Siyuan Jiang

YuPeng Huang, Hong Zhang, Siyuan Jiang et al.

Virtual screening, including molecular docking, plays an essential role in drug discovery. Many traditional and machine-learning based methods are available to fulfil the docking task. The traditional docking methods are normally extensively time-consuming, and their performance in blind docking remains to be improved. Although the runtime of docking based on machine learning is significantly decreased, their accuracy is still limited. In this study, we take the advantage of both traditional and machine-learning based methods, and present a method Deep Site and Docking Pose (DSDP) to improve the performance of blind docking. For the traditional blind docking, the entire protein is covered by a cube, and the initial positions of ligands are randomly generated in the cube. In contract, DSDP can predict the binding site of proteins and provide an accurate searching space and initial positions for the further conformational sampling. The docking task of DSDP makes use of the score function and a similar but modified searching strategy of AutoDock Vina, accelerated by implementation in GPUs. We systematically compare its performance with the state-of-the-art methods, including Autodock Vina, GNINA, QuickVina, SMINA, and DiffDock. DSDP reaches a 29.8% top-1 success rate (RMSD < 2 Å) on an unbiased and challenging test dataset with 1.2 s wall-clock computational time per system. Its performances on DUD-E dataset and the time-split PDBBind dataset used in EquiBind, TankBind, and DiffDock are also effective, presenting a 57.2% and 41.8% top-1 success rate with 0.8 s and 1.0 s per system, respectively.

Aakash Bansal, Siyuan Jiang, Sakib Haque et al.

Source code summarization is the task of writing natural language descriptions of source code behavior. Code summarization underpins software documentation for programmers. Short descriptions of code help programmers understand the program quickly without having to read the code itself. Lately, neural source code summarization has emerged as the frontier of research into automated code summarization techniques. By far the most popular targets for summarization are program subroutines. The idea, in a nutshell, is to train an encoder-decoder neural architecture using large sets of examples of subroutines extracted from code repositories. The encoder represents the code and the decoder represents the summary. However, most current approaches attempt to treat the subroutine as a single unit. For example, by taking the entire subroutine as input to a Transformer or RNN-based encoder. But code behavior tends to depend on the flow from statement to statement. Normally dynamic analysis may shed light on this flow, but dynamic analysis on hundreds of thousands of examples in large datasets is not practical. In this paper, we present a statement-based memory encoder that learns the important elements of flow during training, leading to a statement-based subroutine representation without the need for dynamic analysis. We implement our encoder for code summarization and demonstrate a significant improvement over the state-of-the-art.

Siyuan Jiang, Yan Ding, Yuling Wang et al.

Ultrasound is a vital diagnostic technique in health screening, with the advantages of non-invasive, cost-effective, and radiation free, and therefore is widely applied in the diagnosis of nodules. However, it relies heavily on the expertise and clinical experience of the sonographer. In ultrasound images, a single nodule might present heterogeneous appearances in different cross-sectional views which makes it hard to perform per-nodule examination. Sonographers usually discriminate different nodules by examining the nodule features and the surrounding structures like gland and duct, which is cumbersome and time-consuming. To address this problem, we collected hundreds of breast ultrasound videos and built a nodule reidentification system that consists of two parts: an extractor based on the deep learning model that can extract feature vectors from the input video clips and a real-time clustering algorithm that automatically groups feature vectors by nodules. The system obtains satisfactory results and exhibits the capability to differentiate ultrasound videos. As far as we know, it's the first attempt to apply re-identification technique in the ultrasonic field.

