ChemReasoner - Catalyst Discovery via Large Language Model-driven Reasoning( 32832-E)
ChemReasoner - Catalyst Discovery via Large Language Model-driven Reasoning
Choudhury, Sutanay [Pacific Northwest National Lab↗
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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Implementing Ordinary Differential Equation Solvers in Rust Programming Language for Modeling Vehicle Powertrain Systems: Preprint
Efficient and accurate ordinary differential equation (ODE) solvers are necessary for powertrain and vehicle dynamics modeling. However, current commercial ODE solvers can be financially prohibitive, leading to a need for accessible, effective, open-source ODE solvers designed for powertrain modeling. Rust is a compiled programming language that has the potential to be used for fast and easy-to-use powertrain models, given its exceptional computational performance, robust package ecosystem, and short time required for modelers to become proficient. However, of the three commonly used (>3,000 downloads) packages in Rust with ODE solver capabilities, only one has more than four numerical methods implemented, and none are designed specifically for modeling physical systems. Therefore, the goal of the Differential Equation System Solver (DESS) was to implement accurate ODE solvers in Rust designed for the component-based problems often seen in powertrain modeling. DESS is a text-based software package that provides a flexible framework for building and solving systems of ODEs. This allows DESS to be included as a dependency for automotive powertrain models that require a variety of solvers and solver configurations. Seven explicit ODE solver methods have been implemented in DESS: Euler’s, Heun’s, midpoint, Ralston’s, classic Runge-Kutta, Bogacki-Shampine, and Cash-Karp. These represent five fixed-step methods and two adaptive-step methods. This paper shows that the solver implementations increase accuracy and computational efficiency compared to Euler's method when modeling a system of three thermal masses in Rust. DESS also includes features designed for modeling component-based physical systems. Users can define relationships between nodes in their system, which the package then translates into a system of equations, leading to simpler and more intuitive code. In the case of a three-thermal-mass system, the user can specify node thermal properties (e.g., thermal capacitance), how nodes are interconnected, and thermal conductance between nodes rather than providing a system of equations. The core contribution from this work is an open-source, text-based Rust package with ODE solvers for automotive powertrain modeling to support cost-free, fast, and accurate simulation.
ADVANCED PROPULSION SYSTEMS↗
Rapid Adaptation of Chemical Named Entity Recognition Using Few-Shot Learning and LLM Distillation
Named entity recognition (NER) has been widely used in chemical text mining for the automatic identification and extraction of chemical entities. However, existing chemical NER systems primarily focus on scenarios with abundant training data, requiring significant human effort on annotations. This poses challenges for applications in the chemical field, such as catalysis, where many advancements have traditionally relied on trial-and-error investigations and incremental adjustment of variables. This hinders catalysis science and technology progress in addressing emerging energy and environmental crises. In this work, we propose a few-shot NER model that can quickly adapt to extract new types of chemical entities by using only a limited number of annotated examples. Our model employs a metric-learning approach to transfer entity similarity knowledge from high-resource chemical domains (with abundant annotations) to enable effective entity recognition in low-resource specialized domains (limited annotation). We validate the effectiveness of our model on a few-shot chemical NER benchmark built based on six existing chemical NER data sets. Experiments show that the proposed few-shot NER model can achieve reasonable performance with only 5 examples per entity type and shows consistent improvement as the number of examples increases. Furthermore, we demonstrate how the proposed model can be trained with large language model (LLM) annotated data, opening a new pathway for rapid adaptation of NER systems. Furthermore, our approach leverages the knowledge broadness of large language models for chemistry while distilling this knowledge into a lightweight model suitable for efficient and in-house use.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DECIDER
This software offers methods and functions for building failure detectors for deep image classification models with the aid of vision-language models and LLMs. It includes functionalities for training baseline image classifiers, debiasing classifiers using vision-language models and LLMs, evaluating failure between models along with baselines. Developed using PyTorch, this software is compatible with standard neural network architectures used for imaging data. Additionally, it provides capabilities to compute evaluation metrics for assessing the performance and quality of the detectors.
