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Cong Shen

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18 papers

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NeurIPS Conference 2025 Conference Paper

A Single-Loop First-Order Algorithm for Linearly Constrained Bilevel Optimization

Wei Shen
Jiawei Zhang
Minhui Huang
Cong Shen

We study bilevel optimization problems where the lower-level problems are strongly convex and have coupled linear constraints. To overcome the potential non-smoothness of the hyper-objective and the computational challenges associated with the Hessian matrix, we utilize penalty and augmented Lagrangian methods to reformulate the original problem as a single-level one. Especially, we establish a strong theoretical connection between the reformulated function and the original hyper-objective by characterizing the closeness of their values and derivatives. Based on this reformulation, we propose a single-loop, first-order algorithm for linearly constrained bilevel optimization (SFLCB). We provide rigorous analyses of its non-asymptotic convergence rates, showing an improvement over prior double-loop algorithms -- form $O(\epsilon^{-3}\log(\epsilon^{-1}))$ to $O(\epsilon^{-3})$. The experiments corroborate our theoretical findings and demonstrate the practical efficiency of the proposed SFLCB algorithm. Simulation code is provided at https: //github. com/ShenGroup/SFLCB.

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TMLR Journal 2025 Journal Article

FedHERO: A Federated Learning Approach for Node Classification Task on Heterophilic Graphs

Zihan Chen
Xingbo Fu
Yushun Dong
Jundong Li
Cong Shen

Graph neural networks (GNNs) have shown significant success in modeling graph data, and Federated Graph Learning (FGL) empowers clients to collaboratively train GNNs in a distributed manner while preserving data privacy. However, FGL faces unique challenges when the general neighbor distribution pattern of nodes varies significantly across clients. Specifically, FGL methods usually require that the graph data owned by all clients is homophilic to ensure similar neighbor distribution patterns of nodes. Such an assumption ensures that the learned knowledge is consistent across the local models from all clients. Therefore, these local models can be properly aggregated as a global model without undermining the overall performance. Nevertheless, when the neighbor distribution patterns of nodes vary across different clients (e.g., when clients hold graphs with different levels of heterophily), their local models may gain different and even conflict knowledge from their node-level predictive tasks. Consequently, aggregating these local models usually leads to catastrophic performance deterioration on the global model. To address this challenge, we propose FedHERO, an FGL framework designed to harness and share insights from heterophilic graphs effectively. At the heart of FedHERO is a dual-channel GNN equipped with a structure learner, engineered to discern the structural knowledge encoded in the local graphs. With this specialized component, FedHERO enables the local model for each client to identify and learn patterns that are universally applicable across graphs with different patterns of node neighbor distributions. FedHERO not only enhances the performance of individual client models by leveraging both local and shared structural insights but also sets a new precedent in this field to effectively handle graph data with various node neighbor distribution patterns. We conduct extensive experiments to validate the superior performance of FedHERO against existing alternatives.

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NeurIPS Conference 2025 Conference Paper

Greedy Sampling Is Provably Efficient For RLHF

Di Wu
Chengshuai Shi
Jing Yang
Cong Shen

Reinforcement Learning from Human Feedback (RLHF) has emerged as a key technique for post‑training large language models. Despite its empirical success, the theoretical understanding of RLHF is still limited, as learning the KL-regularized target with only preference feedback poses additional challenges compared with canonical RL. Existing works mostly study the reward-based Bradley-Terry (BT) preference model, and extend classical designs utilizing optimism or pessimism. This work, instead, considers the general preference model (whose practical relevance has been observed recently) and obtains performance guarantees with major, order-wise improvements over existing ones. Surprisingly, these results are derived from algorithms that directly use empirical estimates (i. e. , greedy sampling), as opposed to constructing optimistic or pessimistic estimates in previous works. This insight has a deep root in the unique structural property of the optimal policy class under the KL-regularized target, and we further specialize it to the BT model, highlighting the surprising sufficiency of greedy sampling in RLHF.

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NeurIPS Conference 2024 Conference Paper

Efficient Prompt Optimization Through the Lens of Best Arm Identification

Chengshuai Shi
Kun Yang
Zihan Chen
Jundong Li
Jing Yang
Cong Shen

The remarkable instruction-following capability of large language models (LLMs) has sparked a growing interest in automatically finding good prompts, i. e. , prompt optimization. Most existing works follow the scheme of selecting from a pre-generated pool of candidate prompts. However, these designs mainly focus on the generation strategy, while limited attention has been paid to the selection method. Especially, the cost incurred during the selection (e. g. , accessing LLM and evaluating the responses) is rarely explicitly considered. To overcome this limitation, this work provides a principled framework, TRIPLE, to efficiently perform prompt selection under an explicit budget constraint. TRIPLE is built on a novel connection established between prompt optimization and fixed-budget best arm identification (BAI-FB) in multi-armed bandits (MAB); thus, it is capable of leveraging the rich toolbox from BAI-FB systematically and also incorporating unique characteristics of prompt optimization. Extensive experiments on multiple well-adopted tasks using various LLMs demonstrate the remarkable performance improvement of TRIPLE over baselines while satisfying the limited budget constraints. As an extension, variants of TRIPLE are proposed to efficiently select examples for few-shot prompts, also achieving superior empirical performance.

