Runzhong Wang

Runzhong Wang, Yunhao Zhang, Ziao Guo et al.

Encoding constraints into neural networks is attractive. This paper studies how to introduce the popular positive linear satisfiability to neural networks. We propose the first differentiable satisfiability layer based on an extension of the classic Sinkhorn algorithm for jointly encoding multiple sets of marginal distributions. We further theoretically characterize the convergence property of the Sinkhorn algorithm for multiple marginals. In contrast to the sequential decision e.g.\ reinforcement learning-based solvers, we showcase our technique in solving constrained (specifically satisfiability) problems by one-shot neural networks, including i) a neural routing solver learned without supervision of optimal solutions; ii) a partial graph matching network handling graphs with unmatchable outliers on both sides; iii) a predictive network for financial portfolios with continuous constraints. To our knowledge, there exists no one-shot neural solver for these scenarios when they are formulated as satisfiability problems. Source code is available at https://github.com/Thinklab-SJTU/LinSATNet

Montgomery Bohde, Hongxuan Liu, Mrunali Manjrekar et al.

In this work, we present FRIGID, a framework with a novel diffusion language model that generates molecular structures conditioned on mass spectra via intermediate fingerprint representations and determined chemical formulae, training at the scale of hundreds of millions of unlabeled structures. We then demonstrate how forward fragmentation models enable inference-time scaling by identifying spectrum-inconsistent fragments and refining them through targeted remasking and denoising. While FRIGID already achieves strong performance with its diffusion base, inference-time scaling significantly improves its accuracy, surpassing 18% Top-1 accuracy on the challenging MassSpecGym benchmark and tripling the Top-1 accuracy of the leading methods on NPLIB1. Further empirical analyses show that FRIGID exhibits log-linear performance scaling with increasing inference-time compute, opening a promising new direction for continued improvements in de novo structural elucidation. FRIGID code is publicly available at https://github.com/coleygroup/FRIGID

Haoyu Geng, Hang Ruan, Runzhong Wang et al.

Predictive combinatorial optimization, where the parameters of combinatorial optimization (CO) are unknown at the decision-making time, is the precise modeling of many real-world applications, including energy cost-aware scheduling and budget allocation on advertising. Tackling such a problem usually involves a prediction model and a CO solver. These two modules are integrated into the predictive CO pipeline following two design principles: "Predict-then-Optimize (PtO)", which learns predictions by supervised training and subsequently solves CO using predicted coefficients, while the other, named "Predict-and-Optimize (PnO)", directly optimizes towards the ultimate decision quality and claims to yield better decisions than traditional PtO approaches. However, there lacks a systematic benchmark of both approaches, including the specific design choices at the module level, as well as an evaluation dataset that covers representative real-world scenarios. To this end, we develop a modular framework to benchmark 11 existing PtO/PnO methods on 8 problems, including a new industrial dataset for combinatorial advertising that will be released. Our study shows that PnO approaches are better than PtO on 7 out of 8 benchmarks, but there is no silver bullet found for the specific design choices of PnO. A comprehensive categorization of current approaches and integration of typical scenarios are provided under a unified benchmark. Therefore, this paper could serve as a comprehensive benchmark for future PnO approach development and also offer fast prototyping for application-focused development. The code is available at https://github.com/Thinklab-SJTU/PredictiveCO-Benchmark.

Kevin Yu, Jihye Roh, Ziang Li et al.

Computer-aided synthesis planning (CASP) algorithms have demonstrated expert-level abilities in planning retrosynthetic routes to molecules of low to moderate complexity. However, current search methods assume the sufficiency of reaching arbitrary building blocks, failing to address the common real-world constraint where using specific molecules is desired. To this end, we present a formulation of synthesis planning with starting material constraints. Under this formulation, we propose Double-Ended Synthesis Planning (DESP), a novel CASP algorithm under a bidirectional graph search scheme that interleaves expansions from the target and from the goal starting materials to ensure constraint satisfiability. The search algorithm is guided by a goal-conditioned cost network learned offline from a partially observed hypergraph of valid chemical reactions. We demonstrate the utility of DESP in improving solve rates and reducing the number of search expansions by biasing synthesis planning towards expert goals on multiple new benchmarks. DESP can make use of existing one-step retrosynthesis models, and we anticipate its performance to scale as these one-step model capabilities improve.