Narayanaswamy, Vivek Sivaraman↗
MoE-Inference-Bench: Performance Evaluation of Mixture of Expert Large Language and Vision Models
Mixture of Experts (MoE) models have enabled the scaling of Large Language Models (LLMs) and Vision Language Models (VLMs) by achieving massive parameter counts while maintaining computational efficiency. However, MoEs introduce several inference-time challenges, including load imbalance across experts and the additional routing computational overhead. To address these challenges and fully harness the benefits of MoE, a systematic evaluation of hardware acceleration techniques is essential. We present MoE-Inference-Bench, a comprehensive study to evaluate MoE performance across diverse scenarios. We analyze the impact of batch size, sequence length, and critical MoE hyperparameters such as FFN dimensions and number of experts on throughput. We evaluate several optimization techniques on Nvidia H100 GPUs, including pruning, Fused MoE operations, speculative decoding, quantization, and various parallelization strategies. Our evaluation includes MoEs from the Mixtral, DeepSeek, OLMoE and Qwen families. The results reveal performance differences across configurations and provide insights for the efficient deployment of MoEs.
Chitty-Venkata, Krishna Teja↗
Double Visual Defense
This is the official code for the paper "Double Visual Defense: Adversarial Pre-training and Instruction Tuning for Improving Vision-Language Model Robustness". This code can be used to produce vision language models (VLMs), like LLaVA, with enhanced robustness to adversarial attacks (e.g. jailbreaks).
Bartoldson, Brian [Lawrence Livermore National Lab↗
AI4HE: A Python Library for Materials Discovery
Machine learning library for developing scientific transformer models, particularly chemical language models, at scale
Salij, Andrew↗
Transform-Your-World
Machine learning library for developing scientific transformer models, particularly chemical language models, at scale
Salij, Andrew↗
Arbitrary Autoencoder Injection for Interpretability Experimentation
Goes over a simple software library (Python) for utilizing sparse autoencoders for more models than just language models.
Campos, Marco Vinicio↗
Generative AI in Supply Chain Management: Applications, Challenges, and Future Directions
Supply chain management (SCM) is undergoing rapid transformation due to increasing global complexity, demand volatility, and operational disruptions. Generative Artificial Intelligence (GenAI) has emerged as a powerful paradigm capable of synthesizing data, simulating operational scenarios, and enabling adaptive decision-making across supply chain networks. This paper presents a survey of GenAI’s role in SCM, focusing on its applications in predictive analytics, autonomous logistics, and fraud detection. Unlike traditional AI systems that rely primarily on predictive analytics, GenAI models, including large language models, generative adversarial networks, and diffusion-based architectures, enable the creation of synthetic supply chain scenarios and autonomous optimization strategies. This survey provides (1) a taxonomy of GenAI techniques for supply chain applications, (2) a comparative analysis of generative AI approaches with traditional machine learning, reinforcement learning, and blockchain-based methods, and (3) a discussion of key challenges such as data privacy, interpretability, and integration with legacy enterprise systems. Furthermore, we outline open research problems and propose directions for future research toward autonomous, resilient, and sustainable AI-driven supply chains.
15 - GEOTHERMAL ENERGY↗
Towards philosophical reasoning with agentic LLMs: Socratic method for scientific assistance
As large language models (LLMs) become central tools in science, improving their reasoning capabilities is critical for meaningful and trustworthy applications. We introduce a Socratic agent for scientific reasoning, implemented through a structured system prompt that guides LLMs via classical principles of inquiry. Unlike typical prompt engineering or retrieval-based methods, our approach leverages definition, analogy, hypothesis elimination, and other Socratic techniques to generate more coherent, critical, and domain-aware responses. We evaluate the agent across diverse scientific domains and benchmark it on the abstraction and reasoning corpus challenge dataset, achieving 97.15% under a fixed prompting protocol and without fine-tuning or external tools. Expert evaluation shows improved reasoning depth, clarity, and adaptability over conventional LLM outputs, suggesting that structured prompting rooted in philosophical reasoning can improve the scientific utility of language models.
LLM reasoning↗
MSD CoP Webinar: "Generative agents: A new frontier for representing human actors and their behavior in MSD models"
Context: This webinar was hosted by the MultiSector Dynamics Community of Practice (MSD CoP; https://multisectordynamics.org). Talk #1: Behavioral Generative Agents for Energy Operations Presenter: Dr. Cong Chen (Thayer School of Engineering, Dartmouth College) Abstract: Accurately modeling consumer behavior in energy operations remains challenging due to inherent uncertainties, behavioral complexities, and limited empirical data. This talk introduces a novel approach leveraging generative agents--artificial agents powered by large language models--to realistically simulate customer decision-making in dynamic energy operations. Talk #2: Simulating multiple human perspectives in socio-ecological systems using large language models Presenter: Dr. Yongchao Zeng (Institute of Meteorology and Climate Research, Atmospheric Environmental Research (IMK-IFU) of the Karlsruhe Institute of Technology in Germany) Abstract: Understanding socio-ecological systems requires insights from diverse stakeholder perspectives. This talk describes a novel simulation system called HoPeS (Human-oriented Perspective Shifting). HoPeS enables model users to not only explore simulated socio-ecological systems (SESs) from a third-person observer's perspective but also take any of the simulated stakeholder roles, like playing an RPG game. By shifting multiple perspectives, model users can reflect and integrate the situated knowledge learned through the participatory simulation, approximating a more holistic and less biased understanding of SESs. Moderators: Jim Yoon (MSD CoP Human Systems Modeling Working Group Co-Chair); Stefano Galelli (MSD CoP Using AI to Enhance MSD Research Working Group Co-Chair); Patrick M. Reed (MSD CoP Facilitation Team) This webinar was held on: November 13th, 2025 from 12-1 PM EST.
