Author name cluster

Hanlin Wu

Possible papers associated with this exact author name in Arrow. This page groups case-insensitive exact name matches and is not a full identity disambiguation profile.

4 papers

2 author rows

ICLR Conference 2025 Conference Paper

A Periodic Bayesian Flow for Material Generation

Hanlin Wu
Yuxuan Song
Jingjing Gong
Ziyao Cao
Yawen Ouyang
Jianbing Zhang
Hao Zhou 0012
Wei-Ying Ma

Generative modeling of crystal data distribution is an important yet challenging task due to the unique periodic physical symmetry of crystals. Diffusion-based methods have shown early promise in modeling crystal distribution. More recently, Bayesian Flow Networks were introduced to aggregate noisy latent variables, resulting in a variance-reduced parameter space that has been shown to be advantageous for modeling Euclidean data distributions with structural constraints (Song, et al.,2023). Inspired by this, we seek to unlock its potential for modeling variables located in non-Euclidean manifolds e.g. those within crystal structures, by overcoming challenging theoretical issues. We introduce CrysBFN, a novel crystal generation method by proposing a periodic Bayesian flow, which essentially differs from the original Gaussian-based BFN by exhibiting non-monotonic entropy dynamics. To successfully realize the concept of periodic Bayesian flow, CrysBFN integrates a new entropy conditioning mechanism and empirically demonstrates its significance compared to time-conditioning. Extensive experiments over both crystal ab initio generation and crystal structure prediction tasks demonstrate the superiority of CrysBFN, which consistently achieves new state-of-the-art on all benchmarks. Surprisingly, we found that CrysBFN enjoys a significant improvement in sampling efficiency, e.g., 200x speedup (10 v.s. 2000 steps network forwards) compared with previous Diffusion-based methods on MP-20 dataset.

Details

NeurIPS Conference 2025 Conference Paper

Accelerating 3D Molecule Generative Models with Trajectory Diagnosis

Zhilong Zhang
Yuxuan Song
Yichun Wang
Jingjing Gong
Hanlin Wu
Dongzhan Zhou
Hao Zhou
Wei-Ying Ma

Geometric molecule generative models have found expanding applications across various scientific domains, but their generation inefficiency has become a critical bottleneck. Through a systematic investigation of the generative trajectory, we discover a unique challenge for molecule geometric graph generation: generative models require determining the permutation order of atoms in the molecule before refining its atomic feature values. Based on this insight, we decompose the generation process into permutation phase and adjustment phase, and propose a geometric-informed prior and consistency parameter objective to accelerate each phase. Extensive experiments demonstrate that our approach achieves competitive performance with approximately 10 sampling steps, 7. 5 × faster than previous state-of-the-art models and approximately 100 × faster than diffusion-based models, offering a significant step towards scalable molecular generation.

PDF Details

NeurIPS Conference 2025 Conference Paper

MOF-BFN: Metal-Organic Frameworks Structure Prediction via Bayesian Flow Networks

Rui Jiao
Hanlin Wu
Wenbing Huang
Yuxuan Song
Yawen Ouyang
Yu Rong
Tingyang Xu
Pengju Wang

Metal-Organic Frameworks (MOFs) have attracted considerable attention due to their unique properties including high surface area and tunable porosity, and promising applications in catalysis, gas storage, and drug delivery. Structure prediction for MOFs is a challenging task, as these frameworks are intrinsically periodic and hierarchically organized, where the entire structure is assembled from building blocks like metal nodes and organic linkers. To address this, we introduce MOF-BFN, a novel generative model for MOF structure prediction based on Bayesian Flow Networks (BFNs). Given the local geometry of building blocks, MOF-BFN jointly predicts the lattice parameters, as well as the positions and orientations of all building blocks within the unit cell. In particular, the positions are modelled in the fractional coordinate system to naturally incorporate the periodicity. Meanwhile, the orientations are modeled as unit quaternions sampled from learned Bingham distributions via the proposed Bingham BFN, enabling effective orientation generation on the 4D unit hypersphere. Experimental results demonstrate that MOF-BFN achieves state-of-the-art performance across multiple tasks, including structure prediction, geometric property evaluation, and de novo generation, offering a promising tool for designing complex MOF materials.

PDF Details

NeurIPS Conference 2025 Conference Paper

Rationalized All-Atom Protein Design with Unified Multi-Modal Bayesian Flow

Hanlin Wu
Yuxuan Song
Zhe Zhang
Zhilong Zhang
Hao Zhou
Wei-Ying Ma
Jingjing Liu

Designing functional proteins is a critical yet challenging problem due to the intricate interplay between backbone structures, sequences, and side-chains. Current approaches often decompose protein design into separate tasks, which can lead to accumulated errors, while recent efforts increasingly focus on all-atom protein design. However, we observe that existing all-atom generation approaches suffering from an information shortcut issue, where models inadvertently infer sequences from side-chain information, compromising their ability to accurately learn sequence distributions. To address this, we introduce a novel rationalized information flow strategy to eliminate the information shortcut. Furthermore, motivated by the advantages of Bayesian flows over differential equation–based methods, we propose the first Bayesian flow formulation for protein backbone orientations by recasting orientation modeling as an equivalent hyperspherical generation problem with antipodal symmetry. To validate, our method delivers consistently exceptional performance in both peptide and antibody design tasks.

PDF Details