Xiaohua Hu

Yuan An, Jane Greenberg, Alex Kalinowski et al.

We present a comprehensive benchmark dataset for Knowledge Graph Question Answering in Materials Science (KGQA4MAT), with a focus on metal-organic frameworks (MOFs). A knowledge graph for metal-organic frameworks (MOF-KG) has been constructed by integrating structured databases and knowledge extracted from the literature. To enhance MOF-KG accessibility for domain experts, we aim to develop a natural language interface for querying the knowledge graph. We have developed a benchmark comprised of 161 complex questions involving comparison, aggregation, and complicated graph structures. Each question is rephrased in three additional variations, resulting in 644 questions and 161 KG queries. To evaluate the benchmark, we have developed a systematic approach for utilizing the LLM, ChatGPT, to translate natural language questions into formal KG queries. We also apply the approach to the well-known QALD-9 dataset, demonstrating ChatGPT's potential in addressing KGQA issues for different platforms and query languages. The benchmark and the proposed approach aim to stimulate further research and development of user-friendly and efficient interfaces for querying domain-specific materials science knowledge graphs, thereby accelerating the discovery of novel materials.

Vishal Dey, Xiao Hu, Xia Ning

In real-world drug design, molecule optimization requires selectively improving multiple molecular properties up to pharmaceutically relevant levels, while maintaining others that already meet such criteria. However, existing computational approaches and instruction-tuned LLMs fail to capture such nuanced property-specific objectives, limiting their practical applicability. To address this, we introduce C-MuMOInstruct, the first instruction-tuning dataset focused on multi-property optimization with explicit, property-specific objectives. Leveraging C-MuMOInstruct, we develop GeLLMO-Cs, a series of instruction-tuned LLMs that can perform targeted property-specific optimization. Our experiments across 5 in-distribution and 5 out-of-distribution tasks show that GeLLMO-Cs consistently outperform strong baselines, achieving up to 126% higher success rate. Notably, GeLLMO-Cs exhibit impressive 0-shot generalization to novel optimization tasks and unseen instructions. This offers a step toward a foundational LLM to support realistic, diverse optimizations with property-specific objectives. C-MuMOInstruct and code are accessible through https://github.com/ninglab/GeLLMO-C.

Yi Yuan, Joseph Van Duyn, Runze Yan et al. · stanford

Electrocardiogram (ECG) analysis is foundational for cardiovascular disease diagnosis, yet the performance of deep learning models is often constrained by limited access to annotated data. Self-supervised contrastive learning has emerged as a powerful approach for learning robust ECG representations from unlabeled signals. However, most existing methods generate only pairwise augmented views and fail to leverage the rich temporal structure of ECG recordings. In this work, we present a poly-window contrastive learning framework. We extract multiple temporal windows from each ECG instance to construct positive pairs and maximize their agreement via statistics. Inspired by the principle of slow feature analysis, our approach explicitly encourages the model to learn temporally invariant and physiologically meaningful features that persist across time. We validate our approach through extensive experiments and ablation studies on the PTB-XL dataset. Our results demonstrate that poly-window contrastive learning consistently outperforms conventional two-view methods in multi-label superclass classification, achieving higher AUROC (0.891 vs. 0.888) and F1 scores (0.680 vs. 0.679) while requiring up to four times fewer pre-training epochs (32 vs. 128) and 14.8% in total wall clock pre-training time reduction. Despite processing multiple windows per sample, we achieve a significant reduction in the number of training epochs and total computation time, making our method practical for training foundational models. Through extensive ablations, we identify optimal design choices and demonstrate robustness across various hyperparameters. These findings establish poly-window contrastive learning as a highly efficient and scalable paradigm for automated ECG analysis and provide a promising general framework for self-supervised representation learning in biomedical time-series data.