arXiv subjects

Liming Nie

Publications and source records attributed to Liming Nie.

12 recordsLinked to original sources

arXiv2026

EndoGov: A knowledge-governed multi-agent expert system for endometrial cancer risk stratification

Multimodal artificial intelligence models for endometrial cancer (EC) risk stratification typically optimize aggregate predictive performance but provide limited mechanisms for enforcing mandatory guideline overrides, such as assigning POLE-mutated tumors to the low-risk group despite high-grade morphology. We present EndoGov, a two-tier multi-agent expert system that factorizes the decision process as D(x) = G(P(x), R), where specialist agents P extract structured evidence and a governance agent G applies an executable rule set R. Tier 1 comprises pathology, molecular, and clinical agents that independently generate schema-constrained reports from frozen foundation-model features or structured records. Tier 2 queries an evidence-level-weighted Guideline Knowledge Graph, using deterministic hard-path rules for high-priority overrides and constrained soft-path reasoning for ambiguous cases. In TCGA-UCEC (n=541), EndoGov achieved 0.943 accuracy, 0.973 macro AUC, and a conditional logic-violation rate (C-LVR) of 0.93% among trigger-exposed cases. In CPTAC-UCEC (n=95), where reference labels are guideline-derived, EndoGov reached 0.842 accuracy compared with < 0.31 for locked-transfer neural baselines, supporting governance-pathway transfer under distribution shift rather than validation against independent clinical truth. End-to-end safety decomposition localized residual failures primarily to upstream molecular detection rather than downstream governance. Backend-swap experiments further showed that hard-path compliance is invariant to the LLM backend. These findings indicate that explicit clinical-rule governance can provide guideline-compliant, auditable EC risk assignment while preserving competitive discrimination.

cs.MA↗

arXiv2026

SoK: Systematizing Software Artifacts Traceability via Associations, Techniques, and Applications

Software development relies heavily on traceability links between various software artifacts to ensure quality and facilitate maintenance. While automated traceability recovery techniques have advanced for different artifact pairs, the field remains fragmented with an incomplete overview of artifact associations, ambiguous linking techniques, and fragmented knowledge of application scenarios. To bridge these gaps, we conducted a systematic literature review on software traceability recovery to synthesize the linked artifacts, recovery tools, and usage scenarios across the traceability ecosystem. First, we constructed the first global artifacts traceability graph of 23 associations among 22 artifact types, exposing a severe research imbalance that heavily favors code-related links. Second, while recovery techniques are shifting toward deep semantic models, a reproducibility crisis persists (e.g., only 37% of studies released code); to address this, we provided a comprehensive evaluation framework including a technical decision map and standardized benchmarks. Finally, we quantified an industrial adoption gap (i.e., 95% of tools remain confined to academia) and proposed a role-centric framework to dynamically align artifact paths with concrete engineering activities. This review contributes a coherent knowledge framework for artifacts traceability research, identifies current trends, and provides directions for future work.

cs.SE↗

arXiv2025

Mapis: A Knowledge-Graph Grounded Multi-Agent Framework for Evidence-Based PCOS Diagnosis

Polycystic Ovary Syndrome (PCOS) constitutes a significant public health issue affecting 10% of reproductive-aged women, highlighting the critical importance of developing effective diagnostic tools. Previous machine learning and deep learning detection tools are constrained by their reliance on large-scale labeled data and an lack of interpretability. Although multi-agent systems have demonstrated robust capabilities, the potential of such systems for PCOS detection remains largely unexplored. Existing medical multi-agent frameworks are predominantly designed for general medical tasks, suffering from insufficient domain integration and a lack of specific domain knowledge. To address these challenges, we propose Mapis, the first knowledge-grounded multi-agent framework explicitly designed for guideline-based PCOS diagnosis. Specifically, it built upon the 2023 International Guideline into a structured collaborative workflow that simulates the clinical diagnostic process. It decouples complex diagnostic tasks across specialized agents: a gynecological endocrine agent and a radiology agent collaborative to verify inclusion criteria, while an exclusion agent strictly rules out other causes. Furthermore, we construct a comprehensive PCOS knowledge graph to ensure verifiable, evidence-based decision-making. Extensive experiments on public benchmarks and specialized clinical datasets, benchmarking against nine diverse baselines, demonstrate that Mapis significantly outperforms competitive methods. On the clinical dataset, it surpasses traditional machine learning models by 13.56%, single-agent by 6.55%, and previous medical multi-agent systems by 7.05% in Accuracy.

