Ken-Tye Yong

Minh-Duong Nguyen, Senura Hansaja, Le-Tuan Nguyen et al.

Federated Unlearning (FUL) aims to remove specific participants' data contributions from a trained Federated Learning model, thereby ensuring data privacy and compliance with regulatory requirements. Despite its potential, progress in FUL has been limited due to several challenges, including the cross-client knowledge inaccessibility and high computational and communication costs. To overcome these challenges, we propose Federated On-server Unlearning (FOUL), a novel framework that comprises two key stages. The learning-to-unlearn stage serves as a preparatory learning phase, during which the model identifies and encodes the key features associated with the forget clients. This stage is communication-efficient and establishes the basis for the subsequent unlearning process. Subsequently, on-server knowledge aggregation phase aims to perform the unlearning process at the server without requiring access to client data, thereby preserving both efficiency and privacy. We introduce a new data setting for FUL, which enables a more transparent and rigorous evaluation of unlearning. To highlight the effectiveness of our approach, we propose a novel evaluation metric termed time-to-forget, which measures how quickly the model achieves optimal unlearning performance. Extensive experiments conducted on three datasets under various unlearning scenarios demonstrate that FOUL outperforms the Retraining in FUL. Moreover, FOUL achieves competitive or superior results with significantly reduced time-to-forget, while maintaining low communication and computation costs.

Senura Hansaja Wanasekara, Minh-Duong Nguyen, Xiaochen Liu et al.

Generative modeling has become a central paradigm in protein research, extending machine learning beyond structure prediction toward sequence design, backbone generation, inverse folding, and biomolecular interaction modeling. However, the literature remains fragmented across representations, model classes, and task formulations, making it difficult to compare methods or identify appropriate evaluation standards. This survey provides a systematic synthesis of generative AI in protein research, organized around (i) foundational representations spanning sequence, geometric, and multimodal encodings; (ii) generative architectures including $\mathrm{SE}(3)$-equivariant diffusion, flow matching, and hybrid predictor-generator systems; and (iii) task settings from structure prediction and de novo design to protein-ligand and protein-protein interactions. Beyond cataloging methods, we compare assumptions, conditioning mechanisms, and controllability, and we synthesize evaluation best practices that emphasize leakage-aware splits, physical validity checks, and function-oriented benchmarks. We conclude with critical open challenges: modeling conformational dynamics and intrinsically disordered regions, scaling to large assemblies while maintaining efficiency, and developing robust safety frameworks for dual-use biosecurity risks. By unifying architectural advances with practical evaluation standards and responsible development considerations, this survey aims to accelerate the transition from predictive modeling to reliable, function-driven protein engineering.