Artificial Intelligence↗
LLaMP v0.1.0
Reducing hallucination of Large Language Models (LLMs) is imperative for use in the sciences, where reliability and reproducibility are crucial. However, LLMs inherently lack long-term memory, making it a nontrivial, ad hoc, and inevitably biased task to fine-tune them on domain-specific literature and data. LLaMP is a multimodal retrieval-augmented generation (RAG) framework of hierarchical reasoning and acting (ReAct) agents that can dynamically and recursively interact with Materials Project to ground large language models on high-fidelity materials informatics.
Riebesell, Janosh [Lawrence Berkeley National Labo↗
Utilizing Machine Learning to Improve Neutralization Potency of an HIV-1 Antibody Targeting the gp41 N-Heptad Repeat
The N-heptad repeat (NHR) of the HIV-1 gp41 prehairpin intermediate (PHI) is an attractive potential vaccine target with high sequence conservation across diverse strains. However, despite the potency of NHR-targeting peptides and clinical efficacy of the NHR-targeting entry inhibitor enfuvirtide, no potently neutralizing NHR-directed monoclonal antibodies (mAbs) nor antisera have been identified or elicited to date. The lack of potent NHR-binding mAbs both dampens enthusiasm for vaccine development efforts at this target and presents a barrier to performing passive immunization experiments with NHR-targeting antibodies. To address this challenge, we previously developed an improved variant of the NHR-directed mAb D5, called D5_AR, which is capable of neutralizing diverse tier-2 viruses. Building on that work, here we present the 2.7Å-crystal structure of D5_AR bound to NHR mimetic peptide IQN17. We then utilize protein language models and supervised machine learning to generate small (n < 100) libraries of D5_AR variants that are subsequently screened for improved neutralization potency. We identify a variant with 5-fold improved neutralization potency, D5_FI, which is the most potent NHR-directed monoclonal antibody characterized to date and exhibits broad neutralization of tier-2 and −3 pseudoviruses as well as replicating R5 and X4 challenge strains. Additionally, our work highlights the ability of protein language models to efficiently identify improved mAb variants from relatively small libraries.
Biopolymers↗
U.S. Solar Siting Regulation and Zoning Ordinances (2025)
A machine readable collection of documented solar siting ordinances at the state and local (e.g., county, township) level throughout the United States. The data were compiled using the Infrastructure Continuous Ordinance Mapping for Planning and Siting Systems (INFRA-COMPASS) tool, which leverages Large Language Models (LLMs) to automate the collection of local codes and ordinances applicable to energy infrastructure. URLs for the ordinance source documents are included in the Solar Ordinances spreadsheet. The GeoPackage file included below contains the jurisdiction shapes for each ordinance. Note that the GeoPackage file is formatted for ingestion by NLR's reVX setbacks tool and therefore does not contain any of the state-level regulations. NOTE: This data was collected with the help of generative AI. The Large Language Models used for this effort make mistakes. Always validate the data for critical use cases. This data is an update to a previously developed database of wind ordinances found in OEDI Submission 5734: see the "U.S. Solar Siting Regulation and Zoning Ordinances 2022" link below. INFRA-COMPASS version used for collection: v0.11.3 LLMs used for collection: GPT-4.1, GPT-4.1 mini, GPT-4.1 nano
14 SOLAR ENERGY↗
U.S. Wind Siting Regulation and Zoning Ordinances (2025)
A machine readable collection of documented wind siting ordinances at the state and local (e.g., county, township) level throughout the United States. The data were compiled using the Infrastructure Continuous Ordinance Mapping for Planning and Siting Systems (INFRA-COMPASS) tool, which leverages Large Language Models (LLMs) to automate the collection of local codes and ordinances applicable to energy infrastructure. URLs for the ordinance source documents are included in the Wind Ordinances spreadsheet. The GeoPackage file included below contains the jurisdiction shapes for each ordinance. Note that the GeoPackage file is formatted for ingestion by NREL's reVX setbacks tool and therefore does not contain any of the state-level regulations. NOTE: This data was collected with the help of generative AI. The Large Language Models used for this effort make mistakes. Always validate the data for critical use cases. This data is an update to a previously developed database of wind ordinances found in OEDI Submission 5733: see the "U.S. Wind Siting Regulation and Zoning Ordinances 2022" link below. INFRA-COMPASS version used for collection: v0.8.2 LLMs used for collection: GPT-4.1, GPT-4.1 mini, GPT-4.1 nano, GPT-4o mini
