Research in computational engineering spans a methodological arc from physics-informed surrogate modeling to agent-driven discovery, unified by the problem of managing computational expense and uncertainty under real operational constraints. Surrogate acceleration dominates: neural topology optimization via Kolmogorov-Arnold networks, Fourier neural operators with sensitivity-consistent gradients, and differentiable hybrid models for transport processes all replace or augment expensive finite-element and finite-volume solvers, trading fidelity for speed while preserving differentiability for gradient-based design. Uncertainty quantification and calibration emerge as critical, not optional, probabilistic virtual sensing under distribution shift, Bayesian neural networks for additive manufacturing, and sensitivity analysis fusing physics models with experimental data all treat model discrepancy and aleatory variability as integral to optimization, not afterthoughts. Multi-agent and human-in-the-loop workflows increasingly coordinate discovery: LLM agents with physics constraints audit theory-to-code pipelines for soil mechanics, multi-agent organizations navigate long-horizon technological forecasting, and CAE simulation harnesses show that domain knowledge input matters more than architectural complexity when repair budget is fixed. Partitioned co-simulation and non-intrusive boundary methods preserve modularity and black-box solver compatibility, reflecting tension between mathematical elegance and practical software reuse. Across domains, ship vibration, protein design, powder diffraction, stock prediction, 3D concrete printing, the pattern is consistent: geometry and physics structure the representation, neural components learn what hand-derived constitutive laws cannot capture, and validation occurs not against benchmarks alone but against controlled experimental or historical data under realistic operational drift.
Cole Brennan
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Accurate forecasting models are usually large, expensive to update online, and fixed in architecture once trained. We apply ONE-NAS, an online neuroevolutionary architecture search that evolves a population of small recurrent networks as each window of data arrives, to daily cross-sectional stock return prediction, and pilot it on a host and endpoint pipeline: the host runs the search and ships each generation's champion genomes over TCP/IP to a Raspberry Pi 4B, which predicts online. On the Pi a single champion predicts a 50-stock window in 24.6~ms and the ensemble of 40 island champions in 556~ms, far inside the daily decision cycle. On four panels of US mid-cap equities over 2022--2024, reading the population as a rank-mean ensemble of island champions returns $+27.5\%$ net of realised transaction costs, against $+11.3$ to $+14.8\%$ for online LSTM, online GRU and monthly-retrained LSTM baselines and $+4.5\%$ for the single best genome used in prior ONE-NAS work.
Assistants grounded in a small, frequently edited knowledge base can retrieve through tool calls to a live data interface or through vector retrieval-augmented generation (RAG). We compare the two on KyGround, a benchmark of 198 questions drawn from the published records of a Greek--English agricultural platform on Kythera, Greece, with answers verified automatically against the records and each question posed in up to nine forms, including Greek without accents, in capitals and in three Latin-script (Greeklish) schemes. With Claude Haiku 4.5 as router and answer model, a reconstruction of the platform's tool agent answered 71.6\% of canonical Greek questions correctly and vector RAG 95.3\% (difference $-23.6$ percentage points, 95\% CI $-33.1$ to $-15.1$). Letting the router write the vector query changed nothing, and placing the whole knowledge base of about 26,000 tokens in the prompt reached 99.3\%. The tool agent's losses arose in retrieval. Its literal searches returned nothing when the router's arguments did not occur verbatim in a record, for example when it transliterated Greek into Latin script or combined words that occur in a record but not as one phrase, and the agent then abstained. Unaccented and capitalised questions cost the tool agent about 20 points and vector RAG at most 2; accent-insensitive search removed this loss, and matching stemmed tokens raised the tool agent to 83.8\% on canonical Greek. Greeklish cost both designs about 21 to 32 points. Tool interfaces for community knowledge bases need search that tolerates how users type.
