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Zhenyu Xu

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5 papers

2 author rows

AAAI Conference 2026 Conference Paper

CLM-Access: A Specialized Foundation Model for High-Dimensional Single-Cell ATAC-Seq Analysis

Ziqiang Liu
Bowen Li
Zhenyu Xu
Yantao Li
Junwei Zhang
Chulin Sha
Xiaolin Li

Inspired by the success of large language models (LLMs) in natural language processing, cell language models (CLMs) have emerged as a promising paradigm to learn cell representations from high-dimensional single-cell data—particularly transcriptomic profiles from scRNA-seq. These foundation models have shown remarkable potential across a variety of downstream applications. However, there remains a lack of foundation models for scATAC-seq data, which measures chromatin accessibility at single-cell level and is critical for decoding epigenetic regulation. Developing such model is considerably more challenging due to the unique characteristics of scATAC-seq data, including the vast number of chromatin regions, lack of standardized annotations, extreme sparsity, and near-binary distributions. To address these challenges, we systematically explore various strategies and propose CLM-Access, a specialized foundation model for scATAC-seq data. CLM-Access incorporates three main innovations: (1) an unified data processing pipeline that maps 2.8 million cells onto an unified reference of over 1 million chromatin regions; (2) a specialized patching and embedding strategy to effectively manage high-dimensional inputs; and (3) a tailored masking and loss function design that preserves fine-grained regional information while enhancing training efficiency and representation quality. With comprehensive benchmarks, we show that CLM-Access significantly outperforms existing methods in key downstream tasks, including batch effect correction, cell type annotation, RNA expression prediction, and multi-modal integration. This work establishes a scalable and interpretable foundation model for single-cell epigenomic analysis and expands the application of CLMs in single-cell research.

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AAAI Conference 2024 Short Paper

Bridging the Gap between Source Code and Requirements Using GPT (Student Abstract)

Ruoyu Xu
Zhenyu Xu
Gaoxiang Li
Victor S. Sheng

Reverse engineering involves analyzing the design, architecture, and functionality of systems, and is crucial for legacy systems. Legacy systems are outdated software systems that are still in use and often lack proper documentation, which makes their maintenance and evolution challenging. To address this, we introduce SC2Req, utilizing the Generative Pre-trained Transformer (GPT) for automated code analysis and requirement generation. This approach aims to convert source code into understandable requirements and bridge the gap between those two. Through experiments on diverse software projects, SC2Req shows the potential to enhance the accuracy and efficiency of the translation process. This approach not only facilitates faster software development and easier maintenance of legacy systems but also lays a strong foundation for future research, promoting better understanding and communication in software development.

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AAAI Conference 2024 Short Paper

ChatGPT-Generated Code Assignment Detection Using Perplexity of Large Language Models (Student Abstract)

Zhenyu Xu
Ruoyu Xu
Victor S. Sheng

In the era of large language models like Chatgpt, maintaining academic integrity in programming education has become challenging due to potential misuse. There's a pressing need for reliable detectors to identify Chatgpt-generated code. While previous studies have tackled model-generated text detection, identifying such code remains uncharted territory. In this paper, we introduce a novel method to discern Chatgpt-generated code. We employ targeted masking perturbation, emphasizing code sections with high perplexity. Fine-tuned CodeBERT is utilized to replace these masked sections, generating subtly perturbed samples. Our scoring system amalgamates overall perplexity, variations in code line perplexity, and burstiness. In this scoring scheme, a higher rank for the original code suggests it's more likely to be chatgpt-generated. The underlying principle is that code generated by models typically exhibits consistent, low perplexity and reduced burstiness, with its ranking remaining relatively stable even after subtle modifications. In contrast, human-written code, when perturbed, is more likely to produce samples that the model prefers. Our approach significantly outperforms current detectors, especially against OpenAI's text-davinci-003 model, with the average AUC rising from 0.56 (GPTZero baseline) to 0.87.

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ICRA Conference 2024 Conference Paper

Semantic-focused Patch Tokenizer with Multi-branch Mixer for Visual Place Recognition

Zhenyu Xu
Ziliang Ren
Qieshi Zhang
Jie Lou
Dacheng Tao
Jun Cheng 0002

Visual Place Recognition (VPR) is critical for navigation and loop closure in autonomous driving tasks, mitigating the impact of shift errors caused by dynamic changes in the environment. Due to the limited ability of backbone networks and extreme environmental changes, current methods fail to capture foundational semantic details that include the distinctive attributes for unique place identification. To address this problem, we propose a new visual token-guided VPR framework that contains a semantic-focused patch tokenizer and a multi-branch Mixer. To mitigate the inference from place-unrelated objects, the semantic-focused patch tokenizer exploits attention-based channel selection and spatial partition, which efficiently captures important semantic information within the channels and preserve spatial relationships among the backbone features. To extract abstract features with spatial structure information, the multi-branch Mixer utilizes a multi-branch structure to aggregate local and global position information, improving the robustness of global representations to environmental changes. Experimental results demonstrate that our method outperforms state-of-the-art methods, achieving 85. 3% Recall@1 on the MSLS val dataset and 59. 1% Recall@1 on the Nordland dataset when using ResNet18 as the backbone.

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AAAI Conference 2023 Short Paper

Logic Error Localization and Correction with Machine Learning (Student Abstract)

Zhenyu Xu
Victor S. Sheng
Keyi Lu

We aim to propose a system repairing programs with logic errors to be functionally correct among different programming languages. Logic error program repair has always been a thorny problem: First, a logic error is usually harder to repair than a syntax error in a program because it has no diagnostic feedback from compilers. Second, it requires inferring in different ranges (i.e., the distance of related code lines) and tracking symbols across its pseudocode, source code, and test cases. Third, the logic error datasets are scarce, since an ideal logic error dataset should contain lots of components during the development procedure of a program, including a program specification, pseudocode, source code, test cases, and test reports (i.e., test case failure report). In our work, we propose novel solutions to these challenges. First, we introduce pseudocode information to assist logic error localization and correction. We construct a code-pseudocode graph to connect symbols across a source code and its pseudocode and then apply a graph neural network to localize and correct logic errors. Second, we collect logic errors generated in the process of syntax error repairing via DrRepair from 500 programs in the SPoC dataset and reconstruct them to our single logic error dataset, which we leverage to train and evaluate our models. Our experimental results show that we achieve 99.39% localization accuracy and 19.20% full repair accuracy on logic errors with five-fold cross-validation. Based on our current work, we will replenish and construct more complete public logic error datasets and propose a novel system to comprehend different programming languages from several perspectives and correct logic errors to be functionally correct.

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