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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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9 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

CHEMREASONER: Heuristic Search over a Large Language Model’s Knowledge Space using Quantum-Chemical Feedback

The discovery of new catalysts is essential for the design of new and more efficient chemical processes in order to transition to a sustainable future. We introduce an AI-guided computational screening framework unifying linguistic reasoning with quantum-chemistry based feedback from 3D atomistic representations. Our approach formulates catalyst discovery as an uncertain environment where an agent actively searches for highly effective catalysts via the iterative combination of large language model (LLM)-derived hypotheses and atomistic graph neural network (GNN)-derived feedback. Identified catalysts in intermediate search steps undergo structural evaluation based on spatial orientation, reaction pathways, and stability. Scoring functions based on adsorption energies and barriers steer the exploration in the LLM's knowledge space toward energetically favorable, high-efficiency catalysts. We introduce planning methods that automatically guide the exploration without human input, providing competitive performance against expert-enumerated chemical descriptor-based implementations. By integrating language-guided reasoning with computational chemistry feedback, our work pioneers AI-accelerated, trustworthy catalyst discovery.

artificial intelligence↗
DOE OSTI2024

The Influence of the Number of Tree Searches on Maximum Likelihood Inference in Phylogenomics

Maximum likelihood (ML) phylogenetic inference is widely used in phylogenomics. As heuristic searches most likely find suboptimal trees, it is recommended to conduct multiple (e.g., 10) tree searches in phylogenetic analyses. However, beyond its positive role, how and to what extent multiple tree searches aid ML phylogenetic inference remains poorly explored. Here, we found that a random starting tree was not as effective as the BioNJ and parsimony starting trees in inferring the ML gene tree and that RAxML-NG and PhyML were less sensitive to different starting trees than IQ-TREE. We then examined the effect of the number of tree searches on ML tree inference with IQ-TREE and RAxML-NG, by running 100 tree searches on 19,414 gene alignments from 15 animal, plant, and fungal phylogenomic datasets. We found that the number of tree searches substantially impacted the recovery of the best-of-100 ML gene tree topology among 100 searches for a given ML program. In addition, all of the concatenation-based trees were topologically identical if the number of tree searches was ≥10. Quartet-based ASTRAL trees inferred from 1 to 80 tree searches differed topologically from those inferred from 100 tree searches for 6/15 phylogenomic datasets. Lastly, our simulations showed that gene alignments with lower difficulty scores had a higher chance of finding the best-of-100 gene tree topology and were more likely to yield the correct trees.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Clifford Circuit-Based Heuristic Optimization of Fermion-To-Qubit Mappings

Simulation of interacting Fermionic Hamiltonians is one of the most promising applications of quantum computers. However, the feasibility of analyzing Fermionic systems with a quantum computer hinges on the efficiency of Fermion-to-qubit mappings that encode nonlocal Fermionic degrees of freedom in local qubit degrees of freedom. While recent studies have highlighted the importance of designing Fermion-to-qubit mappings that are tailored to specific problem Hamiltonians, the methods proposed so far either are restricted to a narrow class of mappings or they use computationally expensive and unscalable brute-force search algorithms. Here, in this work, we address this challenge by designing a heuristic numerical optimization framework for Fermion-to-qubit mappings. To this end, we first translate the Fermion-to-qubit mapping problem to a Clifford circuit optimization problem and then use simulated annealing to optimize the average Pauli weight of the problem Hamiltonian. For all Fermionic Hamiltonians we have considered, the numerically optimized mappings outperform their conventional counterparts, including ternary-tree-based mappings that are known to be optimal for single creation and annihilation operators. We find that our optimized mappings yield between 15% and 40% improvements on the average Pauli weight when the simulation Hamiltonian has an intermediate level of complexity. Most remarkably, the optimized mappings improve the average Pauli weight for 6 × 6 nearest-neighbor hopping and Hubbard models by more than 40% and 20%, respectively. Surprisingly, we also find specific interaction Hamiltonians for which the optimized mapping outperforms any ternary-tree-based mapping. Our results establish heuristic numerical optimization as an effective method for obtaining mappings tailored for specific Fermionic Hamiltonian.

Hamiltonians↗
DOE OSTI2025

Bigpicc: a graph-based approach to identifying carcinogenic gene combinations from mutation data

Abstract Genome data from cancer patients represents relationships between the presence of a gene mutation and cancer occurrence in a patient. Different types of cancer in human are thought to be caused by combinations of two to nine gene mutations. Identifying these combinations through traditional exhaustive search requires the amount of computation that scales exponentially with the combination size and in most cases is intractable even for cutting-edge supercomputers. We propose a parameter-free heuristic approach that leverages the intrinsic topology of gene-patient mutations to identify carcinogenic combinations. The biological relevance of the identified combinations is measured by using them to predict the presence of tumor in previously unseen samples. The resulting classifiers for 16 cancer types perform on par with exhaustive search results, and score the average of 80.1% sensitivity and 91.6% specificity for the best choice of hit range per cancer type. Our approach is able to find higher-hit carcinogenic combinations targeting which would take years of computations using exhaustive search.

