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Researcher profile

Dan Lu

Dan Lu contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Machine LearningArtificial Intelligencecond-mat.mtrl-scimath.OCNeural and Evolutionary Computingphysics.ao-phphysics.chem-phphysics.comp-ph

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Published work

5 published item(s)

preprint2026arXiv

Physical probes expose and alleviate chemical-environment collapse in molecular representations

Nuclear magnetic resonance (NMR) spectroscopy provides an experimental readout of local chemical environments, but its use in molecular representation learning has been constrained by heterogeneous data and incomplete atom-level assignments. Here we construct complementary high-fidelity experimental and computational 13C NMR resources, which reveal a recurrent form of representational collapse: atoms that are equivalent in molecular topology can remain experimentally distinct in their real chemical environments, whereas explicit 3D descriptions are further limited by static conformations in dynamic regimes. To alleviate this bottleneck, we develop CLAIM (Contrastive Learning for Atom-to-molecule Inference of Molecular NMR), a framework that aligns efficient topological molecular inputs with atom-resolved NMR observables. Through hierarchical chemical priors and cross-level contrastive learning, CLAIM restores lost chemical resolution and markedly improves atom-level molecule-spectrum retrieval. CLAIM remains robust in flexible and tautomeric systems for 13C NMR prediction, improves stereoisomer discrimination without explicit 3D modelling, and transfers to broader molecular property tasks including ADMET prediction and fluorescence estimation. These results establish physically grounded spectral alignment as an effective strategy for alleviating chemical-environment collapse and for guiding experimentally grounded molecular representation learning.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

A Spatiotemporal-Aware Climate Model Ensembling Method for Improving Precipitation Predictability

Multimodel ensembling has been widely used to improve climate model predictions, and the improvement strongly depends on the ensembling scheme. In this work, we propose a Bayesian neural network (BNN) ensembling method, which combines climate models within a Bayesian model averaging framework, to improve the predictive capability of model ensembles. Our proposed BNN approach calculates spatiotemporally varying model weights and biases by leveraging individual models' simulation skill, calibrates the ensemble prediction against observations by considering observation data uncertainty, and quantifies epistemic uncertainty when extrapolating to new conditions. More importantly, the BNN method provides interpretability about which climate model contributes more to the ensemble prediction at which locations and times. Thus, beyond its predictive capability, the method also brings insights and understanding of the models to guide further model and data development. In this study, we apply the BNN weighting scheme to an ensemble of CMIP6 climate models for monthly precipitation prediction over the conterminous United States. In both synthetic and real case studies, we demonstrate that BNN produces predictions of monthly precipitation with higher accuracy than three baseline ensembling methods. BNN can correctly assign a larger weight to the regions and seasons where the individual model fits the observation better. Moreover, its offered interpretability is consistent with our understanding of localized climate model performance. Additionally, BNN shows an increasing uncertainty when the prediction is farther away from the period with constrained data, which appropriately reflects our predictive confidence and trustworthiness of the models in the changing climate.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

PI3NN: Out-of-distribution-aware prediction intervals from three neural networks

We propose a novel prediction interval (PI) method for uncertainty quantification, which addresses three major issues with the state-of-the-art PI methods. First, existing PI methods require retraining of neural networks (NNs) for every given confidence level and suffer from the crossing issue in calculating multiple PIs. Second, they usually rely on customized loss functions with extra sensitive hyperparameters for which fine tuning is required to achieve a well-calibrated PI. Third, they usually underestimate uncertainties of out-of-distribution (OOD) samples leading to over-confident PIs. Our PI3NN method calculates PIs from linear combinations of three NNs, each of which is independently trained using the standard mean squared error loss. The coefficients of the linear combinations are computed using root-finding algorithms to ensure tight PIs for a given confidence level. We theoretically prove that PI3NN can calculate PIs for a series of confidence levels without retraining NNs and it completely avoids the crossing issue. Additionally, PI3NN does not introduce any unusual hyperparameters resulting in a stable performance. Furthermore, we address OOD identification challenge by introducing an initialization scheme which provides reasonably larger PIs of the OOD samples than those of the in-distribution samples. Benchmark and real-world experiments show that our method outperforms several state-of-the-art approaches with respect to predictive uncertainty quality, robustness, and OOD samples identification.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

A Novel Evolution Strategy with Directional Gaussian Smoothing for Blackbox Optimization

We propose an improved evolution strategy (ES) using a novel nonlocal gradient operator for high-dimensional black-box optimization. Standard ES methods with $d$-dimensional Gaussian smoothing suffer from the curse of dimensionality due to the high variance of Monte Carlo (MC) based gradient estimators. To control the variance, Gaussian smoothing is usually limited in a small region, so existing ES methods lack nonlocal exploration ability required for escaping from local minima. We develop a nonlocal gradient operator with directional Gaussian smoothing (DGS) to address this challenge. The DGS conducts 1D nonlocal explorations along $d$ orthogonal directions in $\mathbb{R}^d$, each of which defines a nonlocal directional derivative as a 1D integral. We then use Gauss-Hermite quadrature, instead of MC sampling, to estimate the $d$ 1D integrals to ensure high accuracy (i.e., small variance). Our method enables effective nonlocal exploration to facilitate the global search in high-dimensional optimization. We demonstrate the superior performance of our method in three sets of examples, including benchmark functions for global optimization, and real-world science and engineering applications.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Application of variational policy gradient to atomic-scale materials synthesis

Atomic-scale materials synthesis via layer deposition techniques present a unique opportunity to control material structures and yield systems that display unique functional properties that cannot be stabilized using traditional bulk synthetic routes. However, the deposition process itself presents a large, multidimensional space that is traditionally optimized via intuition and trial and error, slowing down progress. Here, we present an application of deep reinforcement learning to a simulated materials synthesis problem, utilizing the Stein variational policy gradient (SVPG) approach to train multiple agents to optimize a stochastic policy to yield desired functional properties. Our contributions are (1) A fully open source simulation environment for layered materials synthesis problems, utilizing a kinetic Monte-Carlo engine and implemented in the OpenAI Gym framework, (2) Extension of the Stein variational policy gradient approach to deal with both image and tabular input, and (3) Developing a parallel (synchronous) implementation of SVPG using Horovod, distributing multiple agents across GPUs and individual simulation environments on CPUs. We demonstrate the utility of this approach in optimizing for a material surface characteristic, surface roughness, and explore the strategies used by the agents as compared with a traditional actor-critic (A2C) baseline. Further, we find that SVPG stabilizes the training process over traditional A2C. Such trained agents can be useful to a variety of atomic-scale deposition techniques, including pulsed laser deposition and molecular beam epitaxy, if the implementation challenges are addressed.

0 citations0 reviewsNo code linkedOpen access