Penglei Wang

Qi Si, Penglei Wang, Yushuai Wu et al.

Predicting spatial gene expression from routine H\&E enables large-scale molecular profiling, yet current models treat this as isolated pointwise tasks, thereby overlooking essential biological structures like gene coordination and spatial distribution. To preserve these relationships, we introduce \textbf{FLAG}, a diffusion-based framework that redefines this task as structured distribution modeling. At the same time, we identify the critical \textbf{Gene Dimension Curse}, where joint modeling gene expression and their spatial interactions fail in high-dimensional spaces, and FLAG solves this challenge by integrating a spatial graph encoder for topological consistency and utilizing Gene Foundation Model (GFM) alignment for gene-gene fidelity in the generation process. To rigorously assess model performance, we propose a set of novel structural evaluation metrics, including Gene Structural Correlation (\textbf{GSC}) and Spatial Structural Correlation (\textbf{SSC}). Our experiments demonstrate that FLAG is highly competitive in traditional accuracy (PCC/MSE) while achieving significantly enhanced structural fidelity in capturing both gene-gene and gene-spatial relationships. The code is available at https://github.com/darkflash03/FLAG.

Qi Si, Xuyang Liu, Penglei Wang et al.

RNA inverse folding, designing sequences to form specific 3D structures, is critical for therapeutics, gene regulation, and synthetic biology. Current methods, focused on sequence recovery, struggle to address structural objectives like secondary structure consistency (SS), minimum free energy (MFE), and local distance difference test (LDDT), leading to suboptimal structural accuracy. To tackle this, we propose a reinforcement learning (RL) framework integrated with a latent diffusion model (LDM). Drawing inspiration from the success of diffusion models in RNA inverse folding, which adeptly model complex sequence-structure interactions, we develop an LDM incorporating pre-trained RNA-FM embeddings from a large-scale RNA model. These embeddings capture co-evolutionary patterns, markedly improving sequence recovery accuracy. However, existing approaches, including diffusion-based methods, cannot effectively handle non-differentiable structural objectives. By contrast, RL excels in this task by using policy-driven reward optimization to navigate complex, non-gradient-based objectives, offering a significant advantage over traditional methods. In summary, we propose the Step-wise Optimization of Latent Diffusion Model (SOLD), a novel RL framework that optimizes single-step noise without sampling the full diffusion trajectory, achieving efficient refinement of multiple structural objectives. Experimental results demonstrate SOLD surpasses its LDM baseline and state-of-the-art methods across all metrics, establishing a robust framework for RNA inverse folding with profound implications for biotechnological and therapeutic applications.

Yaowei Jin, Junjie Wang, Cheng Cao et al.

Structure-Based Drug Design (SBDD) aims to discover bioactive ligands. Conventional approaches construct probability paths separately in Euclidean and probabilistic spaces for continuous atomic coordinates and discrete chemical categories, leading to a mismatch with the underlying statistical manifolds. We address this issue from an information-geometric perspective by modeling molecules as composite exponential-family distributions and defining generative flows along exponential geodesics under the Fisher-Rao metric. To avoid the instantaneous trajectory collapse induced by geodesics directly targeting Dirac distributions, we propose Evolving Exponential Geodesic Flow for SBDD (EvoEGF-Mol), which replaces static Dirac targets with dynamically concentrating distributions, ensuring stable training via a progressive-parameter-refinement architecture. Our model approaches a reference-level PoseBusters passing rate (93.4%) on CrossDock, demonstrating remarkable geometric precision and interaction fidelity, while outperforming baselines on real-world MolGenBench tasks by recovering bioactive scaffolds and generating candidates that meet established MedChem filters.

Xinze Li, Penglei Wang, Tianfan Fu et al.

Structure-based drug design (SBDD), which aims to generate molecules that can bind tightly to the target protein, is an essential problem in drug discovery, and previous approaches have achieved initial success. However, most existing methods still suffer from invalid local structure or unrealistic conformation issues, which are mainly due to the poor leaning of bond angles or torsional angles. To alleviate these problems, we propose AUTODIFF, a diffusion-based fragment-wise autoregressive generation model. Specifically, we design a novel molecule assembly strategy named conformal motif that preserves the conformation of local structures of molecules first, then we encode the interaction of the protein-ligand complex with an SE(3)-equivariant convolutional network and generate molecules motif-by-motif with diffusion modeling. In addition, we also improve the evaluation framework of SBDD by constraining the molecular weights of the generated molecules in the same range, together with some new metrics, which make the evaluation more fair and practical. Extensive experiments on CrossDocked2020 demonstrate that our approach outperforms the existing models in generating realistic molecules with valid structures and conformations while maintaining high binding affinity.