Chaolong Ying

Zihan Zhou, Ruiying Liu, Chaolong Ying et al.

Molecular conformation generation, a critical aspect of computational chemistry, involves producing the three-dimensional conformer geometry for a given molecule. Generating molecular conformation via diffusion requires learning to reverse a noising process. Diffusion on inter-atomic distances instead of conformation preserves SE(3)-equivalence and shows superior performance compared to alternative techniques, whereas related generative modelings are predominantly based upon heuristical assumptions. In response to this, we propose a novel molecular conformation generation approach driven by the observation that the disintegration of a molecule can be viewed as casting increasing force fields to its composing atoms, such that the distribution of the change of inter-atomic distance shifts from Gaussian to Maxwell-Boltzmann distribution. The corresponding generative modeling ensures a feasible inter-atomic distance geometry and exhibits time reversibility. Experimental results on molecular datasets demonstrate the advantages of the proposed shifting distribution compared to the state-of-the-art.

Xuanhao Pan, Chenguang Wang, Chaolong Ying et al.

The ``Heatmap + Monte Carlo Tree Search (MCTS)'' paradigm has recently emerged as a prominent framework for solving the Travelling Salesman Problem (TSP). While considerable effort has been devoted to enhancing heatmap sophistication through advanced learning models, this paper rigorously examines whether this emphasis is justified, critically assessing the relative impact of heatmap complexity versus MCTS configuration. Our extensive empirical analysis across diverse TSP scales, distributions, and benchmarks reveals two pivotal insights: 1) The configuration of MCTS strategies significantly influences solution quality, underscoring the importance of meticulous tuning to achieve optimal results and enabling valid comparisons among different heatmap methodologies. 2) A rudimentary, parameter-free heatmap based on the intrinsic $k$-nearest neighbor structure of TSP instances, when coupled with an optimally tuned MCTS, can match or surpass the performance of more sophisticated, learned heatmaps, demonstrating robust generalizability on problem scale and distribution shift. To facilitate rigorous and fair evaluations in future research, we introduce a streamlined pipeline for standardized MCTS hyperparameter tuning. Collectively, these findings challenge the prevalent assumption that heatmap complexity is the primary determinant of performance, advocating instead for a balanced integration and comprehensive evaluation of both learning and search components within this paradigm. Our code is available at: https://github.com/LOGO-CUHKSZ/rethink_mcts_tsp.

Chaolong Ying, Xinjian Zhao, Tianshu Yu

Recently, there has been an emerging trend to integrate persistent homology (PH) into graph neural networks (GNNs) to enrich expressive power. However, naively plugging PH features into GNN layers always results in marginal improvement with low interpretability. In this paper, we investigate a novel mechanism for injecting global topological invariance into pooling layers using PH, motivated by the observation that filtration operation in PH naturally aligns graph pooling in a cut-off manner. In this fashion, message passing in the coarsened graph acts along persistent pooled topology, leading to improved performance. Experimentally, we apply our mechanism to a collection of graph pooling methods and observe consistent and substantial performance gain over several popular datasets, demonstrating its wide applicability and flexibility.

Xinjian Zhao, Chaolong Ying, Tianshu Yu

Graph Neural Networks (GNNs) learn from graph-structured data by passing local messages between neighboring nodes along edges on certain topological layouts. Typically, these topological layouts in modern GNNs are deterministically computed (e.g., attention-based GNNs) or locally sampled (e.g., GraphSage) under heuristic assumptions. In this paper, we for the first time pose that these layouts can be globally sampled via Langevin dynamics following Boltzmann distribution equipped with explicit physical energy, leading to higher feasibility in the physical world. We argue that such a collection of sampled/optimized layouts can capture the wide energy distribution and bring extra expressivity on top of WL-test, therefore easing downstream tasks. As such, we propose Distributional Edge Layouts (DELs) to serve as a complement to a variety of GNNs. DEL is a pre-processing strategy independent of subsequent GNN variants, thus being highly flexible. Experimental results demonstrate that DELs consistently and substantially improve a series of GNN baselines, achieving state-of-the-art performance on multiple datasets.

Chaolong Ying, Yingqi Ruan, Xuemin Chen et al.

The Maximum Common Edge Subgraph (MCES) problem is a crucial challenge with significant implications in domains such as biology and chemistry. Traditional approaches, which include transformations into max-clique and search-based algorithms, suffer from scalability issues when dealing with larger instances. This paper introduces ``Neural Graduated Assignment'' (NGA), a simple, scalable, unsupervised-training-based method that addresses these limitations. Central to NGA is stacking of differentiable assignment optimization with neural components, enabling high-dimensional parameterization of the matching process through a learnable temperature mechanism. We further theoretically analyze the learning dynamics of NGA, showing its design leads to fast convergence, better exploration-exploitation tradeoff, and ability to escape local optima. Extensive experiments across MCES computation, graph similarity estimation, and graph retrieval tasks reveal that NGA not only significantly improves computation time and scalability on large instances but also enhances performance compared to existing methodologies. The introduction of NGA marks a significant advancement in the computation of MCES and offers insights into other assignment problems.

Chaolong Ying, Yinan Zhang, Lei Zhang et al.

Map-to-map matching is a critical task for aligning spatial data across heterogeneous sources, yet it remains challenging due to the lack of ground truth correspondences, sparse node features, and scalability demands. In this paper, we propose an unsupervised graph-based framework that addresses these challenges through three key innovations. First, our method is an unsupervised learning approach that requires no training data, which is crucial for large-scale map data where obtaining labeled training samples is challenging. Second, we introduce pseudo coordinates that capture the relative spatial layout of nodes within each map, which enhances feature discriminability and enables scale-invariant learning. Third, we design an mechanism to adaptively balance feature and geometric similarity, as well as a geometric-consistent loss function, ensuring robustness to noisy or incomplete coordinate data. At the implementation level, to handle large-scale maps, we develop a tile-based post-processing pipeline with overlapping regions and majority voting, which enables parallel processing while preserving boundary coherence. Experiments on real-world datasets demonstrate that our method achieves state-of-the-art accuracy in matching tasks, surpassing existing methods by a large margin, particularly in high-noise and large-scale scenarios. Our framework provides a scalable and practical solution for map alignment, offering a robust and efficient alternative to traditional approaches.

Yaomin Wang, Chaolong Ying, Xiaodong Luo et al.

Inference in large-scale Markov Random Fields (MRFs) is a critical yet challenging task, traditionally approached through approximate methods like belief propagation and mean field, or exact methods such as the Toulbar2 solver. These strategies often fail to strike an optimal balance between efficiency and solution quality, particularly as the problem scale increases. This paper introduces NeuroLifting, a novel technique that leverages Graph Neural Networks (GNNs) to reparameterize decision variables in MRFs, facilitating the use of standard gradient descent optimization. By extending traditional lifting techniques into a non-parametric neural network framework, NeuroLifting benefits from the smooth loss landscape of neural networks, enabling efficient and parallelizable optimization. Empirical results demonstrate that, on moderate scales, NeuroLifting performs very close to the exact solver Toulbar2 in terms of solution quality, significantly surpassing existing approximate methods. Notably, on large-scale MRFs, NeuroLifting delivers superior solution quality against all baselines, as well as exhibiting linear computational complexity growth. This work presents a significant advancement in MRF inference, offering a scalable and effective solution for large-scale problems.