Wujiang Xu, Runzhong Wang, Xiaobo Guo et al.

Video summarization intends to produce a concise video summary by effectively capturing and combining the most informative parts of the whole content. Existing approaches for video summarization regard the task as a frame-wise keyframe selection problem and generally construct the frame-wise representation by combining the long-range temporal dependency with the unimodal or bimodal information. However, the optimal video summaries need to reflect the most valuable keyframe with its own information, and one with semantic power of the whole content. Thus, it is critical to construct a more powerful and robust frame-wise representation and predict the frame-level importance score in a fair and comprehensive manner. To tackle the above issues, we propose a multimodal hierarchical shot-aware convolutional network, denoted as MHSCNet, to enhance the frame-wise representation via combining the comprehensive available multimodal information. Specifically, we design a hierarchical ShotConv network to incorporate the adaptive shot-aware frame-level representation by considering the short-range and long-range temporal dependency. Based on the learned shot-aware representations, MHSCNet can predict the frame-level importance score in the local and global view of the video. Extensive experiments on two standard video summarization datasets demonstrate that our proposed method consistently outperforms state-of-the-art baselines. Source code will be made publicly available.

Jinpei Guo, Shaofeng Zhang, Runzhong Wang et al. · pku

Vision transformers (ViTs) have recently been used for visual matching beyond object detection and segmentation. However, the original grid dividing strategy of ViTs neglects the spatial information of the keypoints, limiting the sensitivity to local information. Therefore, we propose QueryTrans (Query Transformer), which adopts a cross-attention module and keypoints-based center crop strategy for better spatial information extraction. We further integrate the graph attention module and devise a transformer-based graph matching approach GMTR (Graph Matching TRansformers) whereby the combinatorial nature of GM is addressed by a graph transformer neural GM solver. On standard GM benchmarks, GMTR shows competitive performance against the SOTA frameworks. Specifically, on Pascal VOC, GMTR achieves $\mathbf{83.6\%}$ accuracy, $\mathbf{0.9\%}$ higher than the SOTA framework. On Spair-71k, GMTR shows great potential and outperforms most of the previous works. Meanwhile, on Pascal VOC, QueryTrans improves the accuracy of NGMv2 from $80.1\%$ to $\mathbf{83.3\%}$, and BBGM from $79.0\%$ to $\mathbf{84.5\%}$. On Spair-71k, QueryTrans improves NGMv2 from $80.6\%$ to $\mathbf{82.5\%}$, and BBGM from $82.1\%$ to $\mathbf{83.9\%}$. Source code will be made publicly available.

Runzhong Wang, Yang Li, Junchi Yan et al.

Combinatorial optimization (CO) is the fundamental problem at the intersection of computer science, applied mathematics, etc. The inherent hardness in CO problems brings up challenge for solving CO exactly, making deep-neural-network-based solvers a research frontier. In this paper, we design a family of non-autoregressive neural networks to solve CO problems under positive linear constraints with the following merits. First, the positive linear constraint covers a wide range of CO problems, indicating that our approach breaks the generality bottleneck of existing non-autoregressive networks. Second, compared to existing autoregressive neural network solvers, our non-autoregressive networks have the advantages of higher efficiency and preserving permutation invariance. Third, our offline unsupervised learning has lower demand on high-quality labels, getting rid of the demand of optimal labels in supervised learning. Fourth, our online differentiable search method significantly improves the generalizability of our neural network solver to unseen problems. We validate the effectiveness of this framework in solving representative CO problems including facility location, max-set covering, and traveling salesman problem. Our non-autoregressive neural solvers are competitive to and can be even superior to state-of-the-art solvers such as SCIP and Gurobi, especially when both efficiency and efficacy are considered. Code is available at https://github.com/Thinklab-SJTU/NAR-CO-Solver

Montgomery Bohde, Mrunali Manjrekar, Runzhong Wang et al.

