arXiv subjects

Daniel O'Malley

Publications and source records attributed to Daniel O'Malley.

At least 19 recordsLinked to original sources

arXiv2026

In-context learning enables continental-scale subsurface temperature prediction from sparse local observations

Continental-scale knowledge of subsurface temperature is limited by the cost and sparsity of borehole measurements, but such information is essential for geothermal resource assessment and for understanding heat transport in the shallow crust. The thermal field reflects the interaction between lithology, crustal structure, radiogenic heat production, and advective fluid flow, sometimes producing sharp anomalies that are smoothed by conventional interpolation or difficult to capture with physical models. Here we introduce In-Context Earth, a transformer-based model that uses sparse local borehole observations as geological context to predict continuous temperature-at-depth fields with calibrated uncertainty. In the contiguous United States, the model achieves a mean absolute error of 4.7 {\deg}C, outperforming the physics-informed Stanford Thermal Model, a model based on AlphaEarth embeddings, the multimodal Transparent Earth model, and universal kriging, while resolving sharper thermal gradients in geothermal provinces. Its uncertainty estimates are well calibrated, with a Kolmogorov-Smirnov statistic of 2.5%. Without finetuning, the model adapts to Alberta, Australia, and the United Kingdom (UK) using only 20 local observations at inference time, maintaining high accuracy in geologically distinct test regions with a mean absolute error of 2.2 {\deg}C in Alberta, 6.2 {\deg}C in Australia, and 5.4 {\deg}C in the UK. Interpretability analyses show that the model learns internal representations of subsurface properties it never observes during training, including seismic velocities, geochemistry, and crustal structure, and uses these representations in physically consistent ways. More broadly, this work shows that in-context learning can use sparse borehole observations for continental-scale subsurface characterization, without requiring dense measurements or region-specific retraining.

cs.LG↗

arXiv2026

Physics-informed reservoir characterization from bulk and extreme pressure events with a differentiable simulator

Accurate characterization of subsurface heterogeneity is challenging but essential for applications such as reservoir pressure management, geothermal energy extraction and CO$_2$, H$_2$, and wastewater injection operations. This challenge becomes especially acute in extreme pressure events, which are rarely observed but can strongly affect operational risk. Traditional history matching and inversion techniques rely on expensive full-physics simulations, making it infeasible to handle uncertainty and extreme events at scale. Purely data-driven models often struggle to maintain physics consistency when dealing with sparse observations, complex geology, and extreme events. To overcome these limitations, we introduce a physics-informed machine learning method that embeds a differentiable subsurface flow simulator directly into neural network training. The network infers heterogeneous permeability fields from limited pressure observations, while training minimizes both permeability and pressure losses through the simulator, enforcing physical consistency. Because the simulator is used only during training, inference remains fast once the model is learned. In an initial test, the proposed method reduces the pressure inference error by half compared with a purely data-driven approach. We then extend the test over eight distinct data scenarios, and in every case, our method produces significantly lower pressure inference errors than the purely data-driven model. We also evaluate our method on extreme events, which represent high-consequence data in the tail of the sample distribution. Similar to the bulk distribution, the physics-informed model maintains higher pressure inference accuracy in the extreme event regimes. Overall, the proposed method enables rapid, physics-consistent subsurface inversion for real-time reservoir characterization and risk-aware decision-making.

