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Dongbo Bu

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5 papers

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TMLR Journal 2026 Journal Article

GGFlow: A Graph Flow Matching Method with Efficient Optimal Transport

Xiaoyang Hou
Tian Zhu
Milong Ren
Dongbo Bu
Xin Gao
Chunming Zhang
Shiwei Sun

Generating graph-structured data is crucial in various domains but remains challenging due to the complex interdependencies between nodes and edges. While diffusion models have demonstrated their superior generative capabilities, they often suffer from unstable training and inefficient sampling. To enhance generation performance and training stability, we propose GGFlow, a discrete flow matching generative model incorporating an efficient optimal transport for graph structures and it incorporates an edge-augmented graph transformer to enable direct communications among edges. Additionally, GGFlow introduces a novel goal-guided generation framework to control the generative trajectory of our model towards desired properties. GGFlow demonstrates superior performance on both unconditional and conditional generation tasks, outperforming existing baselines and underscoring its effectiveness and potential for wider application.

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NeurIPS Conference 2024 Conference Paper

NeuralSteiner: Learning Steiner Tree for Overflow-avoiding Global Routing in Chip Design

Ruizhi Liu
Zhisheng Zeng
Shizhe Ding
Jingyan Sui
Xingquan Li
Dongbo Bu

Global routing plays a critical role in modern chip design. The routing paths generated by global routers often form a rectilinear Steiner tree (RST). Recent advances from the machine learning community have shown the power of learning-based route generation; however, the yielded routing paths by the existing approaches often suffer from considerable overflow, thus greatly hindering their application in practice. We propose NeuralSteiner, an accurate approach to overflow-avoiding global routing in chip design. The key idea of NeuralSteiner approach is to learn Steiner trees: we first predict the locations of highly likely Steiner points by adopting a neural network considering full-net spatial and overflow information, then select appropriate points by running a graph-based post-processing algorithm, and finally connect these points with the input pins to yield overflow-avoiding RSTs. NeuralSteiner offers two advantages over previous learning-based models. First, by using the learning scheme, NeuralSteiner ensures the connectivity of generated routes while significantly reducing congestion. Second, NeuralSteiner can effectively scale to large nets and transfer to unseen chip designs without any modifications or fine-tuning. Extensive experiments over public large-scale benchmarks reveal that, compared with the state-of-the-art deep generative methods, NeuralSteiner achieves up to a 99. 8\% reduction in overflow while speeding up the generation and maintaining a slight wirelength loss within only 1. 8\%.

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NeurIPS Conference 2023 Conference Paper

Accurate Interpolation for Scattered Data through Hierarchical Residual Refinement

Shizhe Ding
Boyang Xia
Dongbo Bu

Accurate interpolation algorithms are highly desired in various theoretical and engineering scenarios. Unlike the traditional numerical algorithms that have exact zero-residual constraints on observed points, the neural network-based interpolation methods exhibit non-zero residuals at these points. These residuals, which provide observations of an underlying residual function, can guide predicting interpolation functions, but have not been exploited by the existing approaches. To fill this gap, we propose Hierarchical INTerpolation Network (HINT), which utilizes the residuals on observed points to guide target function estimation in a hierarchical fashion. HINT consists of several sequentially arranged lightweight interpolation blocks. The first interpolation block estimates the main component of the target function, while subsequent blocks predict the residual components using observed points residuals of the preceding blocks. The main component and residual components are accumulated to form the final interpolation results. Furthermore, under the assumption that finer residual prediction requires a more focused attention range on observed points, we utilize hierarchical local constraints in correlation modeling between observed and target points. Extensive experiments demonstrate that HINT outperforms existing interpolation algorithms significantly in terms of interpolation accuracy across a wide variety of datasets, which underscores its potential for practical scenarios.

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NeurIPS Conference 2023 Conference Paper

Predicting mutational effects on protein-protein binding via a side-chain diffusion probabilistic model

Shiwei Liu
Tian Zhu
Milong Ren
Chungong Yu
Dongbo Bu
Haicang Zhang

Many crucial biological processes rely on networks of protein-protein interactions. Predicting the effect of amino acid mutations on protein-protein binding is important in protein engineering, including therapeutic discovery. However, the scarcity of annotated experimental data on binding energy poses a significant challenge for developing computational approaches, particularly deep learning-based methods. In this work, we propose SidechainDiff, a novel representation learning-based approach that leverages unlabelled experimental protein structures. SidechainDiff utilizes a Riemannian diffusion model to learn the generative process of side-chain conformations and can also give the structural context representations of mutations on the protein-protein interface. Leveraging the learned representations, we achieve state-of-the-art performance in predicting the mutational effects on protein-protein binding. Furthermore, SidechainDiff is the first diffusion-based generative model for side-chains, distinguishing it from prior efforts that have predominantly focused on the generation of protein backbone structures.

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TCS Journal 2009 Journal Article

Finding compact structural motifs

Dongbo Bu
Ming Li
Shuai Cheng Li
Jianbo Qian
Jinbo Xu

Protein structural motif detection has important applications in structural genomics. Compared with sequence motifs, structural motifs are more sensitive in revealing the evolutionary relationships among proteins. A variety of algorithms have been proposed to attack this problem. However, they are either heuristic without theoretical performance guarantee, or inefficient due to employing exhaustive search strategies. This paper studies a reasonably restricted version of this problem: the compact structural motif problem. We prove that this restricted version is still NP-hard, and we present a polynomial-time approximation scheme to solve it. This is the first approximation algorithm with a guaranteed ratio for the protein structural motif problem. 1 1 A preliminary version of this paper appeared in CPM’2007.

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