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JBHI Journal 2024 Journal Article

Geometric Molecular Graph Representation Learning Model for Drug-Drug Interactions Prediction

Zhenyu Jiang
Pingjian Ding
Cong Shen
Xiaopeng Dai

Drug-drug interaction (DDI) can trigger many adverse effects in patients and has emerged as a threat to medicine and public health. Therefore, it is important to predict potential drug interactions since it can provide combination strategies of drugs for systematic and effective treatment. Existing deep learning-based methods often rely on DDI functional networks, or use them as an important part of the model information source. However, it is difficult to discover the interactions of a new drug. To address the above limitations, we propose a geometric molecular graph representation learning model (Mol-DDI) for DDI prediction based on the basic assumption that structure determines function. Mol-DDI only considers the covalent and non-covalent bond information of molecules, then it uses the pre-training idea of large-scale models to learn drug molecular representations and predict drug interactions during the fine-tuning process. Experimental results show that the Mol-DDI model outperforms others on the three datasets and performs better in predicting new drug interaction experiments.

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TMLR Journal 2024 Journal Article

Harnessing the Power of Federated Learning in Federated Contextual Bandits

Chengshuai Shi
Ruida Zhou
Kun Yang
Cong Shen

Federated learning (FL) has demonstrated great potential in revolutionizing distributed machine learning, and tremendous efforts have been made to extend it beyond the original focus on supervised learning. Among many directions, federated contextual bandits (FCB), a pivotal integration of FL and sequential decision-making, has garnered significant attention in recent years. Despite substantial progress, existing FCB approaches have largely employed their tailored FL components, often deviating from the canonical FL framework. Consequently, even renowned algorithms like FedAvg remain under-utilized in FCB, let alone other FL advancements. Motivated by this disconnection, this work takes one step towards building a tighter relationship between the canonical FL study and the investigations on FCB. In particular, a novel FCB design, termed FedIGW, is proposed to leverage a regression-based CB algorithm, i.e., inverse gap weighting. Compared with existing FCB approaches, the proposed FedIGW design can better harness the entire spectrum of FL innovations, which is concretely reflected as (1) flexible incorporation of (both existing and forthcoming) FL protocols; (2) modularized plug-in of FL analyses in performance guarantees; (3) seamless integration of FL appendages (such as personalization, robustness, and privacy). We substantiate these claims through rigorous theoretical analyses and empirical evaluations.

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NeurIPS Conference 2024 Conference Paper

Mixture of Demonstrations for In-Context Learning

Song Wang
Zihan Chen
Chengshuai Shi
Cong Shen
Jundong Li

In-Context Learning (ICL) empowers Large Language Models (LLMs) to tackle various tasks by providing input-output examples as additional inputs, referred to as demonstrations. Nevertheless, the performance of ICL could be easily impacted by the quality of selected demonstrations. Existing efforts generally learn a retriever model to score each demonstration for selecting suitable demonstrations, however, the effect is suboptimal due to the large search space and the noise from unhelpful demonstrations. In this study, we introduce MoD, which partitions the demonstration pool into groups, each governed by an expert to reduce search space. We further design an expert-wise training strategy to alleviate the impact of unhelpful demonstrations when optimizing the retriever model. During inference, experts collaboratively retrieve demonstrations for the input query to enhance the ICL performance. We validate MoD via experiments across a range of NLP datasets and tasks, demonstrating its state-of-the-art performance and shedding new light on the future design of retrieval methods for ICL.

