Liming Nie

Chao Huang, Kun Wang, Liming Nie et al.

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.

Shangqing Tong, Hengrong Lan, Liming Nie et al.

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.

Zhifei Chen, Lata Yi, Liming Nie et al.

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.

Weiye Dai, Liyun Shi, Zanxiang He et al.

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.

Wei Ma, Shangqing Liu, Zhihao Lin et al.

Large language models~(LLMs) demonstrate significant potential to revolutionize software engineering (SE) by exhibiting outstanding performance in SE tasks such as code and document generation. However, the high reliability and risk control requirements in software engineering raise concerns about the lack of interpretability of LLMs. To address this concern, we conducted a study to evaluate the capabilities of LLMs and their limitations for code analysis in SE. We break down the abilities needed for artificial intelligence~(AI) models to address SE tasks related to code analysis into three categories: 1) syntax understanding, 2) static behavior understanding, and 3) dynamic behavior understanding. Our investigation focused on the ability of LLMs to comprehend code syntax and semantic structures, which include abstract syntax trees (AST), control flow graphs (CFG), and call graphs (CG). We employed four state-of-the-art foundational models, GPT4, GPT3.5, StarCoder and CodeLlama-13b-instruct. We assessed the performance of LLMs on cross-language tasks involving C, Java, Python, and Solidity. Our findings revealed that while LLMs have a talent for understanding code syntax, they struggle with comprehending code semantics, particularly dynamic semantics. We conclude that LLMs possess capabilities similar to an Abstract Syntax Tree (AST) parser, demonstrating initial competencies in static code analysis. Furthermore, our study highlights that LLMs are susceptible to hallucinations when interpreting code semantic structures and fabricating nonexistent facts. These results indicate the need to explore methods to verify the correctness of LLM output to ensure its dependability in SE. More importantly, our study provides an initial answer to why the codes generated by LLM are usually syntax-correct but vulnerable.

He Jiang, Liming Nie, Zeyi Sun et al.

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

Liming Nie, He Jiang, Zhilei Ren et al.

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.