reflecting the difficulty of capturing spatial information from text. These results establish that pretrained language models can effectively extract complex feature-property relationships from textual material descriptions.

cs.CL↗

arXiv2025

Meta-Learning for Cross-Task Generalization in Protein Mutation Property Prediction

Protein mutations can have profound effects on biological function, making accurate prediction of property changes critical for drug discovery, protein engineering, and precision medicine. Current approaches rely on fine-tuning protein-specific transformers for individual datasets, but struggle with cross-dataset generalization due to heterogeneous experimental conditions and limited target domain data. We introduce two key innovations: (1) the first application of Model-Agnostic Meta-Learning (MAML) to protein mutation property prediction, and (2) a novel mutation encoding strategy using separator tokens to directly incorporate mutations into sequence context. We build upon transformer architectures integrating them with MAML to enable rapid adaptation to new tasks through minimal gradient steps rather than learning dataset-specific patterns. Our mutation encoding addresses the critical limitation where standard transformers treat mutation positions as unknown tokens, significantly degrading performance. Evaluation across three diverse protein mutation datasets (functional fitness, thermal stability, and solubility) demonstrates significant advantages over traditional fine-tuning. In cross-task evaluation, our meta-learning approach achieves 29% better accuracy for functional fitness with 65% less training time, and 94% better accuracy for solubility with 55% faster training. The framework maintains consistent training efficiency regardless of dataset size, making it particularly valuable for industrial applications and early-stage protein design where experimental data is limited. This work establishes a systematic application of meta-learning to protein mutation analysis and introduces an effective mutation encoding strategy, offering transformative methodology for cross-domain generalization in protein engineering.

cs.LG↗

arXiv2025

LLM-guided Chemical Process Optimization with a Multi-Agent Approach

Chemical process optimization maximizes production efficiency and economic performance, but optimization algorithms, including gradient-based solvers, numerical methods, and parameter grid searches, become impractical when operating constraints are ill-defined or unavailable. We present a multi-agent LLM framework that autonomously infers operating constraints from minimal process descriptions, then collaboratively guides optimization. Our AutoGen-based framework employs OpenAI's o3 model with specialized agents for constraint generation, parameter validation, simulation, and optimization guidance. Through autonomous constraint generation and iterative multi-agent optimization, the framework eliminates the need for predefined operational bounds. Validated on hydrodealkylation across cost, yield, and yield-to-cost ratio metrics, the framework achieved competitive performance with conventional methods while reducing wall-time 31-fold relative to grid search, converging in under 20 minutes. The reasoning-guided search demonstrates sophisticated process understanding, correctly identifying utility trade-offs and applying domain-informed heuristics. Unlike conventional methods requiring predefined constraints, our approach uniquely combines autonomous constraint generation with interpretable parameter exploration. Model comparison reveals reasoning-capable architectures (o3, o1) are essential for successful optimization, while standard models fail to converge. This approach is particularly valuable for emerging processes and retrofit applications where operational constraints are poorly characterized or unavailable.

cs.LG↗

arXiv2025

Reframing Generative Models for Physical Systems using Stochastic Interpolants

Generative models have recently emerged as powerful surrogates for physical systems, demonstrating increased accuracy, stability, and/or statistical fidelity. Most approaches rely on iteratively denoising a Gaussian, a choice that may not be the most effective for autoregressive prediction tasks in PDEs and dynamical systems such as climate. In this work, we benchmark generative models across diverse physical domains and tasks, and highlight the role of stochastic interpolants. By directly learning a stochastic process between current and future states, stochastic interpolants can leverage the proximity of successive physical distributions. This allows for generative models that can use fewer sampling steps and produce more accurate predictions than models relying on transporting Gaussian noise. Our experiments suggest that generative models need to balance deterministic accuracy, spectral consistency, and probabilistic calibration, and that stochastic interpolants can potentially fulfill these requirements by adjusting their sampling. This study establishes stochastic interpolants as a competitive baseline for physical emulation and gives insight into the abilities of different generative modeling frameworks.

cs.LG↗

arXiv2025

Hamiltonian Neural PDE Solvers through Functional Approximation

Designing neural networks within a Hamiltonian framework offers a principled way to ensure that conservation laws are respected in physical systems. While promising, these capabilities have been largely limited to discrete, analytically solvable systems. In contrast, many physical phenomena are governed by PDEs, which govern infinite-dimensional fields through Hamiltonian functionals and their functional derivatives. Building on prior work, we represent the Hamiltonian functional as a kernel integral parameterized by a neural field, enabling learnable function-to-scalar mappings and the use of automatic differentiation to calculate functional derivatives. This allows for an extension of Hamiltonian mechanics to neural PDE solvers by predicting a functional and learning in the gradient domain. We show that the resulting Hamiltonian Neural Solver (HNS) can be an effective surrogate model through improved stability and conserving energy-like quantities across 1D and 2D PDEs. This ability to respect conservation laws also allows HNS models to better generalize to longer time horizons or unseen initial conditions.

cs.LG↗

arXiv2025

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.

cs.CL↗

arXiv2025

RT-Cache: Training-Free Retrieval for Real-Time Manipulation

Real robots are expected to repeat the same behavior in new environments with very little new data, yet modern controllers either incur heavy per-step inference or require deployment-time fine-tuning. We propose RT-Cache, a training-free retrieval-as-control pipeline that caches diverse image action trajectories in a unified vector memory and, at test time, embeds the current frame to retrieve and replay multi-step snippets, replacing per-step model calls. A hierarchical search keeps lookups sub-second at million scale, shifting cost from compute to storage and enabling real-time control on modest GPUs. Across real-robot tasks and large open logs, RT-Cache achieves higher success and lower completion time than strong retrieval baselines (approximately x2 higher success and ~30% faster in our settings), and a single-episode anchoring study shows immediate adaptation to a more complex, contact-rich task without fine-tuning. RT-Cache turns experience into an append-only memory, offering a simple, scalable path to few-shot deployment today and a foundation for multimodal keys and optional integration with high-level policies. Project page: https://rt-cache.github.io/.

cs.RO↗

arXiv2025

PinchBot: Long-Horizon Deformable Manipulation with Guided Diffusion Policy

Pottery creation is a complicated art form that requires dexterous, precise and delicate actions to slowly morph a block of clay to a meaningful, and often useful 3D goal shape. In this work, we aim to create a robotic system that can create simple pottery goals with only pinch-based actions. This pinch pottery task allows us to explore the challenges of a highly multi-modal and long-horizon deformable manipulation task. To this end, we present PinchBot, a goal-conditioned diffusion policy model that when combined with pre-trained 3D point cloud embeddings, task progress prediction and collision-constrained action projection, is able to successfully create a variety of simple pottery goals. For experimental videos and access to the demonstration dataset, please visit our project website: https://sites.google.com/andrew.cmu.edu/pinchbot/home.

cs.RO↗