cs.LG↗

arXiv2025

Benchmarking Large Language Models with Integer Sequence Generation Tasks

We present a novel benchmark designed to rigorously evaluate the capabilities of large language models (LLMs) in mathematical reasoning and algorithmic code synthesis tasks. The benchmark comprises integer sequence generation tasks sourced from the Online Encyclopedia of Integer Sequences (OEIS), testing LLMs' abilities to accurately and efficiently generate Python code to compute these sequences without using lookup tables. Our comprehensive evaluation includes leading models from OpenAI (including the specialized reasoning-focused o-series), Anthropic, Meta, and Google across a carefully selected set of 1000 OEIS sequences categorized as ``easy'' or ``hard.'' Half of these sequences are classical sequences from the early days of OEIS and half were recently added to avoid contamination with the models' training data. To prevent models from exploiting memorized sequence values, we introduce an automated cheating detection mechanism that flags usage of lookup tables, validated by comparison with human expert evaluations. Experimental results demonstrate that reasoning-specialized models (o3, o3-mini, o4-mini from OpenAI, and Gemini 2.5-pro from Google) achieve substantial improvements in accuracy over non-reasoning models, especially on more complex tasks. However, overall model performance on the hard sequences is poor, highlighting persistent challenges in algorithmic reasoning. Our benchmark provides important insights into the strengths and limitations of state-of-the-art LLMs, particularly emphasizing the necessity for further advancements to reliably solve complex mathematical reasoning tasks algorithmically.

cs.LG↗

arXiv2025

The Transparent Earth: A Multimodal Foundation Model for the Earth's Subsurface

We present the Transparent Earth, a transformer-based architecture for reconstructing subsurface properties from heterogeneous datasets that vary in sparsity, resolution, and modality, where each modality represents a distinct type of observation (e.g., stress angle, mantle temperature, tectonic plate type). The model incorporates positional encodings of observations together with modality encodings, derived from a text embedding model applied to a description of each modality. This design enables the model to scale to an arbitrary number of modalities, making it straightforward to add new ones not considered in the initial design. We currently include eight modalities spanning directional angles, categorical classes, and continuous properties such as temperature and thickness. These capabilities support in-context learning, enabling the model to generate predictions either with no inputs or with an arbitrary number of additional observations from any subset of modalities. On validation data, this reduces errors in predicting stress angle by more than a factor of three. The proposed architecture is scalable and demonstrates improved performance with increased parameters. Together, these advances make the Transparent Earth an initial foundation model for the Earth's subsurface that ultimately aims to predict any subsurface property anywhere on Earth.

cs.LG↗

arXiv2025

Differentiable multiphase flow model for physics-informed machine learning in reservoir pressure management

Accurate subsurface reservoir pressure control is extremely challenging due to geological heterogeneity and multiphase fluid-flow dynamics. Predicting behavior in this setting relies on high-fidelity physics-based simulations that are computationally expensive. Yet, the uncertain, heterogeneous properties that control these flows make it necessary to perform many of these expensive simulations, which is often prohibitive. To address these challenges, we introduce a physics-informed machine learning workflow that couples a fully differentiable multiphase flow simulator, which is implemented in the DPFEHM framework with a convolutional neural network (CNN). The CNN learns to predict fluid extraction rates from heterogeneous permeability fields to enforce pressure limits at critical reservoir locations. By incorporating transient multiphase flow physics into the training process, our method enables more practical and accurate predictions for realistic injection-extraction scenarios compare to previous works. To speed up training, we pretrain the model on single-phase, steady-state simulations and then fine-tune it on full multiphase scenarios, which dramatically reduces the computational cost. We demonstrate that high-accuracy training can be achieved with fewer than three thousand full-physics multiphase flow simulations -- compared to previous estimates requiring up to ten million. This drastic reduction in the number of simulations is achieved by leveraging transfer learning from much less expensive single-phase simulations.

cs.LG↗

arXiv2025

Block encoding the 3D heterogeneous Poisson equation with application to fracture flow

