publications

publications by categories in reversed chronological order. generated by jekyll-scholar.

2026

Reward Score Matching: Unifying Reward-based Fine-tuning for Flow and Diffusion Models

Jeongjae Lee, Jinho Chang, Jeongsol Kim, and 1 more author

In arxiv, 2026
PCPO: Proportionate Credit Policy Optimization for Preference Alignment of Image Generation Models

Jeongjae Lee, and Jong Chul Ye

In The Fourteenth International Conference on Learning Representations, 2026

2024

Fast and accurate protein structure search with Foldseek

Michel Kempen, Stephanie S. Kim, Charlotte Tumescheit, and 5 more authors

Nature Biotechnology, 2024

Abs DOI

As structure prediction methods are generating millions of publicly available protein structures, searching these databases is becoming a bottleneck. Foldseek aligns the structure of a query protein against a database by describing tertiary amino acid interactions within proteins as sequences over a structural alphabet. Foldseek decreases computation times by four to five orders of magnitude with 86%, 88% and 133% of the sensitivities of Dali, TM-align and CE, respectively.