cs.MA↗

arXiv2024

A Comprehensive Study on Dark Patterns

As digital interfaces become increasingly prevalent, certain manipulative design elements have emerged that may harm user interests, raising associated ethical concerns and bringing dark patterns into focus as a significant research topic. Manipulative design strategies are widely used in user interfaces (UI) primarily to guide user behavior in ways that favor service providers, often at the cost of the users themselves. This paper addresses three main challenges in dark pattern research: inconsistencies and incompleteness in classification, limitations of detection tools, and insufficient comprehensiveness in existing datasets. In this study, we propose a comprehensive analytical framework--the Dark Pattern Analysis Framework (DPAF). Using this framework, we developed a taxonomy comprising 68 types of dark patterns, each annotated in detail to illustrate its impact on users, potential scenarios, and real-world examples, validated through industry surveys. Furthermore, we evaluated the effectiveness of current detection tools and assessed the completeness of available datasets. Our findings indicate that, among the 8 detection tools studied, only 31 types of dark patterns are identifiable, resulting in a coverage rate of just 45.5%. Similarly, our analysis of four datasets, encompassing 5,561 instances, reveals coverage of only 30 types of dark patterns, with an overall coverage rate of 44%. Based on the available datasets, we standardized classifications and merged datasets to form a unified image dataset and a unified text dataset. These results highlight significant room for improvement in the field of dark pattern detection. This research not only deepens our understanding of dark pattern classification and detection tools but also offers valuable insights for future research and practice in this domain.

cs.HC↗

arXiv2024

SoK: Detection and Repair of Accessibility Issues

There is an increasing global emphasis on information accessibility, with numerous researchers actively developing automated tools to detect and repair accessibility issues, thereby ensuring that individuals with diverse abilities can independently access software products and services. However, current research still encounters significant challenges in two key areas: the absence of a comprehensive taxonomy of accessibility issue types, and the lack of comprehensive analysis of the capabilities of detection and repair tools, as well as the status of corresponding datasets. To address these challenges, this paper introduces the Accessibility Issue Analysis (AIA) framework. Utilizing this framework, we develop a comprehensive taxonomy that categorizes 55 types of accessibility issues across four pivotal dimensions: Perceivability, Operability, Understandability, and Robustness. This taxonomy has been rigorously recognized through a questionnaire survey (n=130). Building on this taxonomy, we conduct an in-depth analysis of existing detection and repair tools, as well as the status of corresponding datasets. In terms of tools, our findings indicate that 14 detection tools can identify 31 issue types, achieving a 56.3% rate (31/55). Meanwhile, 9 repair tools address just 13 issue types, with a 23.6% rate. In terms of datasets, those for detection tools cover 21 issue types, at a 38.1% coverage rate, whereas those for repair tools cover only 7 types, at a 12.7% coverage rate.

cs.SE↗

arXiv2024

SoK: Comprehensive Analysis of Rug Pull Causes, Datasets, and Detection Tools in DeFi