Predicting metal-organic framework (MOF) structures from given building blocks requires recovering their positions and orientations in a periodic crystal. The spatial effects of rotation errors are geometry-dependent and anisotropic. The same angular error can produce different atomic displacements depending on block size, shape, and rotation axis. Angular error alone, without reference to the specific block geometry, therefore cannot fully describe the spatial consequences of a pose error. We introduce AnchorPose, a meso-grained pose generation framework that incorporates this geometric dependence into its generative representation. It represents each block through a small set of representative atoms, combines their local geometry with the current spatial state, and generates their coordinates with Bayesian Flow Networks. Known atom correspondences enable rigid alignment to recover complete building-block poses and return geometrically consistent points to the generation process. This design connects point-level spatial prediction with block-level structural constraints. Geometry participates in the pose state and its prediction, while rigid reconstruction preserves intra-block structure without treating all atomic coordinates as assembly variables. On the MOF benchmark, AnchorPose improves single-candidate match rates over the compared block-level and all-atom baselines.
Recovering complete phase sets from powder X-ray diffraction (PXRD) is challenging when weak-phase peaks overlap stronger signals. A natural strategy is to identify phases iteratively, removing the contribution of each identified phase from the observed pattern before predicting the next. However, even after a phase is correctly identified, misestimating its contribution can distort the residual and cause subsequent errors. We introduce PhaseMatcher, an autoregressive framework for complete phase-set identification with physics-guided spectral decomposition. After each phase prediction, PhaseMatcher re-estimates the contributions of all selected phases and the residual from the original observation and all selected reference patterns, accounting for physically plausible variation between reference patterns and the corresponding phase contributions in the observation. The resulting residual guides subsequent phase identification, while a separate stopping module determines when the phase set is complete. On synthetic mixtures and controlled mixtures constructed from measured single-phase patterns, PhaseMatcher improves complete-set identification over the evaluated baselines. On PhaseMix-135K, it also estimates contributions and residuals more accurately than scalar subtraction.
The central challenge in de novo protein design is generating plausible, mutually compatible structures and sequences, such that each designed sequence folds into its intended structure and the structure accommodates that sequence. Compared to typical two-stage design methods, which decouple the modeling of the interdependent modalities, co-design models improve the cross-modal consistency by jointly generating sequences and structures. However, naively generating sequences and structures simultaneously does not ensure their consistency. To address this challenge, we propose CODesign framework. We improve data consistency by generating approximately 105,000 consistency-distilled dimers. We further promote consistency through a multimodal joint flow model that captures the joint distribution of sequences, backbone structures, and local atomic configurations, together with a consistency-aware joint resampling strategy that iteratively refines sequences and side chains. Experiments show that CODesign achieves state-of-the-art performance with the highest in silico success rates on both protein- and ligand-target binder design. Ablation studies also demonstrate our distilled dataset increases performance by 70.9%, which can be further improved by our proposed resampling mechanism with negligible additional computational cost. Code, model weights and the new dataset will be completely open-source.
Multi-agent LLM systems are increasingly structured like organizations, with roles, critics and shared memory, yet they are evaluated on tasks that last minutes. We ask how such an organization behaves when the ground it stands on keeps moving. Frontier Autolab is a long-horizon testbed in which one simulated firm, voiced by sixteen role personas and a dedicated Red Team, must re-found itself in nine technology eras from 1990 to 2040. Each era is temporally gated: the firm decides from a dated briefing, a historian-judge then reveals what happened and scores the decision on a five-dimension rubric, and lessons enter a persistent Playbook. Six eras are scored against history, one against the live market and two are open forecasts. Across four trajectories (36 era decisions, 180 subscores) we find a consistent foresight-commitment gap: in all 24 historically scored eras the judge rated the firm's recognition of the coming shift above its choice of where to build (mean gap 1.9 points on a 10-point scale), because boards chose the layer their existing assets could reach. Organizational design shaped long-run character. A Red Team armed with numeric kill gates produced fifty years of gated pilots and no product, and the rubric rated this firm highest; firms whose memory stored market-structure lessons pivoted every era, while a firm whose memory stored only validation procedure kept one method throughout. We also show why such results are hard to trust. Scores rise across eras in every run while the judge's own hindsight subscore falls (within-run r = -0.58), so apparent learning is confounded with recall of history, and we trace further distortions to self-judging, briefing selection and score aggregation. We release all records and an API harness, and specify fictional and post-cutoff eras that would turn the testbed into a benchmark.