Mass spectrometry plays a fundamental role in elucidating the structures of unknown molecules and subsequent scientific discoveries. One formulation of the structure elucidation task is the conditional de novo generation of molecular structure given a mass spectrum. Toward a more accurate and efficient scientific discovery pipeline for small molecules, we present DiffMS, a formula-restricted encoder-decoder generative network that achieves state-of-the-art performance on this task. The encoder utilizes a transformer architecture and models mass spectra domain knowledge such as peak formulae and neutral losses, and the decoder is a discrete graph diffusion model restricted by the heavy-atom composition of a known chemical formula. To develop a robust decoder that bridges latent embeddings and molecular structures, we pretrain the diffusion decoder with fingerprint-structure pairs, which are available in virtually infinite quantities, compared to structure-spectrum pairs that number in the tens of thousands. Extensive experiments on established benchmarks show that DiffMS outperforms existing models on de novo molecule generation. We provide several ablations to demonstrate the effectiveness of our diffusion and pretraining approaches and show consistent performance scaling with increasing pretraining dataset size. DiffMS code is publicly available at https://github.com/coleygroup/DiffMS.

Runzhong Wang, Rui-Xi Wang, Mrunali Manjrekar et al.

Molecular machine learning has gained popularity with the advancements of geometric deep learning. In parallel, retrieval-augmented generation has become a principled approach commonly used with language models. However, the optimal integration of retrieval augmentation into molecular machine learning remains unclear. Graph neural networks stand to benefit from clever matching to understand the structural alignment of retrieved molecules to a query molecule. Neural graph matching offers a compelling solution by explicitly modeling node and edge affinities between two structural graphs while employing a noise-robust, end-to-end neural network to learn affinity metrics. We apply this approach to mass spectrum simulation and introduce MARASON, a novel model that incorporates neural graph matching to enhance a fragmentation-based neural network. Experimental results highlight the effectiveness of our design, with MARASON achieving 28% top-1 accuracy, a substantial improvement over the non-retrieval state-of-the-art accuracy of 19%. Moreover, MARASON outperforms both naive retrieval-augmented generation methods and traditional graph matching approaches. Code is publicly available at https://github.com/coleygroup/ms-pred

Hao-Shu Fang, Jianhua Sun, Runzhong Wang et al.

Instance segmentation requires a large number of training samples to achieve satisfactory performance and benefits from proper data augmentation. To enlarge the training set and increase the diversity, previous methods have investigated using data annotation from other domain (e.g. bbox, point) in a weakly supervised mechanism. In this paper, we present a simple, efficient and effective method to augment the training set using the existing instance mask annotations. Exploiting the pixel redundancy of the background, we are able to improve the performance of Mask R-CNN for 1.7 mAP on COCO dataset and 3.3 mAP on Pascal VOC dataset by simply introducing random jittering to objects. Furthermore, we propose a location probability map based approach to explore the feasible locations that objects can be placed based on local appearance similarity. With the guidance of such map, we boost the performance of R101-Mask R-CNN on instance segmentation from 35.7 mAP to 37.9 mAP without modifying the backbone or network structure. Our method is simple to implement and does not increase the computational complexity. It can be integrated into the training pipeline of any instance segmentation model without affecting the training and inference efficiency. Our code and models have been released at https://github.com/GothicAi/InstaBoost

Yang Li, Jinpei Guo, Runzhong Wang et al.