Rug pulls pose a grave threat to the cryptocurrency ecosystem, leading to substantial financial loss and undermining trust in decentralized finance (DeFi) projects. With the emergence of new rug pull patterns, research on rug pull is out of state. To fill this gap, we first conducted an extensive analysis of the literature review, encompassing both scholarly and industry sources. By examining existing academic articles and industrial discussions on rug pull projects, we present a taxonomy inclusive of 34 root causes, introducing six new categories inspired by industry sources: burn, hidden owner, ownership transfer, unverified contract, external call, and fake LP lock. Based on the developed taxonomy, we evaluated current rug pull datasets and explored the effectiveness and limitations of existing detection mechanisms. Our evaluation indicates that the existing datasets, which document 2,448 instances, address only 7 of the 34 root causes, amounting to a mere 20% coverage. It indicates that existing open-source datasets need to be improved to study rug pulls. In response, we have constructed a more comprehensive dataset containing 2,360 instances, expanding the coverage to 54% with the best effort. In addition, the examination of 14 detection tools showed that they can identify 25 of the 34 root causes, achieving a coverage of 73.5%. There are nine root causes (Fake LP Lock, Hidden Fee, and Destroy Token, Fake Money Transfer, Ownership Transfer, Liquidity Pool Block, Freeze Account, Wash-Trading, Hedge) that the existing tools cannot cover. Our work indicates that there is a significant gap between current research and detection tools, and the actual situation of rug pulls.

cs.SE↗

arXiv2023

Score-based Generative Models for Photoacoustic Image Reconstruction with Rotation Consistency Constraints

Photoacoustic tomography (PAT) is a newly emerged imaging modality which enables both high optical contrast and acoustic depth of penetration. Reconstructing images of photoacoustic tomography from limited amount of senser data is among one of the major challenges in photoacoustic imaging. Previous works based on deep learning were trained in supervised fashion, which directly map the input partially known sensor data to the ground truth reconstructed from full field of view. Recently, score-based generative models played an increasingly significant role in generative modeling. Leveraging this probabilistic model, we proposed Rotation Consistency Constrained Score-based Generative Model (RCC-SGM), which recovers the PAT images by iterative sampling between Langevin dynamics and a constraint term utilizing the rotation consistency between the images and the measurements. Our proposed method can generalize to different measurement processes (32.29 PSNR with 16 measurements under random sampling, whereas 28.50 for supervised counterpart), while supervised methods need to train on specific inverse mappings.

cs.CV↗

arXiv2023

A Comprehensive Study on Quality Assurance Tools for Java

Quality assurance (QA) tools are receiving more and more attention and are widely used by developers. Given the wide range of solutions for QA technology, it is still a question of evaluating QA tools. Most existing research is limited in the following ways: (i) They compare tools without considering scanning rules analysis. (ii) They disagree on the effectiveness of tools due to the study methodology and benchmark dataset. (iii) They do not separately analyze the role of the warnings. (iv) There is no large-scale study on the analysis of time performance. To address these problems, in the paper, we systematically select 6 free or open-source tools for a comprehensive study from a list of 148 existing Java QA tools. To carry out a comprehensive study and evaluate tools in multi-level dimensions, we first mapped the scanning rules to the CWE and analyze the coverage and granularity of the scanning rules. Then we conducted an experiment on 5 benchmarks, including 1,425 bugs, to investigate the effectiveness of these tools. Furthermore, we took substantial effort to investigate the effectiveness of warnings by comparing the real labeled bugs with the warnings and investigating their role in bug detection. Finally, we assessed these tools' time performance on 1,049 projects. The useful findings based on our comprehensive study can help developers improve their tools and provide users with suggestions for selecting QA tools.

cs.SE↗

arXiv2023

Exploring Code Analysis: Zero-Shot Insights on Syntax and Semantics with LLMs

Code analysis is fundamental in Software Engineering, supporting debugging, optimization, and security assessment. Human developers approach it through syntax parsing, static semantics inference, and dynamic reasoning. Traditional tools are effective but limited by language specificity and weak cross-language generalization. Large language models (LLMs) are promising for code tasks, yet their capabilities for fundamental code analysis remain underexplored. We structure our study around three aspects aligned with human practices: syntax parsing, static semantics inference, and dynamic reasoning. We evaluate 21 state-of-the-art LLMs across nine tasks in four languages (C, Java, Python, Solidity), including AST generation, CFG construction, data dependency, taint analysis, and flaky test reasoning. We apply a three-layer evaluation protocol (automated metrics, expert adjudication, consistency validation) to 3,124 code samples, achieving high inter-rater reliability (Cohen's kappa = 0.844-0.936) and strong human-machine agreement (Gwet's AC1 = 0.500-0.727, F1 = 0.791-0.882). While the best LLMs excel in syntax parsing (AST 90%+, expression matching 84-100%) and show promise in static analysis, their dynamic reasoning remains limited (<70%) with high data-shift sensitivity (per-project F1 varying 0-1.0). This hierarchy holds across model families and scales, suggesting fundamental rather than transient limitations. These findings show how LLMs complement traditional analyzers: they offer cross-language generalization but non-deterministic outputs needing validation, while traditional tools give deterministic guarantees but need language-specific configuration. We contribute a validated evaluation framework with comparison against traditional analyzers (Tree-sitter, Soot, Joern) and task-specific applicability tiers. Benchmark: https://github.com/mathieu0905/llm_code_analysis.git

