Jiayang Chen

Yifan Wu, Jiyue Jiang, Xichen Ye et al.

Biological foundation models (BioFMs), pretrained on large-scale biological sequences, have recently shown strong potential in providing meaningful representations for diverse downstream bioinformatics tasks. However, such models often rely on millions to billions of training sequences and billions of parameters, resulting in prohibitive computational costs and significant barriers to reproducibility and accessibility, particularly for academic labs. To address these challenges, we investigate the feasibility of data pruning for BioFM pretraining and propose a post-hoc influence-guided data pruning framework tailored to biological domains. Our approach introduces a subset-based self-influence formulation that enables efficient estimation of sample importance at low computational cost, and builds upon it two simple yet effective selection strategies, namely Top-k Influence (Top I) and Coverage-Centric Influence (CCI). We empirically validate our method on two representative BioFMs, RNA-FM and ESM-C. For RNA, our framework consistently outperforms random selection baselines under an extreme pruning rate of over 99 percent, demonstrating its effectiveness. Furthermore, we show the generalizability of our framework on protein-related tasks using ESM-C. In particular, our coreset even outperforms random subsets that are ten times larger in both RNA and protein settings, revealing substantial redundancy in biological sequence datasets. These findings underscore the potential of influence-guided data pruning to substantially reduce the computational cost of BioFM pretraining, paving the way for more efficient, accessible, and sustainable biological AI research.

Daniel Jason Tan, Jiayang Chen, Dilruk Perera et al.

ICU enteral feeding remains sub-optimal due to limited personalization and uncertainty about appropriate calorie, protein, and fluid targets, particularly under rapidly changing metabolic demands and heterogeneous patient responses. This study introduces DeepEN, a reinforcement learning (RL)-based framework that personalizes enteral nutrition (EN) dosing for critically ill patients using electronic health record data. DeepEN was trained on over 11,000 ICU patients from the MIMIC-IV database to generate 4-hourly, patient-specific targets for caloric, protein, and fluid intake. The model's state space integrates demographics, comorbidities, vital signs, laboratory results, and prior interventions relevant to nutritional management, while its reward function balances short-term physiological and nutrition-related goals with long-term survival. A dueling double deep Q-network with Conservative Q-Learning regularization is used to ensure safe and reliable policy learning from retrospective data. DeepEN achieved a 3.7 $\pm$ 0.17 percentage-point absolute reduction in estimated mortality compared with the clinician policy (18.8% vs 22.5%) and higher expected returns compared with guideline-based dosing (11.89 vs 8.11), with improvements in key nutritional biomarkers. U-shaped associations between deviations from clinician dosing and mortality suggest that the learned policy aligns with high-value clinician actions while diverging from suboptimal ones. These findings demonstrate the feasibility of conservative offline RL for individualized EN therapy and suggest that data-driven personalization may improve outcomes beyond guideline- or heuristic-based approaches.