Tengfei Luo

Gang Liu, Tong Zhao, Jiaxin Xu et al.

Rationale is defined as a subset of input features that best explains or supports the prediction by machine learning models. Rationale identification has improved the generalizability and interpretability of neural networks on vision and language data. In graph applications such as molecule and polymer property prediction, identifying representative subgraph structures named as graph rationales plays an essential role in the performance of graph neural networks. Existing graph pooling and/or distribution intervention methods suffer from lack of examples to learn to identify optimal graph rationales. In this work, we introduce a new augmentation operation called environment replacement that automatically creates virtual data examples to improve rationale identification. We propose an efficient framework that performs rationale-environment separation and representation learning on the real and augmented examples in latent spaces to avoid the high complexity of explicit graph decoding and encoding. Comparing against recent techniques, experiments on seven molecular and four polymer real datasets demonstrate the effectiveness and efficiency of the proposed augmentation-based graph rationalization framework.

Gang Liu, Eric Inae, Tong Zhao et al.

Graph property prediction tasks are important and numerous. While each task offers a small size of labeled examples, unlabeled graphs have been collected from various sources and at a large scale. A conventional approach is training a model with the unlabeled graphs on self-supervised tasks and then fine-tuning the model on the prediction tasks. However, the self-supervised task knowledge could not be aligned or sometimes conflicted with what the predictions needed. In this paper, we propose to extract the knowledge underlying the large set of unlabeled graphs as a specific set of useful data points to augment each property prediction model. We use a diffusion model to fully utilize the unlabeled graphs and design two new objectives to guide the model's denoising process with each task's labeled data to generate task-specific graph examples and their labels. Experiments demonstrate that our data-centric approach performs significantly better than fifteen existing various methods on fifteen tasks. The performance improvement brought by unlabeled data is visible as the generated labeled examples unlike the self-supervised learning.

Gang Liu, Sobin Alosious, Subhamoy Mahajan et al.

Machine learning (ML) offers a powerful path toward discovering sustainable polymer materials, but progress has been limited by the lack of large, high-quality, and openly accessible polymer datasets. The Open Polymer Challenge (OPC) addresses this gap by releasing the first community-developed benchmark for polymer informatics, featuring a dataset with 10K polymers and 5 properties: thermal conductivity, radius of gyration, density, fractional free volume, and glass transition temperature. The challenge centers on multi-task polymer property prediction, a core step in virtual screening pipelines for materials discovery. Participants developed models under realistic constraints that include small data, label imbalance, and heterogeneous simulation sources, using techniques such as feature-based augmentation, transfer learning, self-supervised pretraining, and targeted ensemble strategies. The competition also revealed important lessons about data preparation, distribution shifts, and cross-group simulation consistency, informing best practices for future large-scale polymer datasets. The resulting models, analysis, and released data create a new foundation for molecular AI in polymer science and are expected to accelerate the development of sustainable and energy-efficient materials. Along with the competition, we release the test dataset at https://www.kaggle.com/datasets/alexliu99/neurips-open-polymer-prediction-2025-test-data. We also release the data generation pipeline at https://github.com/sobinalosious/ADEPT, which simulates more than 25 properties, including thermal conductivity, radius of gyration, and density.

Deepak Akhare, Zeping Chen, Richard Gulotty et al.

Chemical vapor infiltration (CVI) is a widely adopted manufacturing technique used in producing carbon-carbon and carbon-silicon carbide composites. These materials are especially valued in the aerospace and automotive industries for their robust strength and lightweight characteristics. The densification process during CVI critically influences the final performance, quality, and consistency of these composite materials. Experimentally optimizing the CVI processes is challenging due to long experimental time and large optimization space. To address these challenges, this work takes a modeling-centric approach. Due to the complexities and limited experimental data of the isothermal CVI densification process, we have developed a data-driven predictive model using the physics-integrated neural differentiable (PiNDiff) modeling framework. An uncertainty quantification feature has been embedded within the PiNDiff method, bolstering the model's reliability and robustness. Through comprehensive numerical experiments involving both synthetic and real-world manufacturing data, the proposed method showcases its capability in modeling densification during the CVI process. This research highlights the potential of the PiNDiff framework as an instrumental tool for advancing our understanding, simulation, and optimization of the CVI manufacturing process, particularly when faced with sparse data and an incomplete description of the underlying physics.

