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Shufeng Kong

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13 papers

2 author rows

AAAI Conference 2026 Conference Paper

MIRNet: Integrating Constrained Graph-Based Reasoning with Pre-training for Diagnostic Medical Imaging

Shufeng Kong
Zijie Wang
Nuan Cui
Hao Tang
Yihan Meng
Yuanyuan Wei
Feifan Chen
Yingheng Wang

Automated interpretation of medical images demands robust modeling of complex visual-semantic relationships while addressing annotation scarcity, label imbalance, and clinical plausibility constraints. We introduce MIRNet (Medical Image Reasoner Network), a novel framework that integrates self-supervised pre-training with constrained graph-based reasoning. Tongue image diagnosis is a particularly challenging domain that requires fine-grained visual and semantic understanding. Our approach leverages self-supervised masked autoencoder (MAE) to learn transferable visual representations from unlabeled data; employs graph attention networks (GAT) to model label correlations through expert-defined structured graphs; enforces clinical priors via constraint-aware optimization using KL divergence and regularization losses; and mitigates imbalance using asymmetric loss (ASL) and boosting ensembles. To address annotation scarcity, we also introduce TongueAtlas-4K, a comprehensive expert-curated benchmark comprising 4,000 images annotated with 22 diagnostic labels–representing the largest public dataset in tongue analysis. Validation shows our method achieves state-of-the-art performance. While optimized for tongue diagnosis, the framework readily generalizes to broader diagnostic medical imaging tasks.

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AAAI Conference 2024 Conference Paper

Conformal Crystal Graph Transformer with Robust Encoding of Periodic Invariance

Yingheng Wang
Shufeng Kong
John M. Gregoire
Carla P. Gomes

Machine learning techniques, especially in the realm of materials design, hold immense promise in predicting the properties of crystal materials and aiding in the discovery of novel crystals with desirable traits. However, crystals possess unique geometric constraints—namely, E(3) invariance for primitive cell and periodic invariance—which need to be accurately reflected in crystal representations. Though past research has explored various construction techniques to preserve periodic invariance in crystal representations, their robustness remains inadequate. Furthermore, effectively capturing angular information within 3D crystal structures continues to pose a significant challenge for graph-based approaches. This study introduces novel solutions to these challenges. We first present a graph construction method that robustly encodes periodic invariance and a strategy to capture angular information in neural networks without compromising efficiency. We further introduce CrystalFormer, a pioneering graph transformer architecture that emphasizes angle preservation and enhances long-range information. Through comprehensive evaluation, we verify our model's superior performance in 5 crystal prediction tasks, reaffirming the efficiency of our proposed methods.

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UAI Conference 2024 Conference Paper

ILP-FORMER: Solving Integer Linear Programming with Sequence to Multi-Label Learning

Shufeng Kong
Caihua Liu
Carla P. Gomes

Integer Linear Programming (ILP) is an essential class of combinatorial optimization problems (COPs). Its inherent NP-hardness has fostered considerable efforts towards the development of heuristic strategies. An emerging approach involves leveraging data-driven methods to automatically learn these heuristics. For example, using deep (reinforcement) learning to recurrently reoptimize an initial solution with Large Neighborhood Search (LNS) has demonstrated exceptional performance across numerous applications. A pivotal challenge within LNS lies in identifying an optimal subset of variables for reoptimization at each stage. Existing methods typically learn a policy to select a subset, either by maintaining a fixed cardinality or by decomposing the subset into independent binary decisions for each variable. However, such strategies overlook the modeling of LNS’s sequential processes and fail to explore the correlations inherent in variable selection. To overcome these shortcomings, we introduce ILP-FORMER, an innovative model that reimagines policy learning as a sequence-to-multi-label classification (MLC) problem. Our approach uniquely integrates a causal transformer encoder to capture the sequential nature of LNS. Additionally, we employ an MLC decoder with contrastive learning to exploit the correlations in variable selection. Our extensive experiments confirm that ILP-FORMER delivers state-of-the-art anytime performance on several ILP benchmarks. Furthermore, ILP-FORMER exhibits impressive generalization capabilities when dealing with larger problem instances.