cs.SE↗

arXiv2017

Query Expansion Based on Crowd Knowledge for Code Search

As code search is a frequent developer activity in software development practices, improving the performance of code search is a critical task. In the text retrieval based search techniques employed in the code search, the term mismatch problem is a critical language issue for retrieval effectiveness. By reformulating the queries, query expansion provides effective ways to solve the term mismatch problem. In this paper, we propose Query Expansion based on Crowd Knowledge (QECK), a novel technique to improve the performance of code search algorithms. QECK identifies software-specific expansion words from the high quality pseudo relevance feedback question and answer pairs on Stack Overflow to automatically generate the expansion queries. Furthermore, we incorporate QECK in the classic Rocchio's model, and propose QECK based code search method QECKRocchio. We conduct three experiments to evaluate our QECK technique and investigate QECKRocchio in a large-scale corpus containing real-world code snippets and a question and answer pair collection. The results show that QECK improves the performance of three code search algorithms by up to 64 percent in Precision, and 35 percent in NDCG. Meanwhile, compared with the state-of-the-art query expansion method, the improvement of QECK Rocchio is 22 percent in Precision, and 16 percent in NDCG.

cs.SE↗

arXiv2017

ROSF: Leveraging Information Retrieval and Supervised Learning for Recommending Code Snippets

When implementing unfamiliar programming tasks, developers commonly search code examples and learn usage patterns of APIs from the code examples or reuse them by copy-pasting and modifying. For providing high-quality code examples, previous studies present several methods to recommend code snippets mainly based on information retrieval. In this paper, to provide better recommendation results, we propose ROSF, Recommending cOde Snippets with multi-aspect Features, a novel method combining both information retrieval and supervised learning. In our method, we recommend Top-Kcode snippets for a givenfree-form query based on two stages, i.e., coarse-grained searching and fine-grained re-ranking. First, we generate a code snippet candidate set by searching a code snippet corpus using an information retrieval method. Second, we predict probability values of the code snippets for different relevance scores in the candidate set by the learned prediction model from a training set, re-rank these candidate code snippets according to the probability values, and recommend the final results to developers. We conduct several experiments to evaluate our method in a large-scale corpus containing 921,713 real-world code snippets. The results show that ROSF is an effective method for code snippets recommendation and outperforms the-state-of-the-art methods by 20%-41% in Precision and 13%-33% in NDCG

cs.SE↗

arXiv2013

Full-Wave Iterative Image Reconstruction in Photoacoustic Tomography with Acoustically Inhomogeneous Media

Existing approaches to image reconstruction in photoacoustic computed tomography (PACT) with acoustically heterogeneous media are limited to weakly varying media, are computationally burdensome, and/or cannot effectively mitigate the effects of measurement data incompleteness and noise. In this work, we develop and investigate a discrete imaging model for PACT that is based on the exact photoacoustic (PA) wave equation and facilitates the circumvention of these limitations. A key contribution of the work is the establishment of a procedure to implement a matched forward and backprojection operator pair associated with the discrete imaging model, which permits application of a wide-range of modern image reconstruction algorithms that can mitigate the effects of data incompleteness and noise. The forward and backprojection operators are based on the k-space pseudospectral method for computing numerical solutions to the PA wave equation in the time domain. The developed reconstruction methodology is investigated by use of both computer-simulated and experimental PACT measurement data.

physics.med-ph↗