Yihan Zhu, Yuhan Liu, Weijiang Li et al.

Despite the success of foundation models in language and vision, molecular graph generation still lacks a unified framework for heterogeneous design tasks with reliable controllability. While reinforcement learning (RL) offers a natural post-training mechanism for task-specific optimization, applying it to graph generative models is hindered by the vast atom-wise action spaces and chemically invalid intermediate states. We propose \textbf{Co}ntrollable \textbf{Mole}cular Generative Foundation Models (CoMole), built with a unified motif-aware graph diffusion pipeline. By learning a motif-aware graph space, CoMole transfers pretrained structural priors into controllable generation, where RL optimizes conditional reverse policies over chemically meaningful decisions. We theoretically characterize the bottleneck of atom-level RL and justify motif-aware policy optimization. Across three heterogeneous benchmarks spanning materials and drug discovery, CoMole ranks first in controllability on all nine targets, reduces MAE by up to 48.2% relative to the strongest baselines, and maintains validity above 0.94 without rule-based correction or post-hoc filtering. We further show that CoMole transfers controllability to unseen properties by optimizing only task embeddings with the generator frozen, achieving performance competitive with strong task-specific baselines.

Gang Liu, Jie Chen, Yihan Zhu et al.

In-context learning allows large models to adapt to new tasks from a few demonstrations, but it has shown limited success in molecular design. Existing databases such as ChEMBL contain molecular properties spanning millions of biological assays, yet labeled data for each property remain scarce. To address this limitation, we introduce demonstration-conditioned diffusion models (DemoDiff), which define task contexts using a small set of molecule-score examples instead of text descriptions. These demonstrations guide a denoising Transformer to generate molecules aligned with target properties. For scalable pretraining, we develop a new molecular tokenizer with Node Pair Encoding that represents molecules at the motif level, requiring 5.5$\times$ fewer nodes. We curate a dataset containing millions of context tasks from multiple sources covering both drugs and materials, and pretrain a 0.7-billion-parameter model on it. Across 33 design tasks in six categories, DemoDiff matches or surpasses language models 100-1000$\times$ larger and achieves an average rank of 3.63 compared to 5.25-10.20 for domain-specific approaches. These results position DemoDiff as a molecular foundation model for in-context molecular design. Our code is available at https://github.com/liugangcode/DemoDiff.

Deepak Akhare, Tengfei Luo, Jian-Xun Wang

The hybrid neural differentiable models mark a significant advancement in the field of scientific machine learning. These models, integrating numerical representations of known physics into deep neural networks, offer enhanced predictive capabilities and show great potential for data-driven modeling of complex physical systems. However, a critical and yet unaddressed challenge lies in the quantification of inherent uncertainties stemming from multiple sources. Addressing this gap, we introduce a novel method, DiffHybrid-UQ, for effective and efficient uncertainty propagation and estimation in hybrid neural differentiable models, leveraging the strengths of deep ensemble Bayesian learning and nonlinear transformations. Specifically, our approach effectively discerns and quantifies both aleatoric uncertainties, arising from data noise, and epistemic uncertainties, resulting from model-form discrepancies and data sparsity. This is achieved within a Bayesian model averaging framework, where aleatoric uncertainties are modeled through hybrid neural models. The unscented transformation plays a pivotal role in enabling the flow of these uncertainties through the nonlinear functions within the hybrid model. In contrast, epistemic uncertainties are estimated using an ensemble of stochastic gradient descent (SGD) trajectories. This approach offers a practical approximation to the posterior distribution of both the network parameters and the physical parameters. Notably, the DiffHybrid-UQ framework is designed for simplicity in implementation and high scalability, making it suitable for parallel computing environments. The merits of the proposed method have been demonstrated through problems governed by both ordinary and partial differentiable equations.

Seongmin Kim, Vincent R. Pascuzzi, Travis S. Humble et al.

