arXiv subjects

Zhi Jin

Publications and source records attributed to Zhi Jin.

At least 55 records · Page 3Linked to original sources

arXiv2026

Toward a CMOS-integrated quantum diamond biosensor based on NV centers

We report progress toward a CMOS-integrated quantum diamond biosensing platform that combines nitrogen-vacancy (NV) centers in diamond with a custom 40 nm CMOS Single-Photon Avalanche Diode (SPAD) array. The system integrates on-chip active quenching and digital readout with external FPGA-based photon counting, compact microwave delivery, and practical optical excitation and collection schemes to support widefield optically detected magnetic resonance (ODMR). System-level design considerations spanning fluorescence collection efficiency, detector count-rate capability, and microwave homogeneity are analyzed with biological compatibility and scalability in mind. Using superparamagnetic iron oxide nanoparticle (SPION)-labeled HEK293T cells as a representative use case, simple dipole-field estimates indicate that sub-$μ$T sensitivity is required to resolve ODMR shifts within typical ensemble linewidths. Based on the proposed architecture and efficiency analysis, a magnetic field sensitivity of approximately 90 nT/$\sqrt{\mathrm{Hz}}$ per pixel is estimated. These results outline a practical path from optics-heavy quantum diamond microscopes toward compact, CMOS-integrated NV-based biosensors for quantitative magnetic imaging in complex biological environments.

physics.app-ph↗

arXiv2026

ReqElicitGym: An Evaluation Environment for Interview Competence in Conversational Requirements Elicitation

With the rapid improvement of LLMs' coding capabilities, the bottleneck of LLM-based automated software development is shifting from generating correct code to eliciting users' requirements. Despite growing interest, the interview competence of LLMs in conversational requirements elicitation remains fully underexplored. Existing evaluations often depend on a few scenarios, real user interaction, and subjective human scoring, which hinders systematic and quantitative comparison. To address these challenges, we propose ReqElicitGym, an interactive and automatic evaluation environment for assessing interview competence in conversational requirements elicitation. Specifically, ReqElicitGym introduces a new evaluation dataset and designs both an interactive oracle user and a task evaluator. The dataset contains 101 website requirements elicitation scenarios spanning 10 application types. Both the oracle user and the task evaluator achieve high agreement with real users and expert judgment. Using our ReqElicitGym, any automated conversational requirements elicitation approach (e.g., LLM-based agents) can be evaluated in a reproducible and quantitative manner through interaction with the environment. Based on our ReqElicitGym, we conduct a systematic empirical study on seven representative LLMs, and the results show that current LLMs still exhibit limited interview competence in uncovering implicit requirements. Particularly, they elicit less than half of the users' implicit requirements, and their effective elicitation questions often emerge in later turns of the dialogue. Besides, we found LLMs can elicit interaction and content implicit requirements, but consistently struggle with style-related requirements. We believe ReqElicitGym will facilitate the evaluation and development of automated conversational requirements elicitation.

cs.SE↗

arXiv2026

aiXcoder-7B-v2: Training LLMs to Fully Utilize the Long Context in Repository-level Code Completion

Large Language Models (LLMs) have shown promising results in repository-level code completion, which completes code based on the in-file and cross-file context of a repository. The cross-file context typically contains different types of information (e.g., relevant APIs and similar code) and is lengthy. In this paper, we found that LLMs struggle to fully utilize the information in the cross-file context. We hypothesize that one of the root causes of the limitation is the misalignment between pre-training (i.e., relying on nearby context) and repo-level code completion (i.e., frequently attending to long-range cross-file context). To address the above misalignment, we propose Code Long-context Alignment - COLA, a purely data-driven approach to explicitly teach LLMs to focus on the cross-file context. Specifically, COLA constructs a large-scale repo-level code completion dataset - COLA-132K, where each sample contains the long cross-file context (up to 128K tokens) and requires generating context-aware code (i.e., cross-file API invocations and code spans similar to cross-file context). Through a two-stage training pipeline upon COLA-132K, LLMs learn the capability of finding relevant information in the cross-file context, thus aligning LLMs with repo-level code completion. We apply COLA to multiple popular LLMs (e.g., aiXcoder-7B) and extensive experiments on COLA-132K and a public benchmark - CrossCodeEval. Our experiments yield the following results. 1) Effectiveness. COLA substantially improves the performance of multiple LLMs in repo-level code completion. For example, it improves aiXcoder-7B by up to 19.7% in exact match. 2) Generalizability. The capability learned by COLA can generalize to new languages. 3) Enhanced Context Utilization Capability. We design two probing experiments, which show COLA improves the capability of LLMs in utilizing the information in cross-file context.