Teal Amore, Nathan Berman, Siyuan Jiang

Automated testing is crucial for maintaining open-source software quality. However, motivating contributors to include tests for code changes remains a challenge. While existing interventions, such as code coverage metrics and reviewer feedback, are often reactive and applied only after a pull request is opened, this study investigates whether documentation on testing can serve as a proactive measure to encourage testing behavior. In this work, we investigate the relationship between documentation on testing and contributor testing behavior. We introduce the Test Engagement Ratio (TER) to help understand testing frequency. Using data from 160 OSS repositories, we analyze the relationship between documentation comprehensiveness and TER. Our results show a weak but statistically significant positive correlation ($ρ=0.36$, $p<0.001$), which strengthens to a moderate relationship ($ρ=0.44$) in repositories with higher pull request activity. Documentation categories such as How to Run Tests and How to Write Tests show the strongest correlation with testing engagement. Furthermore, TER is found to be moderately correlated ($ρ=0.52$, $p<0.001$) with Test Code Ratio, providing preliminary evidence of its validity. Our findings suggest that documentation on testing may be associated with increased testing engagement. Future work will explore causality, documentation quality at a granular level, and cross-repository exposure effects.

Xinyang Xiong, Siyuan jiang, Pengcheng Zeng

Clustering functional data in the presence of phase variation is challenging, as temporal misalignment can obscure intrinsic shape differences and degrade clustering performance. Most existing approaches treat registration and clustering as separate tasks or rely on restrictive parametric assumptions. We present \textbf{NeuralFLoC}, a fully unsupervised, end-to-end deep learning framework for joint functional registration and clustering based on Neural ODE-driven diffeomorphic flows and spectral clustering. The proposed model learns smooth, invertible warping functions and cluster-specific templates simultaneously, effectively disentangling phase and amplitude variation. We establish universal approximation guarantees and asymptotic consistency for the proposed framework. Experiments on functional benchmarks show state-of-the-art performance in both registration and clustering, with robustness to missing data, irregular sampling, and noise, while maintaining scalability. Code is available at https://anonymous.4open.science/r/NeuralFLoC-FEC8.

Siyuan Jiang, Yihan Hu, Wenjie Li et al.

Functional data, representing curves or trajectories, are ubiquitous in fields like biomedicine and motion analysis. A fundamental challenge is phase variability -- temporal misalignments that obscure underlying patterns and degrade model performance. Current methods often address registration (alignment) and classification as separate, sequential tasks. This paper introduces DeepFRC, an end-to-end deep learning framework that jointly learns diffeomorphic warping functions and a classifier within a unified architecture. DeepFRC combines a neural deformation operator for elastic alignment, a spectral representation using Fourier basis for smooth functional embedding, and a class-aware contrastive loss that promotes both intra-class coherence and inter-class separation. We provide the first theoretical guarantees for such a joint model, proving its ability to approximate optimal warpings and establishing a data-dependent generalization bound that formally links registration fidelity to classification performance. Extensive experiments on synthetic and real-world datasets demonstrate that DeepFRC consistently outperforms state-of-the-art methods in both alignment quality and classification accuracy, while ablation studies validate the synergy of its components. DeepFRC also shows notable robustness to noise, missing data, and varying dataset scales. Code is available at https://github.com/Drivergo-93589/DeepFRC.

Marcos V. Conde, Radu Timofte, Zihao Lu et al.

This paper reviews the NTIRE 2025 RAW Image Restoration and Super-Resolution Challenge, highlighting the proposed solutions and results. New methods for RAW Restoration and Super-Resolution could be essential in modern Image Signal Processing (ISP) pipelines, however, this problem is not as explored as in the RGB domain. The goal of this challenge is two fold, (i) restore RAW images with blur and noise degradations, (ii) upscale RAW Bayer images by 2x, considering unknown noise and blur. In the challenge, a total of 230 participants registered, and 45 submitted results during thee challenge period. This report presents the current state-of-the-art in RAW Restoration.

Marcos V. Conde, Florin-Alexandru Vasluianu, Radu Timofte et al.

This paper reviews the NTIRE 2024 RAW Image Super-Resolution Challenge, highlighting the proposed solutions and results. New methods for RAW Super-Resolution could be essential in modern Image Signal Processing (ISP) pipelines, however, this problem is not as explored as in the RGB domain. Th goal of this challenge is to upscale RAW Bayer images by 2x, considering unknown degradations such as noise and blur. In the challenge, a total of 230 participants registered, and 45 submitted results during thee challenge period. The performance of the top-5 submissions is reviewed and provided here as a gauge for the current state-of-the-art in RAW Image Super-Resolution.

