Computational Engineering
MUFASA: An Information Utility-Aware Preprocessing Framework for Reliable Model Reasoning in Computational Pathology
Rathinaraja Jeyaraj, Barathi Subramanian, Songmi Noh et al. (+7 more)
Reliable computational pathology depends on preprocessing methods that identify informative tissue regions while excluding artifacts and low-utility regions from whole-slide images (WSI). However, existing preprocessing pipelines often retain such regions or discard diagnostically relevant tissue, thereby limiting downstream model performance, reliability, and robustness across heterogeneous cohorts. Here, we systematically evaluate how these regions affect downstream AI model performance across multiple clinically relevant applications and introduce MUFASA, a generalizable, information utility-aware preprocessing framework for H&E-stained WSI that excludes artifacts and low-utility regions while preserving biologically meaningful tissue. MUFASA integrates slide-level artifact masking, stain-aware tile filtering, reconstruction-based utility stratification of tiles, and targeted recovery of tissue tiles that are over-filtered by earlier phases. Across tumor diagnosis, tumor subtyping, biomarker status prediction, and survival prognostication tasks in diverse cancer cohorts, MUFASA consistently improves downstream model performance relative to widely used preprocessing baselines. These gains are accompanied by reduced artifact-associated attribution in model heatmaps, indicating improved
alignment between retained tissue and model
attention. Our findings establish WSI preprocessing as a critical determinant of downstream model performance and validity, revealing that even accurate predictions can conceal important failure modes stemming from anatomically implausible
reasoning driven by retained artifact-containing and low information-utility tiles.
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All authors Rathinaraja Jeyaraj, Barathi Subramanian, Songmi Noh, Mitchell N. Peterson, Terry Guo, George A. Fisher, Nigam H. Shah, Curtis P. Langlotz, Thomas J. Montine, Jeanne Shen
Computational Engineering
Hidden relationships in a document-derived property graph: top-k chunk embeddings and inverse-distance weighting over a dynamically evolving ontology
Bilge Kaan Karamete and Hunter Casten
Large
language models extracting knowledge graphs from text capture only explicitly stated facts, often leaving semantically related entities disconnected across documents. We present an additive, engine-neutral second pass that discovers these latent ties without altering extracted facts. Each document is chunked and embedded once; top-k nearest- neighbor queries across existing chunks yield candidate node pairs via entity membership maps. Candidate pairs are scored using Shepard inverse-distance weighting with a rescaled chord distance metric, avoiding the threshold-collapsing flaw of affine cosine scoring behind a k-NN gate. Un-gated per-pair accumulators form a commutative monoid, ensuring the pipeline is strictly order-independent and scales incrementally without recomputing prior documents. Implemented across FalkorDB, Kinetica, ArangoDB, and Neo4j, our method shows that 768- and 240-dimensional
embeddings retain 92% and 72% edge fidelity against a 3072-D baseline while achieving a 25x faster top-k formulation.
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Computational Engineering
Lightweight Adaptation of EEG Foundation Models for Stroke Motor Imagery Decoding: Domain Shift and Subject-Level Robustness
Anh T. Nguyen, Zihua Sun and Michelle J. Johnson
Motor imagery (MI) electroencephalography (
EEG) decoding could support post-stroke rehabilitation, but models developed on healthy cohorts may not transfer reliably to pathological
EEG. We evaluated whether Low-Rank Adaptation (LoRA) can efficiently adapt three pretrained
EEG foundation models (i.e., LaBraM-base, REVE-base, and REVE-large) for binary left- versus right-hand MI decoding. Frozen-backbone head-only baselines and LoRA adaptation were evaluated using subject-wise five-fold cross-validation on the PhysioNet
EEG Motor Movement/Imagery
Dataset and a binary subset of the UET175
dataset comprising 30 stroke participants. On EEGMMIDB, LoRA increased accuracy to 0.822 for LaBraM-base and 0.957 for REVE-base. On UET175, all head-only models performed near chance. With LoRA, LaBraM-base remained near chance (0.499$\pm$0.009), whereas REVE-base reached 0.847$\pm$0.194 and outperformed REVE-large (0.806$\pm$0.178), indicating that increased model capacity alone did not improve stroke-domain adaptation. The strongest stroke configuration, REVE-base LoRA, was further evaluated using within-cohort leave-one-subject-out cross-validation (LOOCV), showing 0.952 mean accuracy, but subject-wise accuracy ranged from 0.586 to 1.000, revealing a small low-performing tail. Zero-shot transfer from EEGMMIDB to UET175 remained near chance (0.464$\pm$0.072). These findings show that healthy-
benchmark performance does not ensure transfer to stroke
EEG. Translation of
EEG foundation models to pseudo-online or real-time rehabilitation BCIs should therefore include target-domain adaptation and subject-level assessment of temporal informativeness, spatial sensitivity, and physiological discriminability.