Ship structural vibrations contribute to noise, fatigue, and equipment damage, while dynamic-compliance topology optimization can produce pathological designs near resonance. This study extends neural-reparameterized topology optimization using a convolutional Kolmogorov-Arnold network (KATO) to forced-vibration design with active input power (AIP) as the objective. Applications include a 100 Hz engine-supporting deck panel and an 18 Hz thruster foundation frame. Helmholtz PDE filtering and Heaviside projection control feature sizes and manufacturing tolerance. Across both deck families, all eight optimized layouts reduce AIP relative to size-optimized references and, after finite-depth extrusion, also achieve lower static compliance. For unrestricted, manufacturing-aware, and stress-aware frame variants, KATO matches GCMMA in AIP within 0.5 dB while yielding 22-36x lower static compliance after matched-volume binary re-analysis. In a near-resonant 300 Hz case, both methods reduce initial AIP by more than 32 dB; KATO maintains a connected design, achieves 59x lower binary static compliance, and reduces maximum AIP over 1-500 Hz by 2.7 dB. KATO runs 6.4-10.4x faster than GCMMA for the implemented stress-aware formulations. The results demonstrate neural AIP-driven topology optimization as an efficient approach for designing connected, feature-size-controlled ship structures with improved forced-vibration performance.
Nonlinear contacts and friction strongly influence the vibration response of assembled structures, but their accurate numerical treatment is computationally demanding. The harmonic balance method is widely used to compute periodic steady-state responses, yet the required alternating frequency-time scheme becomes costly for nonsmooth and hysteretic nonlinearities and must be repeated throughout the nonlinear solution process. Here we show that this procedure can be replaced by neural networks that directly map displacement Fourier coefficients to nonlinear force coefficients and provide the corresponding Jacobian through automatic differentiation. The surrounding solver and continuation algorithms remain unchanged for the computation of frequency response curves. The neural networks exclusively learn individual nonlinear elements rather than complete system responses. Physics-based nondimensionalization and phase normalization facilitate the learning process and enable a single trained network to cover a wide range of parameter combinations. Building on the cubic spring, unilateral spring, and Jenkins elements considered here, the approach points toward a reusable library of nonlinear-element surrogates that can be combined in arbitrary number and location within a mechanical system. By bypassing the iterative force evaluation in time domain, the method offers favorable computational scaling for high-resolution analyses and systems with many nonlinear elements.
Topology optimization (TO) remains computationally intensive due to repeated finite element analysis (FEA) evaluations required at each iteration. While neural network-based surrogates offer potential acceleration, existing approaches often suffer from gradient inconsistency between predicted objectives and sensitivities, leading to optimization instability. This work presents KATOsuper, an objective-agnostic framework that couples neural-reparameterized topology optimization with a Sensitivity-Consistent Fourier Neural Operator (SC-FNO). The framework employs the forward_split architecture, which derives deployed sensitivities via automatic differentiation through the predicted objective field and thereby preserves consistency between the predicted objective and the gradient used for optimization. The case studies include three 2D benchmark problems and three 3D structures considering compliance or stress minimization. A physics-informed multi-channel input encoding with Fourier position embedding enables resolution-invariant learning, supporting zero-shot extrapolation beyond the training resolution, with useful performance at moderate scaling factors and topology-preserving exploration at up to 64x without retraining. The framework extends to 3D through KATO3D, featuring novel KANConv3D blocks with learnable B-spline activations. KATOsuper demonstrates 15--110x deployment-time speedup over MATLAB baselines while maintaining competitive optimality, with the clearest gains observed in complex 3D and stress-optimization cases. The insight that sensitivity direction matters more than magnitude enables robust optimization even with approximate physics evaluation, extensible to other differentiable physics-driven design objectives.