Pengcheng Zeng, Siyuan Jiang

We propose Path Signatures Logistic Regression (PSLR), a semi-parametric framework for classifying vector-valued functional data with scalar covariates. Classical functional logistic regression models rely on linear assumptions and fixed basis expansions, which limit flexibility and degrade performance under irregular sampling. PSLR overcomes these issues by leveraging truncated path signatures to construct a finite-dimensional, basis-free representation that captures nonlinear and cross-channel dependencies. By embedding trajectories as time-augmented paths, PSLR extracts stable, geometry-aware features that are robust to sampling irregularity without requiring a common time grid, while still preserving subject-specific timing patterns. We establish theoretical guarantees for the existence and consistent estimation of the optimal truncation order, along with non-asymptotic risk bounds. Experiments on synthetic and real-world datasets show that PSLR outperforms traditional functional classifiers in accuracy, robustness, and interpretability, particularly under non-uniform sampling schemes. Our results highlight the practical and theoretical benefits of integrating rough path theory into modern functional data analysis.

Siyuan Jiang, Jia Li, He Zong et al. · pku

Large Language Models (LLMs) have been widely used in code completion, and researchers are focusing on scaling up LLMs to improve their accuracy. However, larger LLMs have lower inference efficiency, affecting developers' experience and productivity. In this paper, we propose a lightweight and effective LLM for code completion named aiXcoder-7B. Compared to existing LLMs, aiXcoder-7B achieves higher code completion accuracy while having smaller scales (i.e., 7 billion parameters). We attribute the superiority of aiXcoder-7B to three key factors: (1) Multi-objective training. We employ three training objectives, one of which is our proposed Structured Fill-In-the-Middle (SFIM). SFIM considers the syntax structures in code and effectively improves the performance of LLMs for code. (2) Diverse data sampling strategies. They consider inter-file relationships and enhance the capability of LLMs in understanding cross-file contexts. (3) Extensive high-quality data. We establish a rigorous data collection pipeline and consume a total of 1.2 trillion unique tokens for training aiXcoder-7B. This vast volume of data enables aiXcoder-7B to learn a broad distribution of code. We evaluate aiXcoder-7B in five popular code completion benchmarks and a new benchmark collected by this paper. The results show that aiXcoder-7B outperforms the latest six LLMs with similar sizes and even surpasses four larger LLMs (e.g., StarCoder2-15B and CodeLlama-34B), positioning aiXcoder-7B as a lightweight and effective LLM for academia and industry. Finally, we summarize three valuable insights for helping practitioners train the next generations of LLMs for code. aiXcoder-7B has been open-souced and gained significant attention. Until January 2025, aiXcoder-7B has received 2,226 GitHub Stars.

Ying Fu, Yu Li, Shaodi You et al.

The intersection of physics-based vision and deep learning presents an exciting frontier for advancing computer vision technologies. By leveraging the principles of physics to inform and enhance deep learning models, we can develop more robust and accurate vision systems. Physics-based vision aims to invert the processes to recover scene properties such as shape, reflectance, light distribution, and medium properties from images. In recent years, deep learning has shown promising improvements for various vision tasks, and when combined with physics-based vision, these approaches can enhance the robustness and accuracy of vision systems. This technical report summarizes the outcomes of the Physics-Based Vision Meets Deep Learning (PBDL) 2024 challenge, held in CVPR 2024 workshop. The challenge consisted of eight tracks, focusing on Low-Light Enhancement and Detection as well as High Dynamic Range (HDR) Imaging. This report details the objectives, methodologies, and results of each track, highlighting the top-performing solutions and their innovative approaches.

Yihao Huang, Jincao Feng, Hanyue Zheng et al.