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Computational Engineering · Cross-listed from math.NA
Solving the Incompressible Navier-Stokes Equations on Oriented Curved Surfaces Discretized by Point Clouds
Alejandra Foggia and Ivo F. Sbalzarini
We present a meshfree numerical solver for the incompressible Navier-Stokes equations on oriented curved surfaces that are represented by surface point clouds. On curved surfaces, numerical challenges pertaining to stiffness and pressure-velocity coupling are exacerbated. Moreover, vector calculus on curved surfaces differs from its Euclidean counterpart. The presented method operates on surface point clouds in an Eulerian frame of reference without requiring a computational grid or mesh. It achieves consistent approximation in space and time with high order of accuracy; we demonstrate up to order six. The incompressibility constraint is locally imposed as a weak artificial compressibility approximation, avoiding global
matrix inversion. We show that the method provides consistent and convergent approximations of surface vector fields and differential operators. We study the relationship between error, spatial resolution, and artificial Mach number and characterize the frequency spectrum of the artificial oscillations. We provide numerical solutions of the incompressible Navier-Stokes equations on symmetric surfaces, such as the sphere and
torus, and on parametric and non-parametric asymmetric surfaces. Since the proposed method works directly on unstructured surface point clouds, it provides a promising approach for simulations on image-derived geometries, such as in biological morphogenesis from microscopy
videos.
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Computational Engineering
Ordinal Gates, Cardinal Bets: Matching LLM Confidence to the Financial Decision Operator
Rayansh Singh and Sara Rezaeimanesh
LLM confidence scores are not independently deployable objects: their decision value depends on the downstream operator and exposure controller that consume them. Monotone recalibration cannot change a coverage-matched rank-based gate, whereas position sizing consumes score magnitude, so changing a confidence map can invalidate a scale fitted to the previous score distribution. We test this on FactSet news for Nasdaq-100 equities, fitting maps and scales on 2021 and evaluating nine open-weight LLMs out-of-sample on 2022–2023. Cross-applying raw and correctness maps with independently fitted scales shows that the two components are not portable alone: scale transfer reduces certainty-equivalent return (CER) in $8/9$ models and produces large risk-target errors. Matching each map with its fitted scale improves ensemble CER by $9.2$ percentage points per year under frozen-scale control ($p<0.001$), and the effect remains significant when the single largest-contributing model is excluded ($+5.5$pp/yr), so it is not driven by one case. Under an identical adaptive-
volatility controller, however, the incremental effect falls to $+1.6$pp/yr, with a significant controller interaction. Annual walk-forward effects are smaller, although map–scale interaction remains positive in every fold. Confidence transformations should therefore be evaluated jointly with the downstream controllers that consume them.
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Computational Engineering
Viable Pool Sizing for On-Chain FX Liquidity: Amplification, Capital, and Resilience
Ryan Fang, Ivan Bardziyan, Jessica Wang et al. (+1 more)
Financial institutions deploying on-chain FX liquidity face a joint design problem: how much capital to commit, and how to configure the pool, to remain both competitive on trading costs and profitable as a liquidity provider? The StableSwap mechanism (Egorov, 2020) interpolates between constant-product (CPMM) and constant-sum (CSMM)
market makers (Port and Tiruviluamala, 2022) via an amplification factor A, but neither extreme suits institutional FX: CPMM pools require excessive capital and generate high impermanent loss; CSMM pools are capital-efficient near the peg but drain rapidly under
adversarial flow. Using a Merton jump-
diffusion price process (Merton, 1976) and the loss-versus-rebalancing (LVR) framework (Milionis et al., 2022), we map the joint (A, TVL) space to identify configurations that satisfy all three institutional requirements: competitive slippage, positive return, and shock resilience. Minimum viable pool size scales approximately as TVL/Q = 1000/A; ROC at that minimum is thin (about 0.054% per horizon) and independent of A; low-A pools (A <= 10) suffer slippage exceeding 200 bps under a 10x shock, while high-A pools (A >= 500) suffer reserve drain up to 60%, establishing both a capital floor and a practical amplification ceiling.