Many real-world problems are naturally formulated as higher-order optimization (HUBO) tasks involving dense, multi-variable interactions, which are challenging to solve with classical methods. Quantum optimization offers a promising route, but hardware constraints and limitations to quadratic formulations have hampered their practicality. Here, we develop a distributed quantum optimization framework (DQOF) for dense, large-scale HUBO problems. DQOF assigns quantum circuits a central role in directly capturing higher-order interactions, while high-performance computing orchestrates large-scale parallelism and coordination. A clustering strategy enables wide quantum circuits without increasing depth, allowing efficient execution on near-term quantum hardware. We demonstrate high-quality solutions for HUBOs up to 500 variables within 170 seconds, significantly outperforming conventional approaches in solution quality and scalability. Applied to optical metamaterial design, DQOF efficiently discovers high-performance structures and shows that higher-order interactions are important for practical optimization problems. These results establish DQOF as a practical and scalable computational paradigm for large-scale scientific optimization.

Yanfang Ye, Zheyuan Zhang, Tianyi Ma et al.

Cutting-edge Artificial Intelligence (AI) techniques keep reshaping our view of the world. For example, Large Language Models (LLMs) based applications such as ChatGPT have shown the capability of generating human-like conversation on extensive topics. Due to the impressive performance on a variety of language-related tasks (e.g., open-domain question answering, translation, and document summarization), one can envision the far-reaching impacts that can be brought by the LLMs with broader real-world applications (e.g., customer service, education and accessibility, and scientific discovery). Inspired by their success, this paper will offer an overview of state-of-the-art LLMs and their integration into a wide range of academic disciplines, including: (1) arts, letters, and law (e.g., history, philosophy, political science, arts and architecture, law), (2) economics and business (e.g., finance, economics, accounting, marketing), and (3) science and engineering (e.g., mathematics, physics and mechanical engineering, chemistry and chemical engineering, life sciences and bioengineering, earth sciences and civil engineering, computer science and electrical engineering). Integrating humanity and technology, in this paper, we will explore how LLMs are shaping research and practice in these fields, while also discussing key limitations, open challenges, and future directions in the era of generative AI. The review of how LLMs are engaged across disciplines-along with key observations and insights-can help researchers and practitioners interested in exploiting LLMs to advance their works in diverse real-world applications.

Deepak Akhare, Pan Du, Tengfei Luo et al.

Hybrid neural-physics modeling frameworks through differentiable programming have emerged as powerful tools in scientific machine learning, enabling the integration of known physics with data-driven learning to improve prediction accuracy and generalizability. However, most existing hybrid frameworks rely on explicit recurrent formulations, which suffer from numerical instability and error accumulation during long-horizon forecasting. In this work, we introduce Im-PiNDiff, a novel implicit physics-integrated neural differentiable solver for stable and accurate modeling of spatiotemporal dynamics. Inspired by deep equilibrium models, Im-PiNDiff advances the state using implicit fixed-point layers, enabling robust long-term simulation while remaining fully end-to-end differentiable. To enable scalable training, we introduce a hybrid gradient propagation strategy that integrates adjoint-state methods with reverse-mode automatic differentiation. This approach eliminates the need to store intermediate solver states and decouples memory complexity from the number of solver iterations, significantly reducing training overhead. We further incorporate checkpointing techniques to manage memory in long-horizon rollouts. Numerical experiments on various spatiotemporal PDE systems, including advection-diffusion processes, Burgers' dynamics, and multi-physics chemical vapor infiltration processes, demonstrate that Im-PiNDiff achieves superior predictive performance, enhanced numerical stability, and substantial reductions in memory and runtime cost relative to explicit and naive implicit baselines. This work provides a principled, efficient, and scalable framework for hybrid neural-physics modeling.