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IJCAI Conference 2023 Conference Paper

Exploring Leximin Principle for Fair Core-Selecting Combinatorial Auctions: Payment Rule Design and Implementation

Hao Cheng
Shufeng Kong
Yanchen Deng
Caihua Liu
Xiaohu Wu
Bo An
Chongjun Wang

Core-selecting combinatorial auctions (CAs) restrict the auction result in the core such that no coalitions could improve their utilities by engaging in collusion. The minimum-revenue-core (MRC) rule is a widely used core-selecting payment rule to maximize the total utilities of all bidders. However, the MRC rule can suffer from severe unfairness since it ignores individuals' utilities. To address this limitation, we propose to explore the leximin principle to achieve fairness in core-selecting CAs since the leximin principle prefers to maximize the utility of the worst-off; the resulting bidder-leximin-optimal (BLO) payment rule is then theoretically analyzed and an effective algorithm is further provided to compute the BLO outcome. Moreover, we conduct extensive experiments to show that our algorithm returns fairer utility distributions and is faster than existing algorithms of core-selecting payment rules.

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NeurIPS Conference 2022 Conference Paper

Deep Attentive Belief Propagation: Integrating Reasoning and Learning for Solving Constraint Optimization Problems

Yanchen Deng
Shufeng Kong
Caihua Liu
Bo An

Belief Propagation (BP) is an important message-passing algorithm for various reasoning tasks over graphical models, including solving the Constraint Optimization Problems (COPs). It has been shown that BP can achieve state-of-the-art performance on various benchmarks by mixing old and new messages before sending the new one, i. e. , damping. However, existing methods on tuning a static damping factor for BP not only is laborious but also harms their performance. Moreover, existing BP algorithms treat each variable node's neighbors equally when composing a new message, which also limits their exploration ability. To address these issues, we seamlessly integrate BP, Gated Recurrent Units (GRUs), and Graph Attention Networks (GATs) within the massage-passing framework to reason about dynamic weights and damping factors for composing new BP messages. Our model, Deep Attentive Belief Propagation (DABP), takes the factor graph and the BP messages in each iteration as the input and infers the optimal weights and damping factors through GRUs and GATs, followed by a multi-head attention layer. Furthermore, unlike existing neural-based BP variants, we propose a novel self-supervised learning algorithm for DABP with a smoothed solution cost, which does not require expensive training labels and also avoids the common out-of-distribution issue through efficient online learning. Extensive experiments show that our model significantly outperforms state-of-the-art baselines.

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ICML Conference 2022 Conference Paper

Gaussian Mixture Variational Autoencoder with Contrastive Learning for Multi-Label Classification

Junwen Bai
Shufeng Kong
Carla P. Gomes

Multi-label classification (MLC) is a prediction task where each sample can have more than one label. We propose a novel contrastive learning boosted multi-label prediction model based on a Gaussian mixture variational autoencoder (C-GMVAE), which learns a multimodal prior space and employs a contrastive loss. Many existing methods introduce extra complex neural modules like graph neural networks to capture the label correlations, in addition to the prediction modules. We find that by using contrastive learning in the supervised setting, we can exploit label information effectively in a data-driven manner, and learn meaningful feature and label embeddings which capture the label correlations and enhance the predictive power. Our method also adopts the idea of learning and aligning latent spaces for both features and labels. In contrast to previous works based on a unimodal prior, C-GMVAE imposes a Gaussian mixture structure on the latent space, to alleviate the posterior collapse and over-regularization issues. C-GMVAE outperforms existing methods on multiple public datasets and can often match other models’ full performance with only 50% of the training data. Furthermore, we show that the learnt embeddings provide insights into the interpretation of label-label interactions.