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All authors Ryan Fang, Ivan Bardziyan, Jessica Wang, Mayank Anand
Computational Engineering
Finite Element Model Updating-based Load Rating of Bridges with Incomplete As-Built Information
Mehrdad S. Dizaji, Devin K. Harris, Mohamad Alipour et al. (+3 more)
Load rating is the engineering process of determining the safe load-carrying capacity of an existing bridge structure often through analysis of its load-bearing members and their cross sections. However, when structural drawings and details of the structure are missing or insufficient for such calculations, alternative solutions must be used to infer the capacity. This study proposes a rational and consistent engineering solution for capacity inference based on structural identification (St-Id). The proposed approach uses finite element model updating (FEMU) to estimate the unknown characteristics of structures for use in an analytical load rating, which requires the development of an initial model developed in ABAQUS that can be updated based on experimental test data. ABAQUS allowed for the development of an interface with MATLAB, which facilitated the integration of an automatic iterative parameter optimization
algorithm. The optimization
algorithm developed in this investigation incorporated the features of a genetic
algorithm (GA) and a gradient-based scheme to iterate on the unknown parameters. The proposed approach was evaluated on four in-service highway bridges including two concrete slab and two T-beam structures in varying deterioration condition states, which had sufficient plans available but were treated as having varying degrees of unknown details. The results illustrated that the finite element (FE) model updating approach generated load ratings that were within 0-17% of the target load ratings while alleviating the main challenges of the existing alternatives.
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All authors Mehrdad S. Dizaji, Devin K. Harris, Mohamad Alipour, Abdou Ndong, Osman Ozbulut, Abdollah Bagheri
Computational Engineering
Domain-Grounded Tool Orchestration for LLM-Guided Scientific Analysis
Jeff Lee, Sebastien Jourdain, Cory Quammen et al. (+2 more)
Scientific analysis workflows encode deep domain knowledge through sequences of tightly coupled operations where correctness depends on tool selection, execution order, and parameterization. A CFD engineer investigating flow separation must extract wall shear stress, identify zero-crossings in skin friction, and confirm with boundary-layer profiles: a chain that requires both domain expertise and proficiency with visualization tools. Current approaches to LLM-assisted scientific visualization generate scripts that encode this knowledge implicitly, and often incorrectly, producing code that executes but yields wrong results. We present an architecture that separates intent interpretation (LLM) from execution (deterministic domain tools) from explanation (LLM), connected by the Model Context Protocol (MCP) and grounded by domain ontologies that constrain planning to valid analysis chains. We instantiate the architecture in two domains on the same ParaView server infrastructure: computational fluid dynamics post-processing and topological data analysis via the
Topology ToolKit (TTK). Adding the second domain required only an ontology and tool wrappers around existing filters, with no change to the architecture, protocol, or deployment. By construction the design removes whole classes of failure that affect script generation (such as API
hallucination and missing pipeline stages) and narrows the strategic errors that remain. An ablation across both domains locates the ontology's empirical effect: it does not change which tools the planner selects, which is already reliable, but corrects how the model interprets results, raising interpretation accuracy from 0.41 to 0.91, and only when the relevant fact is retrieved in scoped rather than bulk form. ParaView's client-server model carries analysis to production-scale
datasets through a thin browser client.
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All authors Jeff Lee, Sebastien Jourdain, Cory Quammen, Patrick O'Leary, Berk Geveci
Computational Engineering
Sensitivity Hot Spot Penalization: A Robust Topology Optimization Framework against First-Order Worst-Case Perturbations
Junpeng Wang, Niels Aage and Ole Sigmund
Deterministic
topology optimization can efficiently generate high-performance structural designs, but it does not explicitly control localized fragility induced by manufacturing variations and
geometric uncertainties. Such fragility often appears as stress concentrations or hinge-like deformation mechanisms. Conventional robust
topology optimization can suppress these features, but typically requires multiple design realizations and substantially increased computational cost. Recent work by Sigmund et al. (2026) introduced sensitivity hot spot penalization (SHoSP), which augments the nominal objective by a smooth maximum of its sensitivities and suppresses localized fragile features at low additional cost while promoting more even stress distributions. This paper establishes a general connection between SHoSP and a first-order worst-case robust approximation under a material-mass perturbation budget using a Taylor expansion and H{"o}lder's duality. The original penalty weight is identified as a dimensionless norm-bounded perturbation budget relative to the area (2D) or volume (3D) of the design domain. This interpretation explains the suppression of sensitivity hot spots, hinge localization, and stress concentrations by limiting the maximum first-order degradation under budgeted perturbations. It is investigated for compliance minimization and compliant mechanism design. Robustness is assessed using a relaxed worst-case density perturbation and by comparing deterministic and SHoSP designs under equivalent perturbation budgets. Stress-related effects observed on structured meshes are cross-validated by stress-oriented
topology optimization and body-fitted finite element analyses. Extensions to porous infill optimization, multiple load cases, and large-scale 3D examples further demonstrate the applicability and superior scalability of the SHoSP framework.