Quantum linear system (QLS) algorithms offer the potential to solve large-scale linear systems exponentially faster than classical methods. However, applying QLS algorithms to real-world problems remains challenging due to issues such as state preparation, data loading, and efficient information extraction. In this work, we study the feasibility of applying QLS algorithms to solve discretized three-dimensional heterogeneous Poisson equations, with specific examples relating to groundwater flow through geologic fracture networks. We explicitly construct a block encoding for the 3D heterogeneous Poisson matrix by leveraging the sparse local structure of the discretized operator. While classical solvers benefit from preconditioning, we show that block encoding the system matrix and preconditioner separately does not improve the effective condition number that dominates the QLS runtime. This differs from classical approaches where the preconditioner and the system matrix can often be implemented independently. Nevertheless, due to the structure of the problem in three dimensions, the quantum algorithm achieves a runtime of $O(N^{2/3} \ \text{polylog } N \cdot \log(1/\epsilon))$, outperforming the best classical methods (with runtimes of $O(N \log N \cdot \log(1/\epsilon))$) and offering exponential memory savings. These results highlight both the promise and limitations of QLS algorithms for practical scientific computing, and point to effective condition number reduction as a key barrier in achieving quantum advantages.

quant-ph↗

arXiv2025

A Foundation Model for Material Fracture Prediction

Accurately predicting when and how materials fail is critical to designing safe, reliable structures, mechanical systems, and engineered components that operate under stress. Yet, fracture behavior remains difficult to model across the diversity of materials, geometries, and loading conditions in real-world applications. While machine learning (ML) methods show promise, most models are trained on narrow datasets, lack robustness, and struggle to generalize. Meanwhile, physics-based simulators offer high-fidelity predictions but are fragmented across specialized methods and require substantial high-performance computing resources to explore the input space. To address these limitations, we present a data-driven foundation model for fracture prediction, a transformer-based architecture that operates across simulators, a wide range of materials (including plastic-bonded explosives, steel, aluminum, shale, and tungsten), and diverse loading conditions. The model supports both structured and unstructured meshes, combining them with large language model embeddings of textual input decks specifying material properties, boundary conditions, and solver settings. This multimodal input design enables flexible adaptation across simulation scenarios without changes to the model architecture. The trained model can be fine-tuned with minimal data on diverse downstream tasks, including time-to-failure estimation, modeling fracture evolution, and adapting to combined finite-discrete element method simulations. It also generalizes to unseen materials such as titanium and concrete, requiring as few as a single sample, dramatically reducing data needs compared to standard ML. Our results show that fracture prediction can be unified under a single model architecture, offering a scalable, extensible alternative to simulator-specific workflows.

cs.LG↗

arXiv2025

LLM-Assisted Translation of Legacy FORTRAN Codes to C++: A Cross-Platform Study

Large Language Models (LLMs) are increasingly being leveraged for generating and translating scientific computer codes by both domain-experts and non-domain experts. Fortran has served as one of the go to programming languages in legacy high-performance computing (HPC) for scientific discoveries. Despite growing adoption, LLM-based code translation of legacy code-bases has not been thoroughly assessed or quantified for its usability. Here, we studied the applicability of LLM-based translation of Fortran to C++ as a step towards building an agentic-workflow using open-weight LLMs on two different computational platforms. We statistically quantified the compilation accuracy of the translated C++ codes, measured the similarity of the LLM translated code to the human translated C++ code, and statistically quantified the output similarity of the Fortran to C++ translation.

cs.SE↗

arXiv2025

Model-Agnostic Knowledge Guided Correction for Improved Neural Surrogate Rollout

Modeling the evolution of physical systems is critical to many applications in science and engineering. As the evolution of these systems is governed by partial differential equations (PDEs), there are a number of computational simulations which resolve these systems with high accuracy. However, as these simulations incur high computational costs, they are infeasible to be employed for large-scale analysis. A popular alternative to simulators are neural network surrogates which are trained in a data-driven manner and are much more computationally efficient. However, these surrogate models suffer from high rollout error when used autoregressively, especially when confronted with training data paucity. Existing work proposes to improve surrogate rollout error by either including physical loss terms directly in the optimization of the model or incorporating computational simulators as `differentiable layers' in the neural network. Both of these approaches have their challenges, with physical loss functions suffering from slow convergence for stiff PDEs and simulator layers requiring gradients which are not always available, especially in legacy simulators. We propose the Hybrid PDE Predictor with Reinforcement Learning (HyPER) model: a model-agnostic, RL based, cost-aware model which combines a neural surrogate, RL decision model, and a physics simulator (with or without gradients) to reduce surrogate rollout error significantly. In addition to reducing in-distribution rollout error by 47%-78%, HyPER learns an intelligent policy that is adaptable to changing physical conditions and resistant to noise corruption. Code available at https://github.com/scailab/HyPER.