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AAAI Conference 2022 Conference Paper

Pretrained Cost Model for Distributed Constraint Optimization Problems

Yanchen Deng
Shufeng Kong
Bo An

Distributed Constraint Optimization Problems (DCOPs) are an important subclass of combinatorial optimization problems, where information and controls are distributed among multiple autonomous agents. Previously, Machine Learning (ML) has been largely applied to solve combinatorial optimization problems by learning effective heuristics. However, existing ML-based heuristic methods are often not generalizable to different search algorithms. Most importantly, these methods usually require full knowledge about the problems to be solved, which are not suitable for distributed settings where centralization is not realistic due to geographical limitations or privacy concerns. To address the generality issue, we propose a novel directed acyclic graph representation schema for DCOPs and leverage the Graph Attention Networks (GATs) to embed graph representations. Our model, GAT-PCM, is then pretrained with optimally labelled data in an offline manner, so as to construct effective heuristics to boost a broad range of DCOP algorithms where evaluating the quality of a partial assignment is critical, such as local search or backtracking search. Furthermore, to enable decentralized model inference, we propose a distributed embedding schema of GAT-PCM where each agent exchanges only embedded vectors, and show its soundness and complexity. Finally, we demonstrate the effectiveness of our model by combining it with a local search or a backtracking search algorithm. Extensive empirical evaluations indicate that the GAT- PCM-boosted algorithms significantly outperform the stateof-the-art methods in various benchmarks.

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AAAI Conference 2021 Conference Paper

HOT-VAE: Learning High-Order Label Correlation for Multi-Label Classification via Attention-Based Variational Autoencoders

Wenting Zhao
Shufeng Kong
Junwen Bai
Daniel Fink
Carla Gomes

Understanding how environmental characteristics affect biodiversity patterns, from individual species to communities of species, is critical for mitigating effects of global change. A central goal for conservation planning and monitoring is the ability to accurately predict the occurrence of species communities and how these communities change over space and time. This in turn leads to a challenging and long-standing problem in the field of computer science - how to perform accurate multi-label classification with hundreds of labels? The key challenge of this problem is its exponential-sized output space with regards to the number of labels to be predicted. Therefore, it is essential to facilitate the learning process by exploiting correlations (or dependency) among labels. Previous methods mostly focus on modelling the correlation on label pairs; however, complex relations between real-world objects often go beyond second order. In this paper, we propose a novel framework for multi-label classification, Highorder Tie-in Variational Autoencoder (HOT-VAE), which performs adaptive high-order label correlation learning. We experimentally verify that our model outperforms the existing state-of-the-art approaches on a bird distribution dataset on both conventional F1 scores and a variety of ecological metrics. To show our method is general, we also perform empirical analysis on seven other public real-world datasets in several application domains, and Hot-VAE exhibits superior performance to previous methods.

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IJCAI Conference 2020 Conference Paper

Deep Hurdle Networks for Zero-Inflated Multi-Target Regression: Application to Multiple Species Abundance Estimation

Shufeng Kong
Junwen Bai
Jae Hee Lee
Di Chen
Andrew Allyn
Michelle Stuart
Malin Pinsky
Katherine Mills

A key problem in computational sustainability is to understand the distribution of species across landscapes over time. This question gives rise to challenging large-scale prediction problems since (i) hundreds of species have to be simultaneously modeled and (ii) the survey data are usually inflated with zeros due to the absence of species for a large number of sites. The problem of tackling both issues simultaneously, which we refer to as the zero-inflated multi-target regression problem, has not been addressed by previous methods in statistics and machine learning. In this paper, we propose a novel deep model for the zero-inflated multi-target regression problem. To this end, we first model the joint distribution of multiple response variables as a multivariate probit model and then couple the positive outcomes with a multivariate log-normal distribution. By penalizing the difference between the two distributions’ covariance matrices, a link between both distributions is established. The whole model is cast as an end-to-end learning framework and we provide an efficient learning algorithm for our model that can be fully implemented on GPUs. We show that our model outperforms the existing state-of-the-art baselines on two challenging real-world species distribution datasets concerning bird and fish populations.