We present Prema, a tool for Precise Requirement Editing, Modeling and Analysis. It can be used in various fields for describing precise requirements using formal notations and performing rigorous analysis. By parsing the requirements written in formal modeling language, Prema is able to get a model which aptly depicts the requirements. It also provides different rigorous verification and validation techniques to check whether the requirements meet users' expectation and find potential errors. We show that our tool can provide a unified environment for writing and verifying requirements without using tools that are not well inter-related. For experimental demonstration, we use the requirements of the automatic train protection (ATP) system of CASCO signal co. LTD., the largest railway signal control system manufacturer of China. The code of the tool cannot be released here because the project is commercially confidential. However, a demonstration video of the tool is available at https://youtu.be/BX0yv8pRMWs.

Alexander LeClair, Siyuan Jiang, Collin McMillan

Source code summarization -- creating natural language descriptions of source code behavior -- is a rapidly-growing research topic with applications to automatic documentation generation, program comprehension, and software maintenance. Traditional techniques relied on heuristics and templates built manually by human experts. Recently, data-driven approaches based on neural machine translation have largely overtaken template-based systems. But nearly all of these techniques rely almost entirely on programs having good internal documentation; without clear identifier names, the models fail to create good summaries. In this paper, we present a neural model that combines words from code with code structure from an AST. Unlike previous approaches, our model processes each data source as a separate input, which allows the model to learn code structure independent of the text in code. This process helps our approach provide coherent summaries in many cases even when zero internal documentation is provided. We evaluate our technique with a dataset we created from 2.1m Java methods. We find improvement over two baseline techniques from SE literature and one from NLP literature.

Siyuan Jiang, Ameer Armaly, Collin McMillan

Commit messages are a valuable resource in comprehension of software evolution, since they provide a record of changes such as feature additions and bug repairs. Unfortunately, programmers often neglect to write good commit messages. Different techniques have been proposed to help programmers by automatically writing these messages. These techniques are effective at describing what changed, but are often verbose and lack context for understanding the rationale behind a change. In contrast, humans write messages that are short and summarize the high level rationale. In this paper, we adapt Neural Machine Translation (NMT) to automatically "translate" diffs into commit messages. We trained an NMT algorithm using a corpus of diffs and human-written commit messages from the top 1k Github projects. We designed a filter to help ensure that we only trained the algorithm on higher-quality commit messages. Our evaluation uncovered a pattern in which the messages we generate tend to be either very high or very low quality. Therefore, we created a quality-assurance filter to detect cases in which we are unable to produce good messages, and return a warning instead.

Siyuan Jiang, Ameer Armaly, Collin McMillan et al.

When learning to use an Application Programming Interface (API), programmers need to understand the inputs and outputs (I/O) of the API functions. Current documentation tools automatically document the static information of I/O, such as parameter types and names. What is missing from these tools is dynamic information, such as I/O examples---actual valid values of inputs that produce certain outputs. In this paper, we demonstrate a prototype toolset we built to generate I/O examples. Our tool logs I/O values when API functions are executed, for example in running test suites. Then, the tool puts I/O values into API documents as I/O examples. Our tool has three programs: 1) funcWatch, which collects I/O values when API developers run test suites, 2) ioSelect, which selects one I/O example from a set of I/O values, and 3) ioPresent, which embeds the I/O examples into documents. In a preliminary evaluation, we used our tool to generate four hundred I/O examples for three C libraries: ffmpeg, libssh, and protobuf-c.

Siyuan Jiang, Collin McMillan

Committing to a version control system means submitting a software change to the system. Each commit can have a message to describe the submission. Several approaches have been proposed to automatically generate the content of such messages. However, the quality of the automatically generated messages falls far short of what humans write. In studying the differences between auto-generated and human-written messages, we found that 82% of the human-written messages have only one sentence, while the automatically generated messages often have multiple lines. Furthermore, we found that the commit messages often begin with a verb followed by an direct object. This finding inspired us to use a "verb+object" format in this paper to generate short commit summaries. We split the approach into two parts: verb generation and object generation. As our first try, we trained a classifier to classify a diff to a verb. We are seeking feedback from the community before we continue to work on generating direct objects for the commits.