Graph-based protein function analysis is powerful, but protein-protein interaction (PPI) networks exist for only a small fraction of animal and plant genomes. We present LoGoPPI, which infers PPIs from sequence by combining bi-encoder global protein representation with local residue-level late interaction. LoGoPPI matches or exceeds state-of-the-art PLM-based cross-encoders while achieving orders-of-magnitude faster inference, up to ∼1,500-fold, and its local branch provides residue-level signals associated with interaction interfaces and structurally flexible regions. This efficiency enables practical proteome-wide PPI reconstruction at scales prohibitive for cross-encoder models, potentially extending interactome mapping to tens of thousands of animal and plant species. LoGoPPI thus provides a scalable framework for comparative and functional analysis of protein networks across diverse taxa.
The comparison of adopter and non-adopter sample reveals three potential adoption inhibitor, security, data privacy, and portability, which underlines the importance of the technical and security perspectives for research investigating the adoption of technology.
Nattakarn Phaphoom, Xiaofeng Wang, S. Samuel et al.· Journal of Systems and Softw...· 111 citations· ⚡8
This study investigates how Lean internal startup facilitates software product innovation in large companies and identifies its enablers and inhibitors, and shows the potential of the method-in-action framework to investigate the Lean startup approach in non-startup context.
Henry Edison, Nina M. Smørsgård, Xiaofeng Wang et al.· Journal of Systems and Softw...· 78 citations· ⚡6
This paper highlights the challenges to conduct proper affect-related studies with psychology, provides a comprehensive literature review in affect theory, and proposes guidelines for conducting psychoempirical software engineering.
D. Graziotin, Xiaofeng Wang, P. Abrahamsson· SSE@SIGSOFT FSE· 56 citations· ⚡4
This study conducts a multiple case study on twenty European software startups and proposes a prototype-centric learning model in early stage software startups, and identifies factors that occur as barriers but also facilitators for prototyping in earlystage software startups.
Anh Nguyen-Duc, Xiaofeng Wang, P. Abrahamsson· International Conference on...· 44 citations· ⚡5
It is demonstrated that linker-free PROTACs can outperform traditional designs, marking a paradigm shift in PROTAC development for targeted protein degradation.
Pinal, a 16-billion-parameter foundation model that produces protein candidates from natural-language functional descriptions, supports natural language as a high-level interface for candidate generation in protein design, enabling programmable exploration with reduced reliance on manually specified structural or seque...
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
