Abstract Multimodal protein language models (PLMs) deliver strong performance on mutation-effect prediction, but training such models from scratch demands substantial computational resources. In this paper, we propose a fine-tuning framework called InstructPLM-mu and investigate the question: Can a pretrained sequence-...
Jun-De Xu, Ya-Pin Shi, Li-Jun Lang et al.· Briefings in Bioinformatics· 0 citations
An injectively aligned leave-one-cell-out protocol over support x operation grids and SO-OPF, a readout that factors cell energy into support salience and a competitive operation posterior, and a readout that factors cell energy into support salience and a competitive operation posterior are introduced.
Zhong-Yao Wang, Wan-Li Ouyang, Tao-Yong Cui et al.· 0 citations
JEPA-Anything, a domain-agnostic framework based on orthogonal predictive factorization (OPF), achieves the lowest one-step and 100-step molecular errors among compared methods in all four systems and supports a common factorized predictive principle across heterogeneous worlds.
Tao-Yong Cui, Zhong-Yao Wang, Xin-Yue Xu et al.· 2 citations
Immune therapies act across cell-intrinsic programs, tissue ecosystems, and patient-specific immune states, yet most predictors address these scales separately. We used a governed evolutionary AI Scientist to construct the Immune World Model, an action-conditioned model that learns how interventions move immune states...
Tao-Yong Cui, Xi Wang, Zong-Hang Li et al.· 0 citations
Method, a latent world-modeling framework based on orthogonal predictive factorization, is introduced, a latent world-modeling framework based on orthogonal predictive factorization that can be used by a readout, decoder, planner, or autoregressive rollout of an underlying system.
The results show that alternative transcript diversity extensively enters translation-supported proteoform space and establish a systematic link between transcript variation and protein functional diversification.
Felicia T. Jiang, Dengwang Chen, Ziwei Wang et al.· bioRxiv· 1 citation
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