4 papers
Language Models for Controllable DNA Sequence Design
Xingyu Su, Xiner Li, Yuchao Lin +3
We consider controllable DNA sequence design, where sequences are generated by conditioning on specific biological properties. While language models (LMs) such as GPT and BERT have…
Dynamic Search for Inference-Time Alignment in Diffusion Models
Xiner Li, Masatoshi Uehara, Xingyu Su +5
Diffusion models have shown promising generative capabilities across diverse domains, yet aligning their outputs with desired reward functions remains a challenge, particularly in…
Reward-Guided Iterative Refinement in Diffusion Models at Test-Time with Applications to Protein and DNA Design
Masatoshi Uehara, Xingyu Su, Yulai Zhao +5
To fully leverage the capabilities of diffusion models, we are often interested in optimizing downstream reward functions during inference. While numerous algorithms for reward-gui…
Learning to Discover Regulatory Elements for Gene Expression Prediction
Xingyu Su, Haiyang Yu, Degui Zhi +1
We consider the problem of predicting gene expressions from DNA sequences. A key challenge of this task is to find the regulatory elements that control gene expressions. Here, we i…