cs.LG↗

arXiv2024

Patchfinder: Leveraging Visual Language Models for Accurate Information Retrieval using Model Uncertainty

For decades, corporations and governments have relied on scanned documents to record vast amounts of information. However, extracting this information is a slow and tedious process due to the sheer volume and complexity of these records. The rise of Vision Language Models (VLMs) presents a way to efficiently and accurately extract the information out of these documents. The current automated workflow often requires a two-step approach involving the extraction of information using optical character recognition software and subsequent usage of large language models for processing this information. Unfortunately, these methods encounter significant challenges when dealing with noisy scanned documents, often requiring computationally expensive language models to handle high information density effectively. In this study, we propose PatchFinder, an algorithm that builds upon VLMs to improve information extraction. First, we devise a confidence-based score, called Patch Confidence, based on the Maximum Softmax Probability of the VLMs' output to measure the model's confidence in its predictions. Using this metric, PatchFinder determines a suitable patch size, partitions the input document into overlapping patches, and generates confidence-based predictions for the target information. Our experimental results show that PatchFinder, leveraging Phi-3v, a 4.2-billion-parameter VLM, achieves an accuracy of 94% on our dataset of 190 noisy scanned documents, outperforming ChatGPT-4o by 18.5 percentage points.

cs.CV↗

arXiv2024

Developing a Foundation Model for Predicting Material Failure

Understanding material failure is critical for designing stronger and lighter structures by identifying weaknesses that could be mitigated. Existing full-physics numerical simulation techniques involve trade-offs between speed, accuracy, and the ability to handle complex features like varying boundary conditions, grid types, resolution, and physical models. We present the first foundation model specifically designed for predicting material failure, leveraging large-scale datasets and a high parameter count (up to 3B) to significantly improve the accuracy of failure predictions. In addition, a large language model provides rich context embeddings, enabling our model to make predictions across a diverse range of conditions. Unlike traditional machine learning models, which are often tailored to specific systems or limited to narrow simulation conditions, our foundation model is designed to generalize across different materials and simulators. This flexibility enables the model to handle a range of material properties and conditions, providing accurate predictions without the need for retraining or adjustments for each specific case. Our model is capable of accommodating diverse input formats, such as images and varying simulation conditions, and producing a range of outputs, from simulation results to effective properties. It supports both Cartesian and unstructured grids, with design choices that allow for seamless updates and extensions as new data and requirements emerge. Our results show that increasing the scale of the model leads to significant performance gains (loss scales as $N^{-1.6}$, compared to language models which often scale as $N^{-0.5}$).

physics.geo-ph↗

arXiv2024

Online learning of quadratic manifolds from streaming data for nonlinear dimensionality reduction and nonlinear model reduction

This work introduces an online greedy method for constructing quadratic manifolds from streaming data, designed to enable in-situ analysis of numerical simulation data on the Petabyte scale. Unlike traditional batch methods, which require all data to be available upfront and take multiple passes over the data, the proposed online greedy method incrementally updates quadratic manifolds in one pass as data points are received, eliminating the need for expensive disk input/output operations as well as storing and loading data points once they have been processed. A range of numerical examples demonstrate that the online greedy method learns accurate quadratic manifold embeddings while being capable of processing data that far exceed common disk input/output capabilities and volumes as well as main-memory sizes.

math.NA↗

arXiv2024

Enhancing Code Translation in Language Models with Few-Shot Learning via Retrieval-Augmented Generation

