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Junhao Liu

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6 papers

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TMLR Journal 2026 Journal Article

FL-Sailer: Efficient and Privacy-Preserving Federated Learning for Scalable Single-Cell Epigenetic Data Analysis via Adaptive Sampling

Guangyi Zhang
Yi Dai
Yiyun He
Junhao Liu

Single-cell ATAC-seq (scATAC-seq) enables high-resolution mapping of chromatin accessibility, yet privacy regulations and data size constraints hinder multi-institutional sharing. Federated learning (FL) offers a privacy-preserving alternative, but faces three fundamental barriers in scATAC-seq analysis: ultra-high dimensionality, extreme sparsity, and severe cross-institutional heterogeneity. We propose FL-Sailer, the first FL framework designed for scATAC-seq data. FL-Sailer integrates two key innovations: (i) adaptive leverage score sampling, which selects biologically interpretable features while reducing dimensionality by 80%, and (ii) an invariant VAE architecture, which disentangles biological signals from technical confounders via mutual information minimization. We provide a convergence guarantee, showing that FL-Sailer converges to an approximate solution of the original high-dimensional problem with bounded error. Extensive experiments on synthetic and real epigenomic datasets demonstrate that FL-Sailer not only enables previously infeasible multi-institutional collaborations but also surpasses centralized methods by leveraging adaptive sampling as an implicit regularizer to suppress technical noise. Our work establishes that federated learning, when tailored to domain-specific challenges, can become a superior paradigm for collaborative epigenomic research.

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AAAI Conference 2025 Conference Paper

Hierarchical Context Pruning: Optimizing Real-World Code Completion with Repository-Level Pretrained Code LLMs

Lei Zhang
Yunshui Li
Jiaming Li
Xiaobo Xia
Jiaxi Yang
Run Luo
Minzheng Wang
Longze Chen

Some of the latest released Code Large Language Models (Code LLMs) have been trained on repository-level code data, enabling them to perceive repository structures and utilize cross-file code information. This capability allows us to directly concatenate the content of repository code files in prompts to achieve repository-level code completion. However, in real development scenarios, directly concatenating all code repository files in a prompt can easily exceed the context window of Code LLMs, leading to a significant decline in completion performance. Additionally, overly long prompts can increase completion latency, negatively impacting the user experience. In this study, we conducted extensive experiments, including completion error analysis, topology dependency analysis, and cross-file content analysis, to investigate the factors affecting repository-level code completion. Based on the conclusions drawn from these preliminary experiments, we proposed a strategy called **Hierarchical Context Pruning (HCP)** to construct high-quality completion prompts. We applied the **HCP** to six Code LLMs and evaluated them on the CrossCodeEval dataset. The experimental results showed that, compared to previous methods, the prompts constructed using our **HCP** strategy achieved higher completion accuracy on five out of six Code LLMs. Additionally, the **HCP** managed to keep the prompt length around 8k tokens (whereas the full repository code is approximately 50k tokens), significantly improving completion throughput. Our code and data will be publicly available.

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AAAI Conference 2025 Conference Paper

ReX: A Framework for Incorporating Temporal Information in Model-Agnostic Local Explanation Techniques

Junhao Liu
Xin Zhang

Existing local model-agnostic explanation techniques are ineffective for machine learning models that consider inputs of variable lengths, as they do not consider temporal information embedded in these models. To address this limitation, we propose ReX, a general framework for incorporating temporal information in these techniques. Our key insight is that these techniques typically learn a model surrogate by sampling model inputs and outputs, and we can incorporate temporal information in a uniform way by only changing the sampling process and the surrogate features. We instantiate our approach on three popular explanation techniques: Anchors, LIME, and Kernel SHAP. To evaluate the effectiveness of ReX, we apply our approach to six models in three different tasks. Our evaluation results demonstrate that our approach 1) significantly improves the fidelity of explanations, making model-agnostic techniques outperform a state-of-the-art model-specific technique on its target model, and 2) helps end users better understand the models' behaviors.