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Computational Engineering
Redefining Stablecoins from Nominal to Real Value: A Maximum Likelihood Approach
Tomonori Kanno, Kensuke Ito, Yushi Yoshimura et al. (+1 more)
Stablecoins, typically pegged to fiat currencies, cannot achieve true stability because they inherit fluctuations in the underlying unit of account. To overcome this limitation, we introduce a stablecoin pegged to the Maximum Likelihood Value (MLV), a newly defined unit of account derived as the most probable configuration of latent real-value movements that explains observed nominal-value (price) changes. Grounded in inferential statistics and modern portfolio theory, MLV represents the most stable unit of account, as it enforces a zero real return on the minimum-variance portfolio. Empirical results confirm the operational viability of an MLV-pegged stablecoin: MLV can be computed in real time from 500 asset price series and improves annualized returns and Sharpe ratios while substantially reducing turnover in portfolio optimization.
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All authors Tomonori Kanno, Kensuke Ito, Yushi Yoshimura, Kyohei Shibano
Computational Engineering · Cross-listed from cs.AI
FaVOR: LLM-Based Agentic Framework for Factor Mining via Empirical Validation
Hyeonjin Kim, Minseok Kim, Seunghyeon Jung et al. (+3 more)
Traditional finance relies on experts to hand-craft factors through a principled process grounded in economic rationale. Recent LLM-based multi-
agent systems have automated this process, scaling factor mining far beyond manual effort. However, these automated approaches optimize directly for returns and rarely check whether a generated factor still expresses the economic hypothesis that motivated it. We identify this inconsistency between mathematical form and economic meaning as a structural failure mode of return-oriented automation. The resulting factors blur the line between real signals and spurious correlations and break down across regime shifts. We propose FaVOR (Factor Validation through Observable
Reasoning), an agentic framework that restructures factor mining around hypothesis-level evidence rather than return outcomes. In place of the standard hypothesis-to-formula leap, FaVOR enforces a three-stage consistency loop tying mathematical form to economic rationale throughout. (1) Decomposition splits a broad economic hypothesis into independent observable conditions. (2) Validation checks whether each factor reflects its intended condition. (3) Integration merges them into a composite whose structure remains interpretable. On the CSI 500 and S&P 500 in 2025, FaVOR outperforms existing baselines while remaining effective across regimes. FaVOR shows that hypothesis-grounded factor discovery produces signals that are interpretable by construction, regime-robust, and economically faithful. The code is available at https://github.com/damilab/FaVOR.
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All authors Hyeonjin Kim, Minseok Kim, Seunghyeon Jung, Sujin Pyo, Huisu Jang, Woojin Lee
Computational Engineering
The PUR-1 Cyber-Physical Digital Twin
Vasileios Theos, Jonah Lau, Konstantinos Gkouliaras et al. (+7 more)
Digital twin technologies have the potential to improve operational flexibility and responsiveness capabilities of nuclear systems. To provide decision support, cyber event characterization, state estimation, predictive control, and real-time dynamic processing of operational data, however, an efficient digital twin needs to integrate multiple models (data-driven as well as physics-based) with explainability while at the same time maintain two-way synchronization with the physical facility at a time constant less than its operational cycle. In this work, we present the Purdue University Reactor One Digital Twin (PUR-1 DT), a cyber-physical digital twin with a complete high-fidelity physics-based and AI-driven virtual model stack (neutronics, thermal-hydraulics, point kinetics) which provides closed-loop explainable diagnostics, forecasting, predictive control, and action recommendation back to the reactor via two-way communications and a cyber-physical testbed. We demonstrate real-time synchronized state estimation and short-term forecasting over a full reactor operational cycle and conduct a series of benchmarking experiments to validate accuracy and latency. Our results show good agreement with experimental results and lay the groundwork for further development and experimental demonstration of DT-enabled functionalities in real-world facilities.
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All authors Vasileios Theos, Jonah Lau, Konstantinos Gkouliaras, Zachery Dahm, Konstantinos Vasili, Noah Fillgrove, William Richards, True Miller, Brian Jowers, Stylianos Chatzidakis