The advent of large language models (LLMs) has significantly advanced the field of code translation, enabling automated translation between programming languages. However, these models often struggle with complex translation tasks due to inadequate contextual understanding. This paper introduces a novel approach that enhances code translation through Few-Shot Learning, augmented with retrieval-based techniques. By leveraging a repository of existing code translations, we dynamically retrieve the most relevant examples to guide the model in translating new code segments. Our method, based on Retrieval-Augmented Generation (RAG), substantially improves translation quality by providing contextual examples from which the model can learn in real-time. We selected RAG over traditional fine-tuning methods due to its ability to utilize existing codebases or a locally stored corpus of code, which allows for dynamic adaptation to diverse translation tasks without extensive retraining. Extensive experiments on diverse datasets with open LLM models such as Starcoder, Llama3-70B Instruct, CodeLlama-34B Instruct, Granite-34B Code Instruct, and Mixtral-8x22B, as well as commercial LLM models like GPT-3.5 Turbo and GPT-4o, demonstrate our approach's superiority over traditional zero-shot methods, especially in translating between Fortran and CPP. We also explored varying numbers of shots i.e. examples provided during inference, specifically 1, 2, and 3 shots and different embedding models for RAG, including Nomic-Embed, Starencoder, and CodeBERT, to assess the robustness and effectiveness of our approach.

cs.AI↗

arXiv2024

Travel time and energy dissipation minima in heterogeneous subsurface flows

We establish a number of results concerning conditions for minimum energy dissipation and advective travel time in porous and fractured media. First, we establish a pair of converse results concerning fluid motion along a streamline between two points of fixed head: the minimal advective time is achieved under conditions of constant energy dissipation, and minimal energy dissipation is achieved under conditions of constant velocity along the streamline (implying homogeneous conductivity in the vicinity of the streamline). We also show directly by means of variational methods that minimum advection time along a streamline with a given average conductivity is achieved when the conductivity is constant. Finally, we turn our attention to minimum advection time and energy dissipation in parallel and sequential fracture systems governed by the cubic law: for which fracture cross-section and conductivity are intimately linked. We show that, as in porous domains, flow partitioning between different pathways always acts to minimize system energy dissipation. Finally, we consider minimum advection time as a function of aperture distribution in a sequence of fracture segments. We show that, for a fixed average aperture, a uniform-aperture system displays the shortest advection time. However, we also show that any sufficiently small small perturbations in aperture away from uniformity always act to reduce advection time.

physics.flu-dyn↗

arXiv2024

Hierarchical Multigrid Ansatz for Variational Quantum Algorithms

Quantum computing is an emerging topic in engineering that promises to enhance supercomputing using fundamental physics. In the near term, the best candidate algorithms for achieving this advantage are variational quantum algorithms (VQAs). We design and numerically evaluate a novel ansatz for VQAs, focusing in particular on the variational quantum eigensolver (VQE). As our ansatz is inspired by classical multigrid hierarchy methods, we call it "multigrid" ansatz. The multigrid ansatz creates a parameterized quantum circuit for a quantum problem on $n$ qubits by successively building and optimizing circuits for smaller qubit counts $j < n$, reusing optimized parameter values as initial solutions to next level hierarchy at $j+1$. We show through numerical simulation that the multigrid ansatz outperforms the standard hardware-efficient ansatz in terms of solution quality for the Laplacian eigensolver as well as for a large class of combinatorial optimization problems with specific examples for MaxCut and Maximum $k$-Satisfiability. Our studies establish the multi-grid ansatz as a viable candidate for many VQAs and in particular present a promising alternative to the QAOA approach for combinatorial optimization problems.

quant-ph↗

arXiv2024

A near-term quantum algorithm for solving linear systems of equations based on the Woodbury identity

