Fengbin Zhu
Publications
CAPSUL: A Comprehensive Human Protein Benchmark for Subcellular Localization
Subcellular localization is a crucial biological task for drug target identification and function annotation. Although it has been biologically realized that subcellular localization is closely associated with protein structure, no existing dataset offers comprehensive 3D structural information with detailed subcellular localization annotations, thus severely hindering the application of promising structure-based models on this task. To address this gap, we introduce a new benchmark called $\mathbf{CAPSUL}$, a $\mathbf{C}$omprehensive hum$\mathbf{A}$n $\mathbf{P}$rotein benchmark for $\mathbf{SU}$bcellular $\mathbf{L}$ocalization. It features a dataset that integrates diverse 3D structural representations with fine-grained subcellular localization annotations carefully curated by domain experts. We evaluate this benchmark using a variety of state-of-the-art sequence-based and structure-based models, showcasing the importance of involving structural features in this task. Furthermore, we explore reweighting and single-label classification strategies to facilitate future investigation on structure-based methods for this task. Lastly, we showcase the powerful interpretability of structure-based methods through a case study on the Golgi apparatus, where we discover a decisive localization pattern $α$-helix from attention mechanisms, demonstrating the potential for bridging the gap with intuitive biological interpretability and paving the way for data-driven discoveries in cell biology.
One Adapts to Any: Meta Reward Modeling for Personalized LLM Alignment
Alignment of Large Language Models (LLMs) aims to align outputs with human preferences, and personalized alignment further adapts models to individual users. This relies on personalized reward models that capture user-specific preferences and automatically provide individualized feedback. However, developing these models faces two critical challenges: the scarcity of feedback from individual users and the need for efficient adaptation to unseen users. We argue that addressing these constraints requires a paradigm shift from fitting data to learn user preferences to learn the process of preference adaptation. To realize this, we propose Meta Reward Modeling (MRM), which reformulates personalized reward modeling as a meta-learning problem. Specifically, we represent each user's reward model as a weighted combination of base reward functions, and optimize the initialization of these weights using a Model-Agnostic Meta-Learning (MAML)-style framework to support fast adaptation under limited feedback. To ensure robustness, we introduce the Robust Personalization Objective (RPO), which places greater emphasis on hard-to-learn users during meta optimization. Extensive experiments on personalized preference datasets validate that MRM enhances few-shot personalization, improves user robustness, and consistently outperforms baselines.