Guoyue Xu, Renzheng Zhang, Tengfei Luo

To overcome the inherent inefficiencies of traditional trial-and-error materials discovery, the scientific community is increasingly developing autonomous laboratories that integrate data-driven decision-making into closed-loop experimental workflows. In this work, we realize this concept for thermoresponsive polymers by developing a low-cost, "frugal twin" platform for the optimization of the lower critical solution temperature (LCST) of poly(N-isopropylacrylamide) (PNIPAM). Our system integrates robotic fluid-handling, on-line sensors, and Bayesian optimization (BO) that navigates the multi-component salt solution spaces to achieve user-specified LCST targets. The platform demonstrates convergence to target properties within a minimal number of experiments. It strategically explores the parameter space, learns from informative "off-target" results, and self-corrects to achieve the final targets. By providing an accessible and adaptable blueprint, this work lowers the barrier to entry for autonomous experimentation and accelerates the design and discovery of functional polymers.

Yihan Zhu, Gang Liu, Eric Inae et al.

Polymers are large macromolecules composed of repeating structural units known as monomers and are widely applied in fields such as energy storage, construction, medicine, and aerospace. However, existing graph neural network methods, though effective for small molecules, only model the single unit of polymers and fail to produce consistent vector representations for the true polymer structure with varying numbers of units. To address this challenge, we introduce Graph Repetition Invariance (GRIN), a novel method to learn polymer representations that are invariant to the number of repeating units in their graph representations. GRIN integrates a graph-based maximum spanning tree alignment with repeat-unit augmentation to ensure structural consistency. We provide theoretical guarantees for repetition-invariance from both model and data perspectives, demonstrating that three repeating units are the minimal augmentation required for optimal invariant representation learning. GRIN outperforms state-of-the-art baselines on both homopolymer and copolymer benchmarks, learning stable, repetition-invariant representations that generalize effectively to polymer chains of unseen sizes.

Zeping Chen, Marwa Yacouti, Maryam Shakiba et al.

Carbon fiber-reinforced composites (CFRC) are pivotal in advanced engineering applications due to their exceptional mechanical properties. A deep understanding of CFRC behavior under mechanical loading is essential for optimizing performance in demanding applications such as aerospace structures. While traditional Finite Element Method (FEM) simulations, including advanced techniques like Interface-enriched Generalized FEM (IGFEM), offer valuable insights, they can struggle with computational efficiency. Existing data-driven surrogate models partially address these challenges by predicting propagated damage or stress-strain behavior but fail to comprehensively capture the evolution of stress and damage throughout the entire deformation history, including crack initiation and propagation. This study proposes a novel auto-regressive composite U-Net deep learning model to simultaneously predict stress and damage fields during CFRC deformation. By leveraging the U-Net architecture's ability to capture spatial features and integrate macro- and micro-scale phenomena, the proposed model overcomes key limitations of prior approaches. The model achieves high accuracy in predicting evolution of stress and damage distribution within the microstructure of a CFRC under unidirectional strain, offering a speed-up of over 60 times compared to IGFEM.

Jiaxin Xu, Gang Liu, Ruilan Guo et al.

The advancement of polymer informatics has been significantly propelled by the integration of machine learning (ML) techniques, enabling the rapid prediction of polymer properties and expediting the discovery of high-performance polymeric materials. However, the field lacks a standardized workflow that encompasses prediction accuracy, uncertainty quantification, ML interpretability, and polymer synthesizability. In this study, we introduce POINT$^{2}$ (POlymer INformatics Training and Testing), a comprehensive benchmark database and protocol designed to address these critical challenges. Leveraging the existing labeled datasets and the unlabeled PI1M dataset, a collection of approximately one million virtual polymers generated via a recurrent neural network trained on the realistic polymers, we develop an ensemble of ML models, including Quantile Random Forests, Multilayer Perceptrons with dropout, Graph Neural Networks, and pretrained large language models. These models are coupled with diverse polymer representations such as Morgan, MACCS, RDKit, Topological, Atom Pair fingerprints, and graph-based descriptors to achieve property predictions, uncertainty estimations, model interpretability, and template-based polymerization synthesizability across a spectrum of properties, including gas permeability, thermal conductivity, glass transition temperature, melting temperature, fractional free volume, and density. The POINT$^{2}$ database can serve as a valuable resource for the polymer informatics community for polymer discovery and optimization.

Gang Liu, Jiaxin Xu, Tengfei Luo et al.