cs.SE↗

arXiv2026

FastPhysGS: Accelerating Physics-based Dynamic 3DGS Simulation via Interior Completion and Adaptive Optimization

Extending 3D Gaussian Splatting (3DGS) to 4D physical simulation remains challenging. Based on the Material Point Method (MPM), existing methods either rely on manual parameter tuning or distill dynamics from video diffusion models, limiting the generalization and optimization efficiency. Recent attempts using LLMs/VLMs suffer from a text/image-to-3D perceptual gap, yielding unstable physics behavior. In addition, they often ignore the surface structure of 3DGS, leading to implausible motion. We propose FastPhysGS, a fast and robust framework for physics-based dynamic 3DGS simulation:(1) Instance-aware Particle Filling (IPF) with Monte Carlo Importance Sampling (MCIS) to efficiently populate interior particles while preserving geometric fidelity; (2) Bidirectional Graph Decoupling Optimization (BGDO), an adaptive strategy that rapidly optimizes material parameters predicted from a VLM. Experiments show FastPhysGS achieves high-fidelity physical simulation in 1 minute using only 7 GB runtime memory, outperforming prior works with broad potential applications.

cs.CV↗

arXiv2026

Learning to Evolve: Bayesian-Guided Continual Knowledge Graph Embedding

As social media and the World Wide Web become hubs for information dissemination, effectively organizing and understanding the vast amounts of dynamically evolving Web content is crucial. Knowledge graphs (KGs) provide a powerful framework for structuring this information. However, the rapid emergence of new hot topics, user relationships, and events in social media renders traditional static knowledge graph embedding (KGE) models rapidly outdated. Continual Knowledge Graph Embedding (CKGE) aims to address this issue, but existing methods commonly suffer from catastrophic forgetting, whereby older, but still valuable, information is lost when learning new knowledge (such as new memes or trending events). This means the model cannot effectively learn the evolution of the data. We propose a novel CKGE framework, BAKE. Unlike existing methods, BAKE formulates CKGE as a sequential Bayesian inference problem and utilizes the Bayesian posterior update principle as a natural continual learning strategy. This principle is insensitive to data order and provides theoretical guarantees to preserve prior knowledge as much as possible. Specifically, we treat each batch of new data as a Bayesian update to the model's prior. By maintaining the posterior distribution, the model effectively preserves earlier knowledge even as it evolves over multiple snapshots. Furthermore, to constrain the evolution of knowledge across snapshots, we introduce a continual clustering method that maintains the compact cluster structure of entity embeddings through a regularization term, ensuring semantic consistency while allowing controlled adaptation to new knowledge. We conduct extensive experiments on multiple CKGE benchmarks, which demonstrate that BAKE achieves the top performance in the vast majority of cases compared to existing approaches.

cs.CL↗

arXiv2026

Evaluating Large Language Models for Time Series Anomaly Detection in Aerospace Software