Engineering predictions require physical mechanisms to be translated consistently into equations, discretization, code, and validation, yet errors can propagate despite local checks. Artificial-intelligence (AI) agents automate scientific tasks, but coordinating and independently auditing the theory-to-solver process under physical constraints and human oversight remains unresolved. We introduce a human-in-the-loop, physics-constrained multi-agent workflow where human experts define admissible physics and modeling boundaries, while agents retrieve evidence, derive equations, implement solvers, and audit the theory-to-code chain. Applied to soil-plug evolution during suction-caisson installation, the workflow generated and audited 6 formulations in 2.9 h of agent execution once physical knowledge and inputs were prepared. Among these formulations, adding seepage-driven soil void-ratio evolution to the geometric baseline reduced mean absolute final-heave error from 58.4% to 9.0% across 14 profiles; the selected model further incorporated near-wall dilation and achieved mean absolute percentage errors of 12.4% across 9 final-state cases and 4.2% at the endpoints of 5 process histories. Beyond predictive performance, blinded replay recovered all 9 target problems, while an independent audit uncovered 5 implementation problems after 36 predefined checks had passed. Overall, this work extends multi-agent AI beyond task automation toward human-governed engineering solvers.
Vibroacoustic analysis often requires coupling structural and acoustic solvers based on different numerical formulations and discretizations, making monolithic implementations intrusive and limiting software modularity and reuse. This work presents a partitioned co-simulation framework for exterior vibroacoustic analysis that couples an Isogeometric boundary representation analysis (IBRA) structural solver with an isogeometric boundary element method (IGA-BEM) acoustic solver. The methodology operates directly on the computer-aided design (CAD) boundary representation, preserving the exact geometry throughout the analysis and supporting both weak and strong coupling between non-conforming discretizations. A key contribution is the extension of the Aitken dynamic relaxation and Interface Quasi-Newton with Inverse Least-Squares (IQN-ILS) convergence accelerators to complex-valued interface quantities, allowing the coupling iterations to account directly for both amplitude and phase information. The approach is validated using one-way and two-way coupled vibroacoustic benchmark problems involving thin-shell structures and exterior acoustic domains. The results show excellent agreement with monolithic reference solutions, while the proposed complex-valued convergence accelerators improve the robustness and convergence behavior of the strongly coupled solution procedure without compromising solution accuracy. These results demonstrate that the proposed approach provides an accurate, robust, and modular approach for CAD-integrated frequency-domain vibroacoustic analysis.
The enforcement of essential boundary conditions is a fundamental challenge in unfitted boundary methods. This paper presents a non-intrusive, black-box strategy for imposing such conditions in unfitted meshes. The approach is intended for situations where the user does not have access to the solver's source code or its mathematical formulation, which is often the case when using commercial software. The proposed algorithm allows solvers originally designed for body-fitted meshes to be used in unfitted cases, provided that four conditions are satisfied: (i) the solver must support user customization by means of scripting, (ii) allow the imposition of Dirichlet boundary conditions at the node level through scripting, (iii) permit the deactivation of elements outside the physical domain, and (iv) provide access to the solution gradient within active elements. The last condition can also be satisfied by externally reconstructing the gradient from nodal values and connectivity information, provided the element formulation is known, making it optional in practice. These requirements are very fair demands and are satisfied by the vast majority of production-ready, possibly commercial, codes. In the current work, we show the application of this non-intrusive algorithm in the context of the Finite Element Method (FEM) and Isogeometric Analysis (IGA) discretizations, demonstrating optimal $L^2$-norm error convergence. This is demonstrated using the Kratos Multiphysics code (release \texttt{v10.1}) \emph{from the user API, simply leveraging the capabilities mentioned above.}
Odor quality is commonly represented using high dimensional descriptor profiles, yet their low dimensional organization remains unclear. We investigated whether a two-dimensional hyperbolic embedding can provide an interpretable representation of this structure. We applied hyperbolic metric multidimensional scaling to two complementary datasets: 480 Sagar rating profiles from three participants rating 160 odorants on 15 continuous descriptors, and 4983 GoodScents--Leffingwell molecules annotated with 138 binary descriptors. The embeddings substantially preserved pairwise descriptor distances, supporting subsequent analyses of radial and angular organization. In Sagar, rating profile entropy was strongly and negatively associated with hyperbolic radius, with diffuse profiles closer to the center and concentrated profiles closer to the boundary. This radial organization emerged primarily at the level of the full descriptor profile, rather than any individual descriptor, and remained robust across alternative descriptor representations, participant specific analyses, and averaged ratings. Sweet, musky, fruity, pleasantness showed the strongest directional trends. In GoodScents--Leffingwell, active label entropy, reflecting descriptor multiplicity, increased with radius, whereas orthogonalized descriptor entropy, reflecting spread across orthogonal modes, decreased with radius. Related binary descriptors occupied coherent localized high-density regions. These findings reveal complementary radial and angular organization in the hyperbolic representation of olfactory descriptor data. They support hyperbolic mapping as an interpretable descriptive framework in which radius summarizes global profile properties, while the angular component captures continuous descriptor gradients and categorical organization.