Biochemistry & Molecular Biology↗
DOE OSTI2026

Hierarchical Multi-agent Large Language Model Reasoning for Autonomous Heterogeneous Catalyst Discovery

Artificial intelligence is reshaping scientific exploration, but most methods automate procedural tasks without engaging in scientific reasoning, limiting autonomy in discovery. We demonstrate that hierarchical agentic large language model reasoning can efficiently drive simulation and scientific exploration. Across two chemical applications, CO adsorption on Cu surface transition metal adatoms and on M–N–C catalysts, reasoning-guided exploration reduces required atomistic simulations by up to 90% relative to heuristic or random selection. Comparisons across single-agent, multi-agent, and stochastic baselines show that hierarchical strategies yield more coherent and information-efficient search trajectories. Reasoning traces reveal chemically grounded decisions that cannot be explained by semantic bias or stochastic sampling. We realize these agentic reasoning strategies in Materials Agents for Simulation and Theory in Electronic-structure Reasoning (MASTER), a multimodal system that translates natural language into density functional theory workflows. Altogether, multi-agent collaboration accelerates heterogeneous catalyst discovery and marks a step toward more autonomous, reasoning-guided scientific exploration.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2025

Extending High-Level Synthesis with AI/ML Methods

Artificial Intelligence (AI) and Machine Learning (ML) methods provide significant opportunities of improving quality of results when performing high-level synthesis (HLS). For example, they can be used to model and predict metrics of the final design (e.g., area, considering aspects such as interconnect overhead for different device technologies), facilitating exploration when searching for the best design trade-offs. They can also enable identifying hidden correlations across the various phases of the synthesis and the various optimizations performed, identifying the most effective pipelines. Finally, in more general terms, bio-inspired heuristic algorithms can improve the design space exploration for the synthesis process in terms of time and quality of the result. This paper discusses opportunities and challenges to augment HLS with AI/ML using as example flow the SODA Synthesizer, an open-source hardware generation toolchain which includes SODA-OPT, a hardware/software partitioning and pre-optimization tool developed with the MLIR framework, and PandA-Bambu, a state-of-the art HLS tool. SODA interfaces with OpenROAD to provide a complete end-to-end toolchain.

artificial intelligence↗
DOE OSTI2024

Tensor decompositions for count data that leverage stochastic and deterministic optimization

There is growing interest to extend low-rank matrix decompositions to multi-way arrays, or tensors. One fundamental low-rank tensor decomposition is the canonical polyadic decomposition (CPD). The challenge of fitting a low-rank, nonnegative CPD model to Poisson-distributed count data is of particular interest. Several popular algorithms use local search methods to approximate the maximum likelihood estimator (MLE) of the Poisson CPD model. Here, this work presents two new algorithms that extend state-of-the-art local methods for Poisson CPD. Hybrid GCP-CPAPR combines Generalized Canonical Decomposition (GCP) with stochastic optimization and CP Alternating Poisson Regression (CPAPR), a deterministic algorithm, to increase the probability of converging to the MLE over either method used alone. Restarted CPAPR with SVDrop uses a heuristic based on the singular values of the CPD model unfoldings to identify convergence toward optimizers that are not the MLE and restarts within the feasible domain of the optimization problem, thus reducing overall computational cost when using a multi-start strategy. We provide empirical evidence that indicates our approaches outperform existing methods with respect to converging to the Poisson CPD MLE.

CPAPR↗
DOE OSTI2025

DeepHyper: A Python Package for Massively Parallel Hyperparameter Optimization in Machine Learning

Machine learning models are increasingly applied across scientific disciplines, yet their effectiveness often hinges on heuristic decisions—such as data transformations, training strategies, and model architectures—that are not learned by the models themselves. Automating the selection of these heuristics and analyzing their sensitivity is crucial for building robust and efficient learning workflows. DeepHyper addresses this challenge by democratizing hyperparameter optimization, providing accessible tools to streamline and enhance machine learning workflows from a laptop to the largest supercomputer in the world. Building on top of hyperparameter optimization, it unlocks new capabilities around ensembles of models for improved accuracy and uncertainty quantification. All of these organized around efficient parallel computing.

ensemble↗