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Haiping Lu

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Machine Learning Artificial Intelligence Biomolecules Computer Vision cond-mat.mtrl-sci Information Retrieval

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preprint2026arXiv

Benchmarking bandgap prediction in semiconductors under experimental and realistic evaluation settings

Accurate bandgap prediction is crucial for semiconductor applications, yet machine learning models trained on computational data often struggle to generalize to experimental bandgap measurements. Challenges related to data fidelity, domain generalization, and model interpretability remain insufficiently addressed in existing evaluation frameworks. To bridge this gap, we introduce RealMat-BaG, a benchmark for assessing model reliability under experimentally relevant conditions. We curate an open-access dataset of experimental bandgaps with aligned crystal structures and compare graph neural networks as well as classical machine learning baselines. Our framework evaluates performance across statistical and domain-based splits, examines transfer from DFT-computed to experimental bandgaps, and analyzes interpretability at both elemental-property and structural levels. Our results reveal the fundamental generalization limitations of current bandgap prediction models and establish a benchmark aligned with experimental measurements for developing more reliable learning strategies for materials discovery.

preprint2023arXiv

Interpretable bilinear attention network with domain adaptation improves drug-target prediction

Predicting drug-target interaction is key for drug discovery. Recent deep learning-based methods show promising performance but two challenges remain: (i) how to explicitly model and learn local interactions between drugs and targets for better prediction and interpretation; (ii) how to generalize prediction performance on novel drug-target pairs from different distribution. In this work, we propose DrugBAN, a deep bilinear attention network (BAN) framework with domain adaptation to explicitly learn pair-wise local interactions between drugs and targets, and adapt on out-of-distribution data. DrugBAN works on drug molecular graphs and target protein sequences to perform prediction, with conditional domain adversarial learning to align learned interaction representations across different distributions for better generalization on novel drug-target pairs. Experiments on three benchmark datasets under both in-domain and cross-domain settings show that DrugBAN achieves the best overall performance against five state-of-the-art baselines. Moreover, visualizing the learned bilinear attention map provides interpretable insights from prediction results.

preprint2022arXiv

Graph Node-Feature Convolution for Representation Learning

Graph convolutional network (GCN) is an emerging neural network approach. It learns new representation of a node by aggregating feature vectors of all neighbors in the aggregation process without considering whether the neighbors or features are useful or not. Recent methods have improved solutions by sampling a fixed size set of neighbors, or assigning different weights to different neighbors in the aggregation process, but features within a feature vector are still treated equally in the aggregation process. In this paper, we introduce a new convolution operation on regular size feature maps constructed from features of a fixed node bandwidth via sampling to get the first-level node representation, which is then passed to a standard GCN to learn the second-level node representation. Experiments show that our method outperforms competing methods in semi-supervised node classification tasks. Furthermore, our method opens new doors for exploring new GCN architectures, particularly deeper GCN models.

preprint2022arXiv

Knowledge-aware Neural Collective Matrix Factorization for Cross-domain Recommendation

Cross-domain recommendation (CDR) can help customers find more satisfying items in different domains. Existing CDR models mainly use common users or mapping functions as bridges between domains but have very limited exploration in fully utilizing extra knowledge across domains. In this paper, we propose to incorporate the knowledge graph (KG) for CDR, which enables items in different domains to share knowledge. To this end, we first construct a new dataset AmazonKG4CDR from the Freebase KG and a subset (two domain pairs: movies-music, movie-book) of Amazon Review Data. This new dataset facilitates linking knowledge to bridge within- and cross-domain items for CDR. Then we propose a new framework, KG-aware Neural Collective Matrix Factorization (KG-NeuCMF), leveraging KG to enrich item representations. It first learns item embeddings by graph convolutional autoencoder to capture both domain-specific and domain-general knowledge from adjacent and higher-order neighbours in the KG. Then, we maximize the mutual information between item embeddings learned from the KG and user-item matrix to establish cross-domain relationships for better CDR. Finally, we conduct extensive experiments on the newly constructed dataset and demonstrate that our model significantly outperforms the best-performing baselines.

preprint2020arXiv

Tri-graph Information Propagation for Polypharmacy Side Effect Prediction

The use of drug combinations often leads to polypharmacy side effects (POSE). A recent method formulates POSE prediction as a link prediction problem on a graph of drugs and proteins, and solves it with Graph Convolutional Networks (GCNs). However, due to the complex relationships in POSE, this method has high computational cost and memory demand. This paper proposes a flexible Tri-graph Information Propagation (TIP) model that operates on three subgraphs to learn representations progressively by propagation from protein-protein graph to drug-drug graph via protein-drug graph. Experiments show that TIP improves accuracy by 7%+, time efficiency by 83$\times$, and space efficiency by 3$\times$.

preprint2015arXiv

Semi-Orthogonal Multilinear PCA with Relaxed Start

Principal component analysis (PCA) is an unsupervised method for learning low-dimensional features with orthogonal projections. Multilinear PCA methods extend PCA to deal with multidimensional data (tensors) directly via tensor-to-tensor projection or tensor-to-vector projection (TVP). However, under the TVP setting, it is difficult to develop an effective multilinear PCA method with the orthogonality constraint. This paper tackles this problem by proposing a novel Semi-Orthogonal Multilinear PCA (SO-MPCA) approach. SO-MPCA learns low-dimensional features directly from tensors via TVP by imposing the orthogonality constraint in only one mode. This formulation results in more captured variance and more learned features than full orthogonality. For better generalization, we further introduce a relaxed start (RS) strategy to get SO-MPCA-RS by fixing the starting projection vectors, which increases the bias and reduces the variance of the learning model. Experiments on both face (2D) and gait (3D) data demonstrate that SO-MPCA-RS outperforms other competing algorithms on the whole, and the relaxed start strategy is also effective for other TVP-based PCA methods.