Diffusion models have recently advanced Combinatorial Optimization (CO) as a powerful backbone for neural solvers. However, their iterative sampling process requiring denoising across multiple noise levels incurs substantial overhead. We propose to learn direct mappings from different noise levels to the optimal solution for a given instance, facilitating high-quality generation with minimal shots. This is achieved through an optimization consistency training protocol, which, for a given instance, minimizes the difference among samples originating from varying generative trajectories and time steps relative to the optimal solution. The proposed model enables fast single-step solution generation while retaining the option of multi-step sampling to trade for sampling quality, which offers a more effective and efficient alternative backbone for neural solvers. In addition, within the training-to-testing (T2T) framework, to bridge the gap between training on historical instances and solving new instances, we introduce a novel consistency-based gradient search scheme during the test stage, enabling more effective exploration of the solution space learned during training. It is achieved by updating the latent solution probabilities under objective gradient guidance during the alternation of noise injection and denoising steps. We refer to this model as Fast T2T. Extensive experiments on two popular tasks, the Traveling Salesman Problem (TSP) and Maximal Independent Set (MIS), demonstrate the superiority of Fast T2T regarding both solution quality and efficiency, even outperforming LKH given limited time budgets. Notably, Fast T2T with merely one-step generation and one-step gradient search can mostly outperform the SOTA diffusion-based counterparts that require hundreds of steps, while achieving tens of times speedup.

Ziang Chen, Qiao Zhang, Runzhong Wang

Graph neural networks (GNNs) have been widely used in graph-related contexts. It is known that the separation power of GNNs is equivalent to that of the Weisfeiler-Lehman (WL) test; hence, GNNs are imperfect at identifying all non-isomorphic graphs, which severely limits their expressive power. This work investigates $k$-hop subgraph GNNs that aggregate information from neighbors with distances up to $k$ and incorporate the subgraph structure. We prove that under appropriate assumptions, the $k$-hop subgraph GNNs can approximate any permutation-invariant/equivariant continuous function over graphs without cycles of length greater than $2k+1$ within any error tolerance. We also provide an extension to $k$-hop GNNs without incorporating the subgraph structure. Our numerical experiments on established benchmarks and novel architectures validate our theory on the relationship between the information aggregation distance and the cycle size.

Han Lu, Zenan Li, Runzhong Wang et al.

Solving combinatorial optimization (CO) on graphs is among the fundamental tasks for upper-stream applications in data mining, machine learning and operations research. Despite the inherent NP-hard challenge for CO, heuristics, branch-and-bound, learning-based solvers are developed to tackle CO problems as accurately as possible given limited time budgets. However, a practical metric for the sensitivity of CO solvers remains largely unexplored. Existing theoretical metrics require the optimal solution which is infeasible, and the gradient-based adversarial attack metric from deep learning is not compatible with non-learning solvers that are usually non-differentiable. In this paper, we develop the first practically feasible robustness metric for general combinatorial optimization solvers. We develop a no worse optimal cost guarantee thus do not require optimal solutions, and we tackle the non-differentiable challenge by resorting to black-box adversarial attack methods. Extensive experiments are conducted on 14 unique combinations of solvers and CO problems, and we demonstrate that the performance of state-of-the-art solvers like Gurobi can degenerate by over 20% under the given time limit bound on the hard instances discovered by our robustness metric, raising concerns about the robustness of combinatorial optimization solvers.

Runzhong Wang, Zhigang Hua, Gan Liu et al.

Combinatorial Optimization (CO) has been a long-standing challenging research topic featured by its NP-hard nature. Traditionally such problems are approximately solved with heuristic algorithms which are usually fast but may sacrifice the solution quality. Currently, machine learning for combinatorial optimization (MLCO) has become a trending research topic, but most existing MLCO methods treat CO as a single-level optimization by directly learning the end-to-end solutions, which are hard to scale up and mostly limited by the capacity of ML models given the high complexity of CO. In this paper, we propose a hybrid approach to combine the best of the two worlds, in which a bi-level framework is developed with an upper-level learning method to optimize the graph (e.g. add, delete or modify edges in a graph), fused with a lower-level heuristic algorithm solving on the optimized graph. Such a bi-level approach simplifies the learning on the original hard CO and can effectively mitigate the demand for model capacity. The experiments and results on several popular CO problems like Directed Acyclic Graph scheduling, Graph Edit Distance and Hamiltonian Cycle Problem show its effectiveness over manually designed heuristics and single-level learning methods.

Chang Liu, Zetian Jiang, Runzhong Wang et al.