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JBHI Journal 2024 Journal Article

Prediction of LncRNA-Protein Interactions Based on Kernel Combinations and Graph Convolutional Networks

Cong Shen
Dongdong Mao
Jijun Tang
Zhijun Liao
Shengyong Chen

The complexes of long non-coding RNAs bound to proteins can be involved in regulating life activities at various stages of organisms. However, in the face of the growing number of lncRNAs and proteins, verifying LncRNA-Protein Interactions (LPI) based on traditional biological experiments is time-consuming and laborious. Therefore, with the improvement of computing power, predicting LPI has met new development opportunity. In virtue of the state-of-the-art works, a framework called LncRNA-Protein Interactions based on Kernel Combinations and Graph Convolutional Networks (LPI-KCGCN) has been proposed in this article. We first construct kernel matrices by taking advantage of extracting both the lncRNAs and protein concerning the sequence features, sequence similarity features, expression features, and gene ontology. Then reconstruct the existent kernel matrices as the input of the next step. Combined with known LPI interactions, the reconstructed similarity matrices, which can be used as features of the topology map of the LPI network, are exploited in extracting potential representations in the lncRNA and protein space using a two-layer Graph Convolutional Network. The predicted matrix can be finally obtained by training the network to produce scoring matrices w. r. t. lncRNAs and proteins. Different LPI-KCGCN variants are ensemble to derive the final prediction results and testify on balanced and unbalanced datasets. The 5-fold cross-validation shows that the optimal feature information combination on a dataset with 15. 5% positive samples has an AUC value of 0. 9714 and an AUPR value of 0. 9216. On another highly unbalanced dataset with only 5% positive samples, LPI-KCGCN also has outperformed the state-of-the-art works, which achieved an AUC value of 0. 9907 and an AUPR value of 0. 9267.

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NeurIPS Conference 2024 Conference Paper

Transformers as Game Players: Provable In-context Game-playing Capabilities of Pre-trained Models

Chengshuai Shi
Kun Yang
Jing Yang
Cong Shen

The in-context learning (ICL) capability of pre-trained models based on the transformer architecture has received growing interest in recent years. While theoretical understanding has been obtained for ICL in reinforcement learning (RL), the previous results are largely confined to the single-agent setting. This work proposes to further explore the in-context learning capabilities of pre-trained transformer models in competitive multi-agent games, i. e. , in-context game-playing (ICGP). Focusing on the classical two-player zero-sum games, theoretical guarantees are provided to demonstrate that pre-trained transformers can provably learn to approximate Nash equilibrium in an in-context manner for both decentralized and centralized learning settings. As a key part of the proof, constructional results are established to demonstrate that the transformer architecture is sufficiently rich to realize celebrated multi-agent game-playing algorithms, in particular, decentralized V-learning and centralized VI-ULCB.

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NeurIPS Conference 2023 Conference Paper

Federated Linear Bandits with Finite Adversarial Actions

Li Fan
Ruida Zhou
Chao Tian
Cong Shen

We study a federated linear bandits model, where $M$ clients communicate with a central server to solve a linear contextual bandits problem with finite adversarial action sets that may be different across clients. To address the unique challenges of **adversarial finite** action sets, we propose the FedSupLinUCB algorithm, which extends the principles of SupLinUCB and OFUL algorithms in linear contextual bandits. We prove that FedSupLinUCB achieves a total regret of $\tilde{O}(\sqrt{d T})$, where $T$ is the total number of arm pulls from all clients, and $d$ is the ambient dimension of the linear model. This matches the minimax lower bound and thus is order-optimal (up to polylog terms). We study both asynchronous and synchronous cases and show that the communication cost can be controlled as $O(d M^2 \log(d)\log(T))$ and $O(\sqrt{d^3 M^3} \log(d))$, respectively. The FedSupLinUCB design is further extended to two scenarios: (1) variance-adaptive, where a total regret of $\tilde{O} (\sqrt{d \sum \nolimits_{t=1}^{T} \sigma_t^2})$ can be achieved with $\sigma_t^2$ being the noise variance of round $t$; and (2) adversarial corruption, where a total regret of $\tilde{O}(\sqrt{dT} + d C_p)$ can be achieved with $C_p$ being the total corruption budget. Experiment results corroborate the theoretical analysis and demonstrate the effectiveness of \alg on both synthetic and real-world datasets.

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AIIM Journal 2023 Journal Article

Multitask joint learning with graph autoencoders for predicting potential MiRNA-drug associations

Yichen Zhong
Cong Shen
Xiaoting Xi
Yuxun Luo
Pingjian Ding
Lingyun Luo

The occurrence of many diseases is associated with miRNA abnormalities. Predicting potential drug-miRNA associations is of great importance for both disease treatment and new drug discovery. Most computation-based approaches learn one task at a time, ignoring the information contained in other tasks in the same domain. Multitask learning can effectively enhance the prediction performance of a single task by extending the valid information of related tasks. In this paper, we presented a multitask joint learning framework (MTJL) with a graph autoencoder for predicting the associations between drugs and miRNAs. First, we combined multiple pieces of information to construct a high-quality similarity network of both drugs and miRNAs and then used a graph autoencoder (GAE) to learn their embedding representations separately. Second, to further improve the embedding quality of drugs, we added an auxiliary task to classify drugs using the learned representations. Finally, the embedding representations of drugs and miRNAs were linearly transformed to obtain the predictive association scores between them. A comparison with other state-of-the-art models shows that MTJL has the best prediction performance, and ablation experiments show that the auxiliary task can enhance the embedding quality and improve the robustness of the model. In addition, we show that MTJL has high utility in predicting potential associations between drugs and miRNAs by conducting two case studies.