17 WIND ENERGY↗
Agentic AI vs ML-Based Autotuning: A Comparative Study for Loop Reordering Optimization
High Performance Computing (HPC) applications rely heavily on code optimizations to achieve good performance on modern CPU and GPU architectures. Traditional Machine Learning auto-tuning approaches have demonstrated success in exploring high-dimensional spaces, but they often require expensive compile-run evaluations and lack adaptability for large HPC applications. The recent advances in Large Language Models (LLMs) and Agentic AI systems raise intriguing questions about the potential of these approaches to address specific optimization methodologies. This work aims to answer an essential question for the HPC community: “How Agentic AI Systems Compare to Traditional ML Autotuning Techniques?” To address this question, we present a comparative analysis between a traditional ML-based optimization approach and an Agentic AI system, evaluating their respective capabilities and limitations for loop-level optimization. In addition, we introduced a new Agentic AI system named LoopGen-AI using three different Large Language Models: GPT-4.1, Claude 4.0, and Gemini 2.5. A key finding is that LoopGen-AI achieves competitive per-formance with only a few program runs, the reasoning logs from the agents revealed that their decisions rely heavily on the combination of semantic understanding of the target kernel with dynamic feedback from the environment, highlighting a promising new dimension in performance tuning. In contrast, ML-based autotuners focus on statistical exploration, and require orders of magnitude more runs to reach peak performance. Additionally, our analysis shows that prompt engineering, particularly using Persona + Context Manager patterns, significantly impacts the effectiveness of Agentic AI. Our results indicate that while Agentic AI systems are not yet a complete replacement for ML-based autotuners, it can effectively complement traditional methods.
Rosas, Miguel Romero↗
From natural language to control signals: a conceptual framework for semantic channel finding in complex experimental infrastructure
Modern experimental platforms such as particle accelerators, fusion devices, telescopes, and industrial process control systems expose tens to hundreds of thousands of control and diagnostic channels, accumulated over decades of hardware evolution. Operators and AI systems alike depend on informal expert knowledge, inconsistent naming conventions, and scattered documentation to locate the signals required for monitoring, troubleshooting, and automated control, creating a persistent bottleneck for reliability, scalability, and emerging language-model-driven interfaces. We formalize semantic channel finding, the task of mapping natural-language intent to concrete control-system signals, as a general problem in complex experimental infrastructure, and introduce a four-paradigm conceptual framework to guide architecture selection based on facility-specific data regimes. The paradigms span (i) direct in-context lookup over small, curated channel dictionaries, (ii) constrained hierarchical navigation through structured trees, (iii) interactive agent exploration using iterative reasoning and tool-based database queries, and (iv) ontology-grounded semantic search that decouples channel meaning from facility-specific naming conventions. We demonstrate the practical feasibility of each paradigm through proof-of-concept implementations at four operational facilities spanning two orders of magnitude in scale: from compact free-electron lasers to large synchrotron light sources, operating under diverse control-system architectures ranging from clean hierarchical naming schemes to legacy environments with decades of heterogeneous conventions. Where evaluated against expert-curated operational queries, these instantiations achieve 90%–97% accuracy, validating the framework’s applicability across real-world deployment scenarios. To accelerate adoption across the broader scientific and industrial control-system community, we release open-source, plug-and-play implementations of all three interactive paradigms-direct lookup, hierarchical navigation, and middle-layer exploration-within the Osprey framework, together with tools for channel database generation, interactive testing, and minimal-configuration deployment. This work establishes semantic channel finding as a foundational capability for human-centric and agentic AI interfaces at large-scale facilities, providing both a systematic framework for architecture design and practical resources to enable adoption without building custom infrastructure from scratch.
channel finding↗