Protein inverse folding aims to recover amino acid sequences for a given 3D protein structure, underpinning broad applications such as enzyme engineering and drug discovery.Current methods often follow a serial pipeline, in which a structure encoder predicts a coarse sequence, which is then refined by protein language models (PLMs). However, because PLMs only perform post-hoc sequence edits, the refinement is bounded by the quality of upstream predictions.Thanks to recent multimodal protein language models (MPLMs), we could directly encode structure to generate sequences with pretrained structural knowledge, but we observe that they are not effective for inverse folding. Therefore, we introduce a symmetric dual-path architecture that both leverages PLMs for pretrained sequence evolution knowledge and MPLMs for pretrained structural knowledge to iteratively guide protein sequence generation.Through extensive experiments across standard protein inverse folding benchmarks, our method achieves state-of-the-art performance, surpassing prior approaches, and ablation studies validate the rationale of our symmetric design, revealing a promising direction for the community.
GAOKAO-Bench is introduced, an intuitive benchmark that employs questions from the Chinese GAOKAO examination as test samples, including both subjective and objective questions that contribute a robust evaluation benchmark for future large language models and offers valuable insights into the advantages and limitations of such models.
Xiaotian Zhang, Chun-yan Li, Yi Zong et al.· arXiv.org· 216 citations· ⚡17
This work investigates the possibilities of using LLMs in a resume screening setting via a document retrieval framework that simulates job candidate selection and finds that the MTEs are biased, significantly favoring White-associated names in 85% of cases and female-associated names in only 11.1% of cases.
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
Empirically, PRISM reduces the end-to-end time for data selection and model tuning to just 30% of conventional pipelines, and achieves this efficiency while simultaneously enhancing performance, surpassing models fine-tuned on the full dataset across eight multimodal and three language understanding benchmarks.
Jinhe Bi, Yifan Wang, Danqi Yan et al.· arXiv.org· 73 citations· ⚡4
The method, ECCOLA, is presented, which aims at making the high-level AI ethics principles more practical, making it possible for developers to more easily implement them in practice.
Ville Vakkuri, Kai-Kristian Kemell, P. Abrahamsson· EUROMICRO Conference on Soft...· 64 citations· ⚡6
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.
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