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JBHI Journal 2022 Journal Article

Multi-Relation Graph Embedding for Predicting miRNA-Target Gene Interactions by Integrating Gene Sequence Information

Jiawei Luo
Wenjue Ouyang
Cong Shen
Jie Cai

Accumulated studies have found that miRNAs are in charge of many complex diseases such as cancers by modulating gene expression. Predicting miRNA-target interactions is beneficial for uncovering the crucial roles of miRNAs in regulating target genes and the progression of diseases. The emergence of large-scale genomic and biological data as well as the recent development in heterogeneous networks provides new opportunities for miRNA target identification. Compared with conventional methods, computational methods become a decent solution for high efficiency. Thus, designing a method that could excavate valid information from the heterogeneous network and gene sequences is in great demand for improving the prediction accuracy. In this study, we proposed a graph-based model named MRMTI for the prediction of miRNA-target interactions. MRMTI utilized the multi-relation graph convolution module and the Bi-LSTM module to incorporate both network topology and sequential information. The learned embeddings of miRNAs and genes were then used to calculate the prediction scores of miRNA-target pairs. Comparisons with other state-of-the-art graph embedding methods and existing bioinformatic tools illustrated the superiority of MRMTI under multiple criteria metrics. Three variants of MRMTI implied the positive effect of multi-relation. The experimental results of case studies further demonstrated the prominent ability of MRMTI in predicting novel associations.

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NeurIPS Conference 2021 Conference Paper

(Almost) Free Incentivized Exploration from Decentralized Learning Agents

Chengshuai Shi
Haifeng Xu
Wei Xiong
Cong Shen

Incentivized exploration in multi-armed bandits (MAB) has witnessed increasing interests and many progresses in recent years, where a principal offers bonuses to agents to do explorations on her behalf. However, almost all existing studies are confined to temporary myopic agents. In this work, we break this barrier and study incentivized exploration with multiple and long-term strategic agents, who have more complicated behaviors that often appear in real-world applications. An important observation of this work is that strategic agents' intrinsic needs of learning benefit (instead of harming) the principal's explorations by providing "free pulls". Moreover, it turns out that increasing the population of agents significantly lowers the principal's burden of incentivizing. The key and somewhat surprising insight revealed from our results is that when there are sufficiently many learning agents involved, the exploration process of the principal can be (almost) free. Our main results are built upon three novel components which may be of independent interest: (1) a simple yet provably effective incentive-provision strategy; (2) a carefully crafted best arm identification algorithm for rewards aggregated under unequal confidences; (3) a high-probability finite-time lower bound of UCB algorithms. Experimental results are provided to complement the theoretical analysis.

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NeurIPS Conference 2021 Conference Paper

Federated Linear Contextual Bandits

Ruiquan Huang
Weiqiang Wu
Jing Yang
Cong Shen

This paper presents a novel federated linear contextual bandits model, where individual clients face different $K$-armed stochastic bandits coupled through common global parameters. By leveraging the geometric structure of the linear rewards, a collaborative algorithm called Fed-PE is proposed to cope with the heterogeneity across clients without exchanging local feature vectors or raw data. Fed-PE relies on a novel multi-client G-optimal design, and achieves near-optimal regrets for both disjoint and shared parameter cases with logarithmic communication costs. In addition, a new concept called collinearly-dependent policies is introduced, based on which a tight minimax regret lower bound for the disjoint parameter case is derived. Experiments demonstrate the effectiveness of the proposed algorithms on both synthetic and real-world datasets.