Transaction-local controls answer whether one financial request may proceed, but market behavior can be distributed across messages, agents, assets, and time. We study this interpretation gap in a virtual exchange populated by ten role-conditioned language-model agents. The agents communicate, trade reference assets and futures, launch tokens, and manage concentrated-liquidity pools under prescriptive adversarial roles. We analyze eight 72-cycle trajectories across two time-blinded hourly replay paths, with a runner-side wallet policy enabled or disabled. The retained artifacts connect generated outgoing messages, policy events, balances, positions, and cycle-end market state. A focal reconstruction shows a launch--promotion--exit scenario realized across private coordination, public claims, follower positioning, repeatedly withheld exits, and a later non-blocking request aligned with a token balance change. Across policy-enabled runs, the gate withholds direct requests selectively; most policy-categorized candidates are flagged rather than blocked, while the surrounding interaction can continue. Repeated runs also show that category-level and within-trajectory relations can recur even when normalized score-change rankings do not. These findings motivate agent-behavior evaluation that links communication, authorization, and evolving state instead of treating individual transaction verdicts as complete safety judgments.
Computer-aided engineering (CAE) simulation is among the largest and most demanding areas of engineering, where setting up a solver such as OpenFOAM, FEniCS, or COMSOL takes real expertise. Large language model (LLM) agents promise to turn a natural-language request into a working simulation, and recent CAE agents add simulation-specific machinery: multi-agent decomposition, domain retrieval, and scripted reflection. That machinery suited weak base models; modern harnesses already supply multi-turn reasoning, tool use, and execution feedback. We ask what a CAE simulation agent still needs beyond a generic harness. With information access and repair budget held fixed, a single-agent harness matches or beats multi-agent specialized systems (FoamBench 96.4\% vs.\ 88.2\%). Ablations trace this to capabilities the harness already provides: execution-feedback repair lifts FoamBench from 71.8\% with no repair round to 96.4\%, while scripted reflection adds nothing. The one input that still helps is domain knowledge supplied as solver tutorials, our largest measured gain (80.9\% to 96.4\%).
Reliable transport models are essential when modelling and optimising many chemical engineering processes, yet, most models assume hand-picked constitutive laws which may not reflect reality, and often assume initial conditions are known exactly. Both restrictions can significantly bias model predictions and lead to systematic error when used in predictive and control settings. Black-box neural surrogate alternatives for modelling can better match real example data, but are confined to the task they were trained on and cannot be interrogated for physical consistency. Here we introduce a general-purpose differentiable hybrid modelling framework for transport processes, specifically for the case of population balance equations. Our framework integrates a JAX finite volume population balance solver with learnable neural network components which are trained to both discover constitutive laws and fit initial conditions from real experimental data, allowing us to better model real experimental transport systems. Furthermore, we use our framework for process optimisation, using its differentiability to allow us to direct optimising experimental settings for quantities of interest. This work highlights the huge potential of such differentiable hybrid modelling frameworks for learning and optimising any given chemical separation which involves mass, energy, and/or momentum transport.
