Guanlue Li

Weiqi Zhang, Guanlue Li, Jianheng Tang et al.

Data imputation is a crucial task due to the widespread occurrence of missing data. Many methods adopt a two-step approach: initially crafting a preliminary imputation (the "draft") and then refining it to produce the final missing data imputation result, commonly referred to as "draft-then-refine". In our study, we examine this prevalent strategy through the lens of graph Dirichlet energy. We observe that a basic "draft" imputation tends to decrease the Dirichlet energy. Therefore, a subsequent "refine" step is necessary to restore the overall energy balance. Existing refinement techniques, such as the Graph Convolutional Network (GCN), often result in further energy reduction. To address this, we introduce a new framework, the Graph Laplacian Pyramid Network (GLPN). GLPN incorporates a U-shaped autoencoder and residual networks to capture both global and local details effectively. Through extensive experiments on multiple real-world datasets, GLPN consistently outperforms state-of-the-art methods across three different missing data mechanisms. The code is available at https://github.com/liguanlue/GLPN.

Fang Wu, Weihao Xuan, Heli Qi et al.

Deep learning in \emph{de novo} protein design has achieved atomic-level fidelity. However, existing models remain largely non-deliberative: they directly synthesize molecular geometries without explicitly reasoning about which residues or interactions are functionally essential. As a result, design decisions are entangled with continuous sampling dynamics, limiting interpretability, controllability, and systematic reuse of biochemical knowledge. We introduce \textbf{Proteo-R1}, a reasoning-guided protein design framework that explicitly decouples \emph{molecular understanding} from \emph{geometric generation}. Proteo-R1 adopts a dual-expert architecture in which a multimodal large language model (MLLM) serves as an \emph{understanding expert}, analyzing protein sequences, structures, and textual context to identify key functional residues that govern binding and specificity. These residue-level decisions are then passed as hard constraints to a separate diffusion-based \emph{generation expert}, which performs conditional co-design while respecting the fixed interaction anchors. This factorization mirrors how human experts approach molecular engineering: first, reasoning about critical interactions, then optimizing geometry subject to those constraints. By operationalizing reasoning as explicit residue-level commitments rather than latent textual guidance, Proteo-R1 achieves stable, interpretable, and modular integration of LLM reasoning with state-of-the-art geometric generative models. Code, data, and demos are available at https://smiles724.github.io/r1/.

Guanlue Li, Chenran Jiang, Ziqi Gao et al.

Effective generation of molecular structures, or new chemical entities, that bind to target proteins is crucial for lead identification and optimization in drug discovery. Despite advancements in atom- and motif-wise deep learning models for 3D molecular generation, current methods often struggle with validity and reliability. To address these issues, we develop the Atom-Motif Consistency Diffusion Model (AMDiff), utilizing a joint-training paradigm for multi-view learning. This model features a hierarchical diffusion architecture that integrates both atom- and motif-level views of molecules, allowing for comprehensive exploration of complementary information. By leveraging classifier-free guidance and incorporating binding site features as conditional inputs, AMDiff ensures robust molecule generation across diverse targets. Compared to existing approaches, AMDiff exhibits superior validity and novelty in generating molecules tailored to fit various protein pockets. Case studies targeting protein kinases, including Anaplastic Lymphoma Kinase (ALK) and Cyclin-dependent kinase 4 (CDK4), demonstrate the model's capability in structure-based de novo drug design. Overall, AMDiff bridges the gap between atom-view and motif-view drug discovery and speeds up the process of target-aware molecular generation.