Graph matching (GM) has been a building block in various areas including computer vision and pattern recognition. Despite recent impressive progress, existing deep GM methods often have obvious difficulty in handling outliers, which are ubiquitous in practice. We propose a deep reinforcement learning based approach RGM, whose sequential node matching scheme naturally fits the strategy for selective inlier matching against outliers. A revocable action framework is devised to improve the agent's flexibility against the complex constrained GM. Moreover, we propose a quadratic approximation technique to regularize the affinity score, in the presence of outliers. As such, the agent can finish inlier matching timely when the affinity score stops growing, for which otherwise an additional parameter i.e. the number of inliers is needed to avoid matching outliers. In this paper, we focus on learning the back-end solver under the most general form of GM: the Lawler's QAP, whose input is the affinity matrix. Especially, our approach can also boost existing GM methods that use such input. Experiments on multiple real-world datasets demonstrate its performance regarding both accuracy and robustness.

Runzhong Wang, Tianqi Zhang, Tianshu Yu et al.

Graph Edit Distance (GED) is a popular similarity measurement for pairwise graphs and it also refers to the recovery of the edit path from the source graph to the target graph. Traditional A* algorithm suffers scalability issues due to its exhaustive nature, whose search heuristics heavily rely on human prior knowledge. This paper presents a hybrid approach by combing the interpretability of traditional search-based techniques for producing the edit path, as well as the efficiency and adaptivity of deep embedding models to achieve a cost-effective GED solver. Inspired by dynamic programming, node-level embedding is designated in a dynamic reuse fashion and suboptimal branches are encouraged to be pruned. To this end, our method can be readily integrated into A* procedure in a dynamic fashion, as well as significantly reduce the computational burden with a learned heuristic. Experimental results on different graph datasets show that our approach can remarkably ease the search process of A* without sacrificing much accuracy. To our best knowledge, this work is also the first deep learning-based GED method for recovering the edit path.

Runzhong Wang, Junchi Yan, Xiaokang Yang

Graph matching involves combinatorial optimization based on edge-to-edge affinity matrix, which can be generally formulated as Lawler's Quadratic Assignment Problem (QAP). This paper presents a QAP network directly learning with the affinity matrix (equivalently the association graph) whereby the matching problem is translated into a constrained vertex classification task. The association graph is learned by an embedding network for vertex classification, followed by Sinkhorn normalization and a cross-entropy loss for end-to-end learning. We further improve the embedding model on association graph by introducing Sinkhorn based matching-aware constraint, as well as dummy nodes to deal with unequal sizes of graphs. To our best knowledge, this is one of the first network to directly learn with the general Lawler's QAP. In contrast, recent deep matching methods focus on the learning of node/edge features in two graphs respectively. We also show how to extend our network to hypergraph matching, and matching of multiple graphs. Experimental results on both synthetic graphs and real-world images show its effectiveness. For pure QAP tasks on synthetic data and QAPLIB benchmark, our method can perform competitively and even surpass state-of-the-art graph matching and QAP solvers with notable less time cost. We provide a project homepage at http://thinklab.sjtu.edu.cn/project/NGM/index.html.

Runzhong Wang, Junchi Yan, Xiaokang Yang

Graph matching refers to finding node correspondence between graphs, such that the corresponding node and edge's affinity can be maximized. In addition with its NP-completeness nature, another important challenge is effective modeling of the node-wise and structure-wise affinity across graphs and the resulting objective, to guide the matching procedure effectively finding the true matching against noises. To this end, this paper devises an end-to-end differentiable deep network pipeline to learn the affinity for graph matching. It involves a supervised permutation loss regarding with node correspondence to capture the combinatorial nature for graph matching. Meanwhile deep graph embedding models are adopted to parameterize both intra-graph and cross-graph affinity functions, instead of the traditional shallow and simple parametric forms e.g. a Gaussian kernel. The embedding can also effectively capture the higher-order structure beyond second-order edges. The permutation loss model is agnostic to the number of nodes, and the embedding model is shared among nodes such that the network allows for varying numbers of nodes in graphs for training and inference. Moreover, our network is class-agnostic with some generalization capability across different categories. All these features are welcomed for real-world applications. Experiments show its superiority against state-of-the-art graph matching learning methods.