Yanwen Huang

Shikun Feng, Yuyan Ni, Minghao Li et al.

Recently, a noticeable trend has emerged in developing pre-trained foundation models in the domains of CV and NLP. However, for molecular pre-training, there lacks a universal model capable of effectively applying to various categories of molecular tasks, since existing prevalent pre-training methods exhibit effectiveness for specific types of downstream tasks. Furthermore, the lack of profound understanding of existing pre-training methods, including 2D graph masking, 2D-3D contrastive learning, and 3D denoising, hampers the advancement of molecular foundation models. In this work, we provide a unified comprehension of existing pre-training methods through the lens of contrastive learning. Thus their distinctions lie in clustering different views of molecules, which is shown beneficial to specific downstream tasks. To achieve a complete and general-purpose molecular representation, we propose a novel pre-training framework, named UniCorn, that inherits the merits of the three methods, depicting molecular views in three different levels. SOTA performance across quantum, physicochemical, and biological tasks, along with comprehensive ablation study, validate the universality and effectiveness of UniCorn.

Bowen Gao, Minsi Ren, Yuyan Ni et al.

In the field of Structure-based Drug Design (SBDD), deep learning-based generative models have achieved outstanding performance in terms of docking score. However, further study shows that the existing molecular generative methods and docking scores both have lacked consideration in terms of specificity, which means that generated molecules bind to almost every protein pocket with high affinity. To address this, we introduce the Delta Score, a new metric for evaluating the specificity of molecular binding. To further incorporate this insight for generation, we develop an innovative energy-guided approach using contrastive learning, with active compounds as decoys, to direct generative models toward creating molecules with high specificity. Our empirical results show that this method not only enhances the delta score but also maintains or improves traditional docking scores, successfully bridging the gap between SBDD and real-world needs.

Junguang Jiang, Yanwen Huang, Bin Liu et al.

In real-world recommender systems, different retrieval objectives are typically addressed using task-specific datasets with carefully designed model architectures. We demonstrate that Large Language Models (LLMs) can function as universal retrievers, capable of handling multiple objectives within a generative retrieval framework. To model complex user-item relationships within generative retrieval, we propose multi-query representation. To address the challenge of extremely large candidate sets in industrial recommender systems, we introduce matrix decomposition to boost model learnability, discriminability, and transferability, and we incorporate probabilistic sampling to reduce computation costs. Finally, our Universal Retrieval Model (URM) can adaptively generate a set from tens of millions of candidates based on arbitrary given objective while keeping the latency within tens of milliseconds. Applied to industrial-scale data, URM outperforms expert models elaborately designed for different retrieval objectives on offline experiments and significantly improves the core metric of online advertising platform by $3\%$.