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NeurIPS Conference 2023 Conference Paper

A Single-Loop Accelerated Extra-Gradient Difference Algorithm with Improved Complexity Bounds for Constrained Minimax Optimization

Yuanyuan Liu
Fanhua Shang
Weixin An
Junhao Liu
Hongying Liu
Zhouchen Lin

In this paper, we propose a novel extra-gradient difference acceleration algorithm for solving constrained nonconvex-nonconcave (NC-NC) minimax problems. In particular, we design a new extra-gradient difference step to obtain an important quasi-cocoercivity property, which plays a key role to significantly improve the convergence rate in the constrained NC-NC setting without additional structural assumption. Then momentum acceleration is also introduced into our dual accelerating update step. Moreover, we prove that, to find an $\epsilon$-stationary point of the function $f$, our algorithm attains the complexity $\mathcal{O}(\epsilon^{-2})$ in the constrained NC-NC setting, while the best-known complexity bound is $\widetilde{\mathcal{O}}(\epsilon^{-4})$, where $\widetilde{\mathcal{O}}(\cdot)$ hides logarithmic factors compared to $\mathcal{O}(\cdot)$. As the special cases of the constrained NC-NC setting, our algorithm can also obtain the same complexity $\mathcal{O}(\epsilon^{-2})$ for both the nonconvex-concave (NC-C) and convex-nonconcave (C-NC) cases, while the best-known complexity bounds are $\widetilde{\mathcal{O}}(\epsilon^{-2. 5})$ for the NC-C case and $\widetilde{\mathcal{O}}(\epsilon^{-4})$ for the C-NC case. For fair comparison with existing algorithms, we also analyze the complexity bound to find $\epsilon$-stationary point of the primal function $\phi$ for the constrained NC-C problem, which shows that our algorithm can improve the complexity bound from $\widetilde{\mathcal{O}}(\epsilon^{-3})$ to $\mathcal{O}(\epsilon^{-2})$. To the best of our knowledge, this is the first time that the proposed algorithm improves the best-known complexity bounds from $\mathcal{O}(\epsilon^{-4})$ and $\widetilde{\mathcal{O}}(\epsilon^{-3})$ to $\mathcal{O}(\epsilon^{-2})$ in both the NC-NC and NC-C settings.

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AAAI Conference 2020 Conference Paper

Improving Knowledge-Aware Dialogue Generation via Knowledge Base Question Answering

Jian Wang
Junhao Liu
Wei Bi
Xiaojiang Liu
Kejing He
Ruifeng Xu
Min Yang

Neural network models usually suffer from the challenge of incorporating commonsense knowledge into the opendomain dialogue systems. In this paper, we propose a novel knowledge-aware dialogue generation model (called TransDG), which transfers question representation and knowledge matching abilities from knowledge base question answering (KBQA) task to facilitate the utterance understanding and factual knowledge selection for dialogue generation. In addition, we propose a response guiding attention and a multi-step decoding strategy to steer our model to focus on relevant features for response generation. Experiments on two benchmark datasets demonstrate that our model has robust superiority over compared methods in generating informative and ﬂuent dialogues. Our code is available at https: //github. com/siat-nlp/TransDG.

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AAAI Conference 2020 Conference Paper

Interactive Dual Generative Adversarial Networks for Image Captioning

Junhao Liu
Kai Wang
Chunpu Xu
Zhou Zhao
Ruifeng Xu
Ying Shen
Min Yang

Image captioning is usually built on either generationbased or retrieval-based approaches. Both ways have certain strengths but suffer from their own limitations. In this paper, we propose an Interactive Dual Generative Adversarial Network (IDGAN) for image captioning, which mutually combines the retrieval-based and generation-based methods to learn a better image captioning ensemble. IDGAN consists of two generators and two discriminators, where the generation- and retrieval-based generators mutually beneﬁt from each other’s complementary targets that are learned from two dual adversarial discriminators. Speciﬁcally, the generation- and retrieval-based generators provide improved synthetic and retrieved candidate captions with informative feedback signals from the two respective discriminators that are trained to distinguish the generated captions from the true captions and assign top rankings to true captions respectively, thus featuring the merits of both retrieval-based and generation-based approaches. Extensive experiments on MSCOCO dataset demonstrate that the proposed IDGAN model signiﬁcantly outperforms the compared methods for image captioning.

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