Senura Hansaja Wanasekara

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.

Senura Hansaja Wanasekara, Van-Dinh Nguyen, Kok-Seng et al.

Goal-oriented semantic communication (SC) aims to revolutionize communication systems by transmitting only task-essential information. However, current approaches face challenges such as joint training at transceivers, leading to redundant data exchange and reliance on labeled datasets, which limits their task-agnostic utility. To address these challenges, we propose a novel framework called Goal-oriented Invariant Representation-based SC (SC-GIR) for image transmission. Our framework leverages self-supervised learning to extract an invariant representation that encapsulates crucial information from the source data, independent of the specific downstream task. This compressed representation facilitates efficient communication while retaining key features for successful downstream task execution. Focusing on machine-to-machine tasks, we utilize covariance-based contrastive learning techniques to obtain a latent representation that is both meaningful and semantically dense. To evaluate the effectiveness of the proposed scheme on downstream tasks, we apply it to various image datasets for lossy compression. The compressed representations are then used in a goal-oriented AI task. Extensive experiments on several datasets demonstrate that SC-GIR outperforms baseline schemes by nearly 10%,, and achieves over 85% classification accuracy for compressed data under different SNR conditions. These results underscore the effectiveness of the proposed framework in learning compact and informative latent representations.

Long Tan Le, Senura Hansaja Wanasekara, Zerun Niu et al.

Semantic communication (SemCom) has emerged as a promising paradigm for 6G wireless systems by transmitting task-relevant information rather than raw bits, yet existing approaches remain vulnerable to dual sources of uncertainty: semantic misinterpretation arising from imperfect feature extraction and transmission-level perturbations from channel noise. Current deep learning based SemCom systems typically employ domain-specific architectures that lack robustness guarantees and fail to generalize across diverse noise conditions, adversarial attacks, and out-of-distribution data. In this paper, a novel and generalized semantic communication framework called WaSeCom is proposed to systematically address uncertainty and enhance robustness. In particular, Wasserstein distributionally robust optimization is employed to provide resilience against semantic misinterpretation and channel perturbations. A rigorous theoretical analysis is performed to establish the robust generalization guarantees of the proposed framework. Experimental results on image and text transmission demonstrate that WaSeCom achieves improved robustness under noise and adversarial perturbations. These results highlight its effectiveness in preserving semantic fidelity across varying wireless conditions.