Inverse molecular design with diffusion models holds great potential for advancements in material and drug discovery. Despite success in unconditional molecular generation, integrating multiple properties such as synthetic score and gas permeability as condition constraints into diffusion models remains unexplored. We present the Graph Diffusion Transformer (Graph DiT) for multi-conditional molecular generation. Graph DiT integrates an encoder to learn numerical and categorical property representations with the Transformer-based denoiser. Unlike previous graph diffusion models that add noise separately on the atoms and bonds in the forward diffusion process, Graph DiT is trained with a novel graph-dependent noise model for accurate estimation of graph-related noise in molecules. We extensively validate Graph DiT for multi-conditional polymer and small molecule generation. Results demonstrate the superiority of Graph DiT across nine metrics from distribution learning to condition control for molecular properties. A polymer inverse design task for gas separation with feedback from domain experts further demonstrates its practical utility.

Gang Liu, Tong Zhao, Eric Inae et al.

Data imbalance is easily found in annotated data when the observations of certain continuous label values are difficult to collect for regression tasks. When they come to molecule and polymer property predictions, the annotated graph datasets are often small because labeling them requires expensive equipment and effort. To address the lack of examples of rare label values in graph regression tasks, we propose a semi-supervised framework to progressively balance training data and reduce model bias via self-training. The training data balance is achieved by (1) pseudo-labeling more graphs for under-represented labels with a novel regression confidence measurement and (2) augmenting graph examples in latent space for remaining rare labels after data balancing with pseudo-labels. The former is to identify quality examples from unlabeled data whose labels are confidently predicted and sample a subset of them with a reverse distribution from the imbalanced annotated data. The latter collaborates with the former to target a perfect balance using a novel label-anchored mixup algorithm. We perform experiments in seven regression tasks on graph datasets. Results demonstrate that the proposed framework significantly reduces the error of predicted graph properties, especially in under-represented label areas.

Sina Malakpour Estalaki, Cody S. Lough, Robert G. Landers et al.

Variation in the local thermal history during the laser powder bed fusion (LPBF) process in additive manufacturing (AM) can cause microporosity defects. in-situ sensing has been proposed to monitor the AM process to minimize defects, but the success requires establishing a quantitative relationship between the sensing data and the porosity, which is especially challenging for a large number of variables and computationally costly. In this work, we develop machine learning (ML) models that can use in-situ thermographic data to predict the microporosity of LPBF stainless steel materials. This work considers two identified key features from the thermal histories: the time above the apparent melting threshold (/tau) and the maximum radiance (T_{max}). These features are computed, stored for each voxel in the built material, are used as inputs. The binary state of each voxel, either defective or normal, is the output. Different ML models are trained and tested for the binary classification task. In addition to using the thermal features of each voxel to predict its own state, the thermal features of neighboring voxels are also included as inputs. This is shown to improve the prediction accuracy, which is consistent with thermal transport physics around each voxel contributing to its final state. Among the models trained, the F1 scores on test sets reach above 0.96 for random forests. Feature importance analysis based on the ML models shows that T_{max}is more important to the voxel state than /tau. The analysis also finds that the thermal history of the voxels above the present voxel is more influential than those beneath it.

Seunghyun Moon, Ruimin Ma, Ross Attardo et al.

In this study, the effects of surface roughness and pore characteristics on fatigue lives of laser powder bed fusion (LPBF) Ti-6Al-4V parts were investigated. The 197 fatigue bars were printed using the same laser power but with varied scanning speeds. These actions led to variations in the geometries of microscale pores, and such variations were characterized using micro-computed tomography. To generate differences in surface roughness in fatigue bars, half of the samples were grit-blasted and the other half machined. Fatigue behaviors were analyzed with respect to surface roughness and statistics of the pores. For the grit-blasted samples, the contour laser scan in the LPBF strategy led to a pore-depletion zone isolating surface and internal pores with different features. For the machined samples, where surface pores resemble internal pores, the fatigue life was highly correlated with the average pore size and projected pore area in the plane perpendicular to the stress direction. Finally, a machine learning model using a drop-out neural network (DONN) was employed to establish a link between surface and pore features to the fatigue data (logN), and good prediction accuracy was demonstrated. Besides predicting fatigue lives, the DONN can also estimate the prediction uncertainty.