Time series anomaly detection (TSAD) is essential for ensuring the safety and reliability of aerospace software systems. Although large language models (LLMs) provide a promising training-free alternative to unsupervised approaches, their effectiveness in aerospace settings remains under-examined because of complex telemetry, misaligned evaluation metrics, and the absence of domain knowledge. To address this gap, we introduce ATSADBench, the first benchmark for aerospace TSAD. ATSADBench comprises nine tasks that combine three pattern-wise anomaly types, univariate and multivariate signals, and both in-loop and out-of-loop feedback scenarios, yielding 108,000 data points. Using this benchmark, we systematically evaluate state-of-the-art open-source LLMs under two paradigms: Direct, which labels anomalies within sliding windows, and Prediction-Based, which detects anomalies from prediction errors. To reflect operational needs, we reformulate evaluation at the window level and propose three user-oriented metrics: Alarm Accuracy (AA), Alarm Latency (AL), and Alarm Contiguity (AC), which quantify alarm correctness, timeliness, and credibility. We further examine two enhancement strategies, few-shot learning and retrieval-augmented generation (RAG), to inject domain knowledge. The evaluation results show that (1) LLMs perform well on univariate tasks but struggle with multivariate telemetry, (2) their AA and AC on multivariate tasks approach random guessing, (3) few-shot learning provides modest gains whereas RAG offers no significant improvement, and (4) in practice LLMs can detect true anomaly onsets yet sometimes raise false alarms, which few-shot prompting mitigates but RAG exacerbates. These findings offer guidance for future LLM-based TSAD in aerospace software.

cs.SE↗

arXiv2026

PROPHET: An Inferable Future Forecasting Benchmark with Causal Intervened Likelihood Estimation

Predicting future events based on news on the Web stands as one of the ultimate aspirations of artificial intelligence. Recent advances in large language model (LLM)-based systems have shown remarkable potential in forecasting future events, thereby garnering significant interest in the research community. Currently, several benchmarks have been established to evaluate the forecasting capabilities by formalizing the event prediction as a retrieval-augmented generation (RAG)-and-reasoning task. In these benchmarks, each prediction question is answered with relevant retrieved news articles downloaded from the Web. However, because there is no consideration of whether the questions can be supported by valid or sufficient supporting rationales, some of the questions in these benchmarks may be inherently noninferable. To address this issue, we introduce a new benchmark, PROPHET, which comprises inferable forecasting questions paired with relevant news for retrieval. To ensure the inferability of the benchmark, we propose Causal Intervened Likelihood (CIL), a statistical measure that assesses inferability through causal inference. In constructing this benchmark, we first collected recent trend forecasting questions, and then filtered the data using CIL resulting in an inferable benchmark for future forecasting. Through extensive experiments, we first demonstrate the validity of CIL and in-depth investigations into future forecasting with the aid of CIL. Subsequently, we evaluate several representative prediction methods on PROPHET. The overall results draws valuable insights for task of future directions.

cs.CL↗

arXiv2026

REprompt: Prompt Generation for Intelligent Software Development Guided by Requirements Engineering

The rapid development of large language models is transforming software development. Beyond serving as code auto-completion tools in integrated development environments, large language models increasingly function as foundation models within coding agents in vibe-coding scenarios. In such settings, prompts play a central role in agent-based intelligent software development, as they not only guide the behavior of large language models but also serve as carriers of user requirements. Under the dominant conversational paradigm, prompts are typically divided into system prompts and user prompts. System prompts provide high-level instructions to steer model behavior and establish conversational context, while user prompts represent inputs and requirements provided by human users. Despite their importance, designing effective prompts remains challenging, as it requires expertise in both prompt engineering and software engineering, particularly requirements engineering. To reduce the burden of manual prompt construction, numerous automated prompt engineering methods have been proposed. However, most existing approaches neglect the methodological principles of requirements engineering, limiting their ability to generate artifacts that conform to formal requirement specifications in realistic software development scenarios. To address this gap, we propose REprompt, a multi-agent prompt optimization framework guided by requirements engineering. Experiment results demonstrate that REprompt effectively optimizes both system and user prompts by grounding prompt generation in requirements engineering principles.

cs.SE↗

arXiv2026

IntentCoding: Amplifying User Intent in Code Generation

Large Language Models (LLMs) have shown strong capabilities in code generation, but their adherence to fine-grained user intent with multiple constraints remains a significant challenge. Our empirical analysis reveals two key observations: 1) Model performance deteriorates quickly as the number of constraints in the user intent increases, and 2) While user intent does influence the model's logits, such an influence may not be strong enough