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.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent

Molecular dynamics simulations are an essential tool in understanding protein structure, dynamics, and function at the atomic level. However, preparing high quality input files for MD simulations can be a time consuming and error prone process. In this work, we introduce an automated pipeline that leverages Large Language Models (LLMs), specifically Gemini 2.0 Flash, in conjunction with python scripting and Selenium based web automation to streamline the generation of MD input files. The pipeline exploits CHARMM GUI's comprehensive web-based interface for preparing simulation-ready inputs for NAMD. By integrating Gemini's code generation and iterative refinement capabilities, simulation scripts are automatically written, executed, and revised to navigate CHARMM GUI, extract appropriate parameters, and produce the required NAMD input files. Post processing is performed using additional software to further refine the simulation outputs, thereby enabling a complete and largely hands free workflow. Our results demonstrate that this approach reduces setup time, minimizes manual errors, and offers a scalable solution for handling multiple protein systems in parallel. This automated framework paves the way for broader application of LLMs in computational structural biology, offering a robust and adaptable platform for future developments in simulation automation.

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

Chemical process optimization is crucial to maximize production efficiency and economic performance. Traditional methods, including gradient-based solvers, evolutionary algorithms, and parameter grid searches, become impractical when operating constraints are ill-defined or unavailable, requiring engineers to rely on subjective heuristics to estimate feasible parameter ranges. To address this constraint definition bottleneck, we present a multi-agent framework of large language model (LLM) agents that autonomously infer operating constraints from minimal process descriptions, then collaboratively guide optimization using the inferred constraints. Our AutoGen-based agentic framework employs OpenAI's o3 model, with specialized agents for constraint generation, parameter validation, simulation execution, and optimization guidance. Through two phases - autonomous constraint generation using embedded domain knowledge, followed by iterative multi-agent optimization - the framework eliminates the need for predefined operational bounds. Validated on the hydrodealkylation process across cost, yield, and yield-to-cost ratio metrics, the framework demonstrated competitive performance with conventional optimization methods while achieving better computational efficiency, requiring fewer iterations to converge. Our approach converged in under 20 minutes, achieving a 31-fold speedup over grid search. Beyond computational efficiency, the framework's reasoning-guided search demonstrates sophisticated process understanding, correctly identifying utility trade-offs, and applying domain-informed heuristics. This approach shows significant potential for optimization scenarios where operational constraints are poorly characterized or unavailable, particularly for emerging processes and retrofit applications.

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.

Neural Functional: Learning Function to Scalar Maps for Neural PDE Surrogates

Many architectures for neural PDE surrogates have been proposed in recent years, largely based on neural networks or operator learning. In this work, we derive and propose a new architecture, the Neural Functional, which learns function to scalar mappings. Its implementation leverages insights from operator learning and neural fields, and we show the ability of neural functionals to implicitly learn functional derivatives. For the first time, this allows for an extension of Hamiltonian mechanics to neural PDE surrogates by learning the Hamiltonian functional and optimizing its functional derivatives. We demonstrate that the Hamiltonian Neural Functional can be an effective surrogate model through improved stability and conserving energy-like quantities on 1D and 2D PDEs. Beyond PDEs, functionals are prevalent in physics; functional approximation and learning with its gradients may find other uses, such as in molecular dynamics or design optimization.

RT-cache: Efficient Robot Trajectory Retrieval System

This paper introduces RT-cache, a novel trajectorymemory pipeline that accelerates real-world robot inference by leveraging big-data retrieval and learning from experience. While modern Vision-Language-Action (VLA) models can handle diverse robotic tasks, they often incur high per-step inference costs, resulting in significant latency, sometimes minutes per task. In contrast, RT-cache stores a large-scale Memory of previously successful robot trajectories and retrieves relevant multistep motion snippets, drastically reducing inference overhead. By integrating a Memory Builder with a Trajectory Retrieval, we develop an efficient retrieval process that remains tractable even for extremely large datasets. RT-cache flexibly accumulates real-world experiences and replays them whenever the current scene matches past states, adapting quickly to new or unseen environments with only a few additional samples. Experiments on the Open-X Embodiment Dataset and other real-world data demonstrate that RT-cache completes tasks both faster and more successfully than a baseline lacking retrieval, suggesting a practical, data-driven solution for real-time manipulation.

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.

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.

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.

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.