Quantum algorithms for solving linear systems of equations have generated excitement because of the potential speed-ups involved and the importance of solving linear equations in many applications. However, applying these algorithms can be challenging. The Harrow-Hassidim-Lloyd algorithm and improvements thereof require complex subroutines suitable for fault-tolerant hardware such as Hamiltonian simulation, making it ill-suited to current hardware. Variational algorithms, on the other hand, involve expensive optimization loops, which can be prone to barren plateaus and local optima. We describe a quantum algorithm for solving linear systems of equations that avoids these problems. Our algorithm is based on the Woodbury identity, which analytically describes the inverse of a matrix that is a low-rank modification of another (easily-invertible) matrix. This approach only utilizes basic quantum subroutines like the Hadamard test or the swap test, so it is well-suited to current hardware. There is no optimization loop, so barren plateaus and local optima do not present a problem. The low-rank aspect of the identity enables us to efficiently transfer information to and from the quantum computer. This approach can produce accurate results on current hardware. As evidence of this, we estimate an inner product involving the solution of a system of more than 16 million equations with 2% error using IBM's Auckland quantum computer. To our knowledge, no system of equations this large has previously been solved to this level of accuracy on a quantum computer.

quant-ph↗

arXiv2024

Information Extraction from Historical Well Records Using A Large Language Model

To reduce environmental risks and impacts from orphaned wells (abandoned oil and gas wells), it is essential to first locate and then plug these wells. Although some historical documents are available, they are often unstructured, not cleaned, and outdated. Additionally, they vary widely by state and type. Manual reading and digitizing this information from historical documents are not feasible, given the high number of wells. Here, we propose a new computational approach for rapidly and cost-effectively locating these wells. Specifically, we leverage the advanced capabilities of large language models (LLMs) to extract vital information including well location and depth from historical records of orphaned wells. In this paper, we present an information extraction workflow based on open-source Llama 2 models and test them on a dataset of 160 well documents. Our results show that the developed workflow achieves excellent accuracy in extracting location and depth from clean, PDF-based reports, with a 100% accuracy rate. However, it struggles with unstructured image-based well records, where accuracy drops to 70%. The workflow provides significant benefits over manual human digitization, including reduced labor and increased automation. In general, more detailed prompting leads to improved information extraction, and those LLMs with more parameters typically perform better. We provided a detailed discussion of the current challenges and the corresponding opportunities/approaches to address them. Additionally, a vast amount of geoscientific information is locked up in old documents, and this work demonstrates that recent breakthroughs in LLMs enable us to unlock this information more broadly.

cs.IR↗

arXiv2023

Learning the Factors Controlling Mineralization for Geologic Carbon Sequestration

We perform a set of flow and reactive transport simulations within three-dimensional fracture networks to learn the factors controlling mineral reactions. CO$_2$ mineralization requires CO$_2$-laden water, dissolution of a mineral that then leads to precipitation of a CO$_2$-bearing mineral. Our discrete fracture networks (DFN) are partially filled with quartz that gradually dissolves until it reaches a quasi-steady state. At the end of the simulation, we measure the quartz remaining in each fracture within the domain. We observe that a small backbone of fracture exists, where the quartz is fully dissolved which leads to increased flow and transport. However, depending on the DFN topology and the rate of dissolution, we observe a large variability of these changes, which indicates an interplay between the fracture network structure and the impact of geochemical dissolution. In this work, we developed a machine learning framework to extract the important features that support mineralization in the form of dissolution. In addition, we use structural and topological features of the fracture network to predict the remaining quartz volume in quasi-steady state conditions. As a first step to characterizing carbon mineralization, we study dissolution with this framework. We studied a variety of reaction and fracture parameters and their impact on the dissolution of quartz in fracture networks. We found that the dissolution reaction rate constant of quartz and the distance to the flowing backbone in the fracture network are the two most important features that control the amount of quartz left in the system. For the first time, we use a combination of a finite-volume reservoir model and graph-based approach to study reactive transport in a complex fracture network to determine the key features that control dissolution.

cs.CE↗