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q-bio.QM2025
scTREAT: Latent Diffusion for Single-Cell Drug-Response Prediction
Zhaokang Liang, Shuyang Zhuang, Xiaoran Jiao +3
Generating drug-induced transcriptional responses requires a model to account for cellular background together with molecular identity and dose. We present scTREAT, the first diffu…
cs.LG2025
Evolutionary Profiles for Protein Fitness Prediction
Jigang Fan, Xiaoran Jiao, Shengdong Lin +5
Predicting the fitness impact of mutations is central to protein engineering but constrained by limited assays relative to the size of sequence space. Protein language models (pLMs…
cs.LG2025
Revisiting Convolution Architecture in the Realm of DNA Foundation Models
Yu Bo, Weian Mao, Yanjun Shao +6
In recent years, a variety of methods based on Transformer and state space model (SSM) architectures have been proposed, advancing foundational DNA language models. However, there…