6 papers
Genome-Factory: A Library for Tuning, Deploying, and Interpreting Genomic Foundation Models
Weimin Wu, Xuefeng Song, Yibo Wen +5
We introduce Genome-Factory, the first integrated Python library for tuning, deploying, and interpreting genomic foundation models. Our core contribution is to simplify and unify t…
On Flow Matching KL Divergence
Maojiang Su, Jerry Yao-Chieh Hu, Sophia Pi +1
We derive a deterministic, non-asymptotic upper bound on the Kullback-Leibler (KL) divergence of the flow-matching distribution approximation. In particular, if the flow-matc…
NdLinear: Preserving Multi-Dimensional Structure for Parameter-Efficient Neural Networks
Alex Reneau, Jerry Yao-Chieh Hu, Zhongfang Zhuang +6
In deep learning, processing multidimensional inputs (e.g., images, medical scans, and time series) is an important task that often requires flattening the inputs. We introduce $\m…
POLO: Preference-Guided Multi-Turn Reinforcement Learning for Lead Optimization
Ziqing Wang, Yibo Wen, William Pattie +6
Lead optimization in drug discovery requires efficiently navigating vast chemical space through iterative cycles to enhance molecular properties while preserving structural similar…
Are Hallucinations Bad Estimations?
Hude Liu, Jerry Yao-Chieh Hu, Jennifer Yuntong Zhang +2
We formalize hallucinations in generative models as failures to link an estimate to any plausible cause. Under this interpretation, we show that even loss-minimizing optimal estima…
Latent Variable Estimation in Bayesian Black-Litterman Models
Thomas Y. L. Lin, Jerry Yao-Chieh Hu, Paul W. Chiou +1
We revisit the Bayesian Black-Litterman (BL) portfolio model and remove its reliance on subjective investor views. Classical BL requires an investor "view": a forecast vector a…