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arXiv 最近完成扫描:2026-11-12 18:21 · 全站最近入库:2026-11-12 06:37各信源进度 →

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版本更新 · v2arXiv:2609.02126

Scalable Bayesian Optimization of Composite Functions for Image-Based Inverse Problems in Materials Characterization

Dasol Yoon, Poompol Buathong, Chia-Hao Lee, Yujia Zhang, David A. Muller, Peter I. Frazier

原文摘要

Estimating physical parameters from scientific images is a common inverse problem in materials characterization that often relies on expensive physics-based simulations. In electron microscopy, specimen thickness and crystal mistilt are critical parameters that govern how electrons scatter through the sample, and therefore the accuracy of any atomic-scale structure recovered from it. They are commonly inferred by matching experimental position-averaged convergent-beam electron diffraction (PACBED) patterns to simulated ones, but grid searches scale poorly and neural-network methods require extensive pretraining that may not transfer to new conditions. Here, we propose scalable Bayesian optimization of composite functions (SBOCF), a simulation-efficient method that exploits the known composite structure of the image-matching objective and the intermediate information contained in simulated images. By representing PACBED images with patch-level summaries and two correction terms, SBOCF preserves the original pixel-wise objective while reducing the number of modeled outputs from 24,649 to 11. Under a budget of 50 simulator evaluations, SBOCF outperformed standard Bayesian optimization with expected improvement on synthetic SrTiO3 benchmarks with thick and thin specimens, reducing the median final SSE by up to 290 times in the thick-sample case. On experimental data, SBOCF produced parameter estimates consistent with previously reported values without task-specific pretraining. For a simulated mistilted specimen, using the SBOCF estimates in a downstream ptychographic reconstruction recovered sharp atoms that were otherwise blurred. These results establish SBOCF as a promising approach for inverse problems involving expensive simulators and high-dimensional structured outputs.

cs.LG · cond-mat.mtrl-sci

新论文 · v1arXiv:2611.13565

Investigating Composite Modeling in Multi-Objective Bayesian Optimization for Scientific Design

Ricky Ye, Sahas Goli, Muhammad Ali, Poompol Buathong, Peter I. Frazier

原文摘要

Scientific design often requires balancing competing objectives that are expensive to evaluate through experiments or simulations. Multi-objective Bayesian optimization (MOBO) addresses this challenge by using probabilistic models to guide the selection of promising designs. In many applications, tunable inputs map to observable intermediate responses, which are then combined through known functions to compute the final objectives. Prior work on Bayesian optimization of composite functions shows that learning from these intermediate responses, which we call Composite modeling, can substantially improve sampling efficiency in single-objective optimization, compared to methods that condition only on black-box observations of the objective function. The benefits of Composite modeling in MOBO, however, remain understudied. In this work, we study the benefits of Composite modeling in MOBO and investigate the factors driving variation in its gains. We first establish single-objective conditions under which intermediate observations provide no additional predictive information beyond objective values, where composite and black box methods use the same warped Gaussian process prior. Controlled numerical experiments with versions of four MOBO methods across eight synthetic and application-inspired scientific-design benchmarks examine how these conditions relate to optimization gains in the multi-objective setting, where the black box approach models the objective functions with a standard multi-output Gaussian process. Both investigations support the claim that composite modeling tends to help more when the function mapping intermediate responses to final objectives is non-bijective and non-affine.

cs.LG · stat.ML

版本更新 · v2arXiv:2605.06879

Better Protein Function Prediction by Modeling Survivorship Bias

Zhongmou Chao, Poompol Buathong, Ekaterina Selivanovitch, Susan Daniel, Peter I. Frazier

原文摘要

Predicting whether a protein sequence possesses a biochemical property of interest is important for understanding and designing protein functionality. Modern protein sequence databases provide valuable training data for functional prediction, but they exhibit survivorship bias: natural selection favors variants that support organismal survival while eliminating many others before they can be observed, complicating classifier training. This setting motivates positive-unlabeled (PU) learning, which treats observed functional sequences as positive and unobserved sequences as unlabeled rather than nonfunctional. However, existing protein PU methods do not account for cross-sequence heterogeneity in evolutionary accessibility: sequences one nucleotide mutation away from a common variant arise far more readily than distant ones. We introduce PULSE: PU Learning with Surveillance and Evolution, a framework that trains a probabilistic classifier for a target protein function using an evolution-aware observation likelihood. When considering functionality of proteins with high genomic sequence coverage, PULSE combines a probabilistic classifier that estimates whether an amino acid sequence performs the target function with an evolutionary model that estimates the likelihood that its encoding nucleotide sequences emerge and are detected based on mutational accessibility, parental prevalence, and surveillance e!ciency. By coupling these two components, PULSE treats the absence of an evolutionarily accessible sequence as stronger evidence of non-functionality than the absence of one unlikely to arise. Tested on eleven tasks focusing on multiple Spike protein properties spanning five SARS-CoV-2 variants, PULSE ranks first or second on all of them, and achieves the best overall performance among all methods, including standard PU learning, one-class classification methods, and protein language models.

cs.LG · q-bio.QM