8 citations · 8 across the 8 of their papers we have counts for
9 papers
Budgeted Quotient-Residual Guidance for Frozen Pocket-Conditioned Molecular Diffusion
Xinyu Wang, Jinbo Bi, Minghu Song
Pocket-conditioned molecular diffusion updates ambient atom coordinates, but many lead-optimization objectives are expressed on quotient features such as distances, contacts, and a…
PocketVE: Stable and Property-Guided Structure-Based Drug Design with Variance-Exploding Diffusion
Peining Zhang, Jinbo Bi
Protein-conditioned 3D molecule generation is a central challenge in structure-based drug design, requiring a balance between pocket compatibility, molecular properties, and physic…
Q-Steer: Action-Value Guidance for Molecular Policy Optimization
Xinyu Wang, Jinbo Bi, Minghu Song
Oracle-limited molecular optimization gives reward only after a complete molecule is generated, while each rollout requires many local next-token decisions. This delayed-feedback i…
Characterizing the Discrete Geometry of ReLU Networks
Blake B. Gaines, Jinbo Bi
It is well established that ReLU networks define continuous piecewise-linear functions, and that their linear regions are polyhedra in the input space. These regions form a complex…
SIGMA: Semantic Identifier Grouping for Molecular Autoregression
Xinyu Wang, Fei Dou, Jinbo Bi +1
Autoregressive molecular models assign probability to molecular serializations even though chemical identity is invariant to serialization. Equivalent serializations can therefore…
VEDA: Generation of 3D Molecules via Variance-Exploding Diffusion with Annealing
Peining Zhang, Jinbo Bi, Minghu Song
Diffusion models show promise for 3D molecular generation, but face a fundamental trade-off between sampling efficiency and conformational accuracy. While flow-based models are fas…
Zero-Shot Transfer Capabilities of the Sundial Foundation Model for Leaf Area Index Forecasting
Peining Zhang, Hongchen Qin, Haochen Zhang +3
This work investigates the zero-shot forecasting capability of time series foundation models for Leaf Area Index (LAI) forecasting in agricultural monitoring. Using the HiQ dataset…
Unraveling the Potential of Diffusion Models in Small Molecule Generation
Peining Zhang, Daniel Baker, Minghu Song +1
Generative AI presents chemists with novel ideas for drug design and facilitates the exploration of vast chemical spaces. Diffusion models (DMs), an emerging tool, have recently at…
Leveraging Partial SMILES Validation Scheme for Enhanced Drug Design in Reinforcement Learning Frameworks
Xinyu Wang, Jinbo Bi, Minghu Song
SMILES-based molecule generation has emerged as a powerful approach in drug discovery. Deep reinforcement learning (RL) using large language model (LLM) has been incorporated into…