The geometric morphology of deposited filaments can significantly influence the structural performance and stability of 3D concrete-printed (3DCP) structures. However, most finite element (FEM)-based approaches for buildability assessment represent printed layers as simplified rectangles, potentially limiting predictive accuracy. This study proposes a geometry-informed modelling framework that integrates the deep-learning-based filament shape prediction tool ShapeGen3DCP with a layer-activation FEM approach to investigate the effect of realistic filament geometries on buildability. The framework generates geometry-aware numerical models directly from material and process parameters, eliminating the need for experimental filament characterization or computationally intensive fluid-flow simulations. Validation against experimental data and a parametric study of rectilinear walls demonstrate that extrusion parameters and the resulting filament geometry can significantly influence buildability predictions. Realistic filament representations are particularly important for free-flow deposition, whereas layer-pressing strategies are less sensitive to geometric simplifications. Among the investigated representations, an elliptical approximation provides an effective balance between geometric fidelity and modelling simplicity. When rectangular representations are preferred to enable regular computational meshes for faster simulations, defining their dimensions based on volume conservation improves prediction reliability compared with calibrating them using either the maximum filament width or the interlayer contact width. Overall, the proposed methodology demonstrates the importance of incorporating filament geometry into 3DCP simulations and provides practical guidance for selecting efficient and accurate geometric representations for buildability assessment.
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.
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.
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.
Scientific computing is undergoing rapid transformation as advances in artificial intelligence, heterogeneous computing, automation, and data-intensive research reshape not only computational tools but also the institutions, workforce models, and collaborative practices that support scientific discovery. This report synthesizes insights from the 2026 Workshop on Next-Generation Ecosystems for Scientific Computing, the second in a three-year series focused on strengthening scientific computing ecosystems through socio-technical co-design. Workshop discussions identified four interdependent strategic themes: software ecosystems for AI-enabled scientific discovery; trust, validation, and traceability; human-AI teaming and paradigm shifts; and workforce, pedagogy, and governance. The report translates these themes into eight priorities for community action spanning shared research infrastructure, trust and traceability, user experience, human-AI teaming, workforce development, cross-sector coordination, stewardship and sustainability, and evaluation of scientific value. Together, these priorities outline directions for building scientific computing ecosystems that remain trustworthy, sustainable, innovative, and resilient as AI assumes a growing role in scientific work.
Multimodal protein language models (pLMs) learn joint protein sequence-structure distributions, and their generation performance should also depend critically on inference-time sampling strategies. Yet prior work has focused more on model training than on how inference-time strategies behave. In this paper, we establish a three-stage investigation framework to empirically study the inference design space of multimodal pLMs across three representative pLMs and four fundamental tasks. We evaluate vanilla sampling, task-specific classifier-free guidance, and reward-guided beam search on multimodal pLMs, corresponding to controls over sampling distributions, per-step logits, and parallel trajectories. Throughout the complementary advancements centered on exploration-exploitation trade-off, we (1) reveal the suboptimality of default inference protocols and identify task-oriented sampling preferences; (2) observe substantial quantitative gains across tasks, consistently boosting the upper bound performance of multimodal pLMs without updating model parameters; (3) derive conclusions about base models that differ from prior consensus.
Probabilistic full-field reconstruction provides uncertainty-aware response evidence for structural reliability assessment, yet inference from sparse and noisy measurements remains underdetermined. Most existing methods overlook shifts between offline training and operational distributions. Under such shifts, posterior intervals may become miscalibrated, causing the reported uncertainty to lose its probabilistic meaning. This study proposes Modal Residual Flow Matching with Context-Conditioned Affine Spread Transport (MoRF-AST) for calibrated structural virtual sensing under changing operating conditions. MoRF constructs an analytic Gaussian reference posterior in normalized modal coordinates and trains a conditional flow only on posterior-whitened residuals. At deployment, AST estimates response scale from historical measurements at installed sensors and uses gated, mean-preserving Bures-Wasserstein transport to adjust posterior spread. On a bridge-deck benchmark, MoRF achieves a posterior-mean normalized root-mean-square error (NRMSE) of 7.20%, compared with 16.1% and 17.9% for two direct conditional flows. Across eight shifted traffic domains, AST reduces MoRF's cross-domain average coverage error from 0.0535 to 0.0236, a 55.9% reduction, while preserving posterior-mean accuracy. The same transport does not improve the tested alternatives in aggregate, showing that calibration gains require its direction to match the base posterior's dispersion bias. MoRF-AST provides a data-efficient framework for probabilistic full-field reconstruction whose uncertainty remains interpretable under scale-dominated operational distribution shifts. More broadly, this work highlights the need to calibrate uncertainty under changing operational distributions, thereby supporting trustworthy probabilistic modeling and reliability-informed decision-making in civil and infrastructure engineering.