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AAAI Conference 2021 Conference Paper

Federated Multi-Armed Bandits

Chengshuai Shi
Cong Shen

Federated multi-armed bandits (FMAB) is a new bandit paradigm that parallels the federated learning (FL) framework in supervised learning. It is inspired by practical applications in cognitive radio and recommender systems, and enjoys features that are analogous to FL. This paper proposes a general framework of FMAB and then studies two specific federated bandit models. We first study the approximate model where the heterogeneous local models are random realizations of the global model from an unknown distribution. This model introduces a new uncertainty of client sampling, as the global model may not be reliably learned even if the finite local models are perfectly known. Furthermore, this uncertainty cannot be quantified a priori without knowledge of the suboptimality gap. We solve the approximate model by proposing Federated Double UCB (Fed2-UCB), which constructs a novel “double UCB” principle accounting for uncertainties from both arm and client sampling. We show that gradually admitting new clients is critical in achieving an order-optimal regret while explicitly considering the communication cost. The exact model, where the global bandit model is the exact average of heterogeneous local models, is then studied as a special case. We show that, somewhat surprisingly, the order-optimal regret can be achieved independent of the number of clients with a careful choice of the update periodicity. Experiments using both synthetic and real-world datasets corroborate the theoretical analysis and provide interesting insight into the proposed algorithms.

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NeurIPS Conference 2021 Conference Paper

Heterogeneous Multi-player Multi-armed Bandits: Closing the Gap and Generalization

Chengshuai Shi
Wei Xiong
Cong Shen
Jing Yang

Despite the significant interests and many progresses in decentralized multi-player multi-armed bandits (MP-MAB) problems in recent years, the regret gap to the natural centralized lower bound in the heterogeneous MP-MAB setting remains open. In this paper, we propose BEACON -- Batched Exploration with Adaptive COmmunicatioN -- that closes this gap. BEACON accomplishes this goal with novel contributions in implicit communication and efficient exploration. For the former, we propose a novel adaptive differential communication (ADC) design that significantly improves the implicit communication efficiency. For the latter, a carefully crafted batched exploration scheme is developed to enable incorporation of the combinatorial upper confidence bound (CUCB) principle. We then generalize the existing linear-reward MP-MAB problems, where the system reward is always the sum of individually collected rewards, to a new MP-MAB problem where the system reward is a general (nonlinear) function of individual rewards. We extend BEACON to solve this problem and prove a logarithmic regret. BEACON bridges the algorithm design and regret analysis of combinatorial MAB (CMAB) and MP-MAB, two largely disjointed areas in MAB, and the results in this paper suggest that this previously ignored connection is worth further investigation.

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NeurIPS Conference 2020 Conference Paper

Robust Recursive Partitioning for Heterogeneous Treatment Effects with Uncertainty Quantification

Hyun-Suk Lee
Yao Zhang
William Zame
Cong Shen
Jang-Won Lee
Mihaela van der Schaar

Subgroup analysis of treatment effects plays an important role in applications from medicine to public policy to recommender systems. It allows physicians (for example) to identify groups of patients for whom a given drug or treatment is likely to be effective and groups of patients for which it is not. Most of the current methods of subgroup analysis begin with a particular algorithm for estimating individualized treatment effects (ITE) and identify subgroups by maximizing the difference across subgroups of the average treatment effect in each subgroup. These approaches have several weaknesses: they rely on a particular algorithm for estimating ITE, they ignore (in)homogeneity within identified subgroups, and they do not produce good confidence estimates. This paper develops a new method for subgroup analysis, R2P, that addresses all these weaknesses. R2P uses an arbitrary, exogenously prescribed algorithm for estimating ITE and quantifies the uncertainty of the ITE estimation, using a construction that is more robust than other methods. Experiments using synthetic and semi-synthetic datasets (based on real data) demonstrate that R2P constructs partitions that are simultaneously more homogeneous within groups and more heterogeneous across groups than the partitions produced by other methods. Moreover, because R2P can employ any ITE estimator, it also produces much narrower confidence intervals with a prescribed coverage guarantee than other methods.

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IJCAI Conference 2018 Conference Paper

Cost-aware Cascading Bandits

Ruida Zhou
Chao Gan
Jing Yang
Cong Shen

In this paper, we propose a cost-aware cascading bandits model, a new variant of multi-armed bandits with cascading feedback, by considering the random cost of pulling arms. In each step, the learning agent chooses an {\it ordered} list of items and \congr{examines} them sequentially, until certain stopping condition is satisfied. Our objective is then to maximize the expected {\it net reward} in each step, i. e. , the reward obtained in each step minus the total cost incurred in examining the items, by deciding the ordered list of items, as well as when to stop examination. We study both the offline and online settings, depending on whether the state and cost statistics of the items are known beforehand. For the offline setting, we show that the Unit Cost Ranking with Threshold 1 (UCR-T1) policy is optimal. For the online setting, we propose a Cost-aware Cascading Upper Confidence Bound (CC-UCB) algorithm, and show that the cumulative regret scales in $O(\log T)$. We also provide a lower bound for all $\alpha$-consistent policies, which scales in $\Omega(\log T)$ and matches our upper bound. The performance of the CC-UCB algorithm is evaluated with both synthetic and real-world data.

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