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, 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.

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.

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.