Mission-critical intelligent systems often operate under time-varying limitations that reduce control authority and change the admissible safe operating envelope. In such settings, a safety certificate learned under nominal conditions may become invalid as system capability changes. To address this challenge, this paper proposes a degradation-aware, data-driven safety-filtering framework that learns a safe set from data, updates it online, and enforces the resulting learned barrier through a time-varying control barrier function (CBF). A nominal safe envelope is first learned from operational data using a radial basis function (RBF)-kernel support vector machine (SVM), whose decision function serves as the initial CBF candidate. To capture capability-induced safe-set contraction, a continuous-time decremental SVM update law is developed so that selected support-vector coefficients are reduced according to a degradation signal. A homotopy-smoothed SVM-CBF is then introduced to avoid discontinuous changes in the learned barrier during active-set transitions. The resulting time-varying learned barrier is enforced using a quadratic-program-based safety filter under degraded input constraints. Forward invariance of the learned time-varying safe set and recursive feasibility of the safety filter are established. Simulation results on a vertical takeoff and landing (VTOL) model show that the proposed method maintains safety under reduced control authority and avoids abrupt barrier-switching effects during safe-set contraction.
This work presents a data-driven methodology for multi-objective optimization under uncertainty of process parameters in the fused filament fabrication (FFF) process. The proposed approach optimizes the process parameters with the objectives of minimizing the geometric inaccuracy and maximizing the filament bond quality of the manufactured part. First, experiments are conducted to collect data pertaining to the part quality. Then, Bayesian neural network (BNN) models are constructed to predict the geometric inaccuracy and bond quality as functions of the process parameters. The BNN model captures the model uncertainty caused by the lack of knowledge about model parameters (neuron weights) and the input variability due to the intrinsic randomness in the input parameters. Using the stochastic predictions from these models, different robustness-based design optimization formulations are investigated, wherein process parameters such as nozzle temperature, nozzle speed, and layer thickness are optimized under uncertainty for different multi-objective scenarios. Epistemic uncertainty in the prediction model and the aleatory uncertainty in the input is considered in the optimization. Finally, Pareto surfaces are constructed to estimate the tradeoffs between the objectives. Both the BNN models and the effectiveness of the proposed optimization methodology are validated using the actual manufacturing of the parts.
This paper develops a computational framework to optimize the process parameters such that the bond quality between extruded polymer filaments is maximized in fused filament fabrication (FFF). A transient heat transfer analysis providing an estimate of the temperature profile of the filaments is coupled with a sintering neck growth model to assess the bond quality that occurs at the interfaces between adjacent filaments. Predicting the variability in the FFF process is essential for achieving proactive quality control of the manufactured part; however, the models used to predict the variability are affected by assumptions and approximations. This paper systematically quantifies the uncertainty in the bond quality model prediction due to various sources of uncertainty, both aleatory and epistemic, and includes the uncertainty and the model discrepancy in the process parameter optimization. Variance-based sensitivity analysis based on Sobol indices is used to quantify the relative contributions of the different uncertainty sources to the uncertainty in the bond quality. A Gaussian process (GP) surrogate model is constructed to compute and include the model discrepancy within the optimization. Physical experiments are conducted for calibration and validation of the physics model and also for validation of the optimum solution. The results show that the proposed formulation for process parameter optimization under uncertainty results in high bond quality between adjoining filaments of the FFF product.
When computational models (either physics-based or data-driven) are used for the sensitivity analysis of engineering systems, the sensitivity estimate is affected by the accuracy and uncertainty of the model. This paper considers global sensitivity analysis (GSA) for situations where both a physics-based model and experimental observations are available, and investigates physics-informed machine learning strategies to effectively combine the two sources of information in order to maximize the accuracy of the sensitivity estimate. Two representative machine learning (ML) techniques are considered, namely, deep neural networks (DNN) and Gaussian process (GP) modeling, and two strategies for incorporating physics knowledge within these techniques are investigated, namely: (i) incorporating loss functions in the ML models to enforce physics constraints, and (ii) pre-training and updating the ML model using simulation and experimental data respectively. Four different models are built for each type (DNN and GP), and the uncertainties in these models are included in the Sobol indices computation. The DNN-based models, with many degrees of freedom in terms of model parameters and training options, are found to result in smaller bounds on the sensitivity estimates when compared to the GP-based models. The proposed methods are illustrated for additive manufacturing and lake temperature modeling examples.
This paper develops an adaptive surrogate modeling method for problems with very high-dimensional spatio-temporal outputs. The analysis of spatio-temporal multi-physics systems is computationally expensive and consists of a large number of inputs and outputs. Surrogate models are often constructed to replace the physics-based model to achieve computational efficiency in analyses such as uncertainty quantification and optimization that require many function calls. In order to address the challenge introduced by the high dimensionality of spatio-temporal output, a dimension reduction method is first employed to map the high-dimensional output to a low-dimensional latent space. This is followed by the construction of the surrogate model in the low-dimensional space. The prediction error in the original space, which includes both the reconstruction error and surrogate model error, is evaluated using different error metrics. Based on the prediction accuracy of the surrogate model, new training points are identified for adaptive improvement of the surrogate model. We present a novel adaptive sampling technique that combines exploration and exploitation to improve the surrogate model accuracy with the fewest possible runs of the expensive physics-based model. Thermo-mechanical analysis of a gas turbine engine blade is used to analyze the effectiveness of the proposed method.
Systems that generate scientific research questions are evaluated today by expert scores, LLM-as-judge ratings, or curated case studies -- all subjective, none falsifiable. We formalize historical backtesting as an alternative: a system generates questions from a corpus frozen at a historical cutoff, the questions are frozen before any access to later literature, and a temporally isolated future corpus then determines whether each question was subsequently answered, partially addressed, independently posed, or ignored, and whether its underlying premise was supported or refuted. The protocol is model-agnostic: any system that emits frozen questions can be scored. We release reproducible astronomy instances with temporally isolated corpora, frozen questions, auditable labels, four reference baselines, and a submission interface. Two findings result. First, evidence-structure-first generation outperforms LLM-only prompting: across a generator decomposition crossed with a four-cutoff stress test (2010-2024, 798 judged questions) whose last window postdates model training, LLM-only generation shows memorized relevance without specific foresight, while a generator using no model weights at all finds questions whose premises the future refutes in every era. Second, a seven-rater agreement study (two blinded human annotators, five judge models, 90 items) indicts the outcome taxonomy rather than the judge: two careful humans agree at kappa = 0.17, every judge model agrees with the professional annotator as well or better (0.17-0.26), and frontier models agree with one another at 0.60 -- certifying an LLM judge by model-model agreement would have overstated its reliability threefold. A prospective instance -- 200 questions frozen 2026-08-17, scored 2027-2030 -- is released so the central claims become contamination-free tests that time itself will grade.
Large language models can write parametric CAD programs from a natural-language description (text-to-CAD generation), but a single sample is often wrong. Increasing test-time compute by sampling multiple candidates only helps if a good candidate can be identified, yet no ground-truth model is available at generation time. Existing systems often require a separate verifier, such as a vision-language judge, to select among candidates. We investigate whether the candidate pool itself provides enough signal for effective selection and a verifier-free alternative. We introduce 3D CAD consensus selection, hereafter consensus selection: sample $N$ parametric CAD programs, compile them to 3D models, and return the candidate that agrees most with the rest of the pool. The method is training-free and compatible with existing CAD agents. We investigate geometric and topological notions of agreement, each of which improves its corresponding evaluation metric. On the exact candidate pools of a state-of-the-art CAD generation method, geometric consensus improves all three geometric metrics over the method's verifier, while topological consensus matches it on topology. Across every tested LLM and prompt variant, geometric consensus also improves geometric accuracy over random selection from the same pool, reducing Chamfer distance by $1-10\%$.