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IJCAI Conference 2020 Conference Paper

Disentangled Variational Autoencoder based Multi-Label Classification with Covariance-Aware Multivariate Probit Model

Junwen Bai
Shufeng Kong
Carla Gomes

Multi-label classification is the challenging task of predicting the presence and absence of multiple targets, involving representation learning and label correlation modeling. We propose a novel framework for multi-label classification, Multivariate Probit Variational AutoEncoder (MPVAE), that effectively learns latent embedding spaces as well as label correlations. MPVAE learns and aligns two probabilistic embedding spaces for labels and features respectively. The decoder of MPVAE takes in the samples from the embedding spaces and models the joint distribution of output targets under a Multivariate Probit model by learning a shared covariance matrix. We show that MPVAE outperforms the existing state-of-the-art methods on important computational sustainability applications as well as on other application domains, using public real-world datasets. MPVAE is further shown to remain robust under noisy settings. Lastly, we demonstrate the interpretability of the learned covariance by a case study on a bird observation dataset.

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JAAMAS Journal 2018 Journal Article

A new distributed algorithm for efficient generalized arc-consistency propagation

Shufeng Kong
Jae Hee Lee
Sanjiang Li

Abstract Generalized arc-consistency propagation is predominantly used in constraint solvers to efficiently prune the search space when solving constraint satisfaction problems. Although many practical applications can be modelled as distributed constraint satisfaction problems, no distributed arc-consistency algorithms so far have considered the privacy of individual agents. In this paper, we propose a new distributed arc-consistency algorithm, called \(\mathsf {DisAC3. 1}\), which leaks less private information of agents than existing distributed arc-consistency algorithms. In particular, \(\mathsf {DisAC3. 1}\) uses a novel termination determination mechanism, which allows the agents to share domains, constraints and communication addresses only with relevant agents. We further extend \(\mathsf {DisAC3. 1}\) to \(\mathsf {DisGAC3. 1}\), which is the first distributed algorithm that enforces generalized arc-consistency on k -ary ( \(k\ge 2\) ) constraint satisfaction problems. Theoretical analyses show that our algorithms are efficient in both time and space. Experiments also demonstrate that \(\mathsf {DisAC3. 1}\) outperforms the state-of-the-art distributed arc-consistency algorithm and that \(\mathsf {DisGAC3. 1}\) ’s performance scales linearly in the number of agents.

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AAAI Conference 2018 Conference Paper

Multiagent Simple Temporal Problem: The Arc-Consistency Approach

Shufeng Kong
Jae Hee Lee
Sanjiang Li

The Simple Temporal Problem (STP) is a fundamental temporal reasoning problem and has recently been extended to the Multiagent Simple Temporal Problem (MaSTP). In this paper we present a novel approach that is based on enforcing arc-consistency (AC) on the input (multiagent) simple temporal network. We show that the AC-based approach is suf- ﬁcient for solving both the STP and MaSTP and provide ef- ﬁcient algorithms for them. As our AC-based approach does not impose new constraints between agents, it does not violate the privacy of the agents and is superior to the state-ofthe-art approach to MaSTP. Empirical evaluations on diverse benchmark datasets also show that our AC-based algorithms for STP and MaSTP are signiﬁcantly more efﬁcient than existing approaches.

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AAMAS Conference 2017 Conference Paper

A Deterministic Distributed Algorithm for Reasoning with Connected Row-Convex Constraints

Shufeng Kong
Jae Hee Lee
Sanjiang Li

The class of CRC constraints generalizes several tractable classes of constraints and is expressive enough to model problems in domains such as temporal reasoning, geometric reasoning, and scene labelling. This paper presents the first distributed deterministic algorithm for connected row-convex (CRC) constraints. Our distributed (partial) path consistency algorithm efficiently transforms a CRC constraint network into an equivalent constraint network, where all constraints are minimal (i. e. , they are the tightest constraints) and generating all solutions can be done in a backtrackfree manner. When compared with the state-of-the-art distributed algorithm for CRC constraints, which is a randomized one, our algorithm guarantees to generate a solution for satisfiable CRC constraint networks and it is applicable to solve large networks in real distributed systems. The experimental evaluations show that our algorithm outperforms the state-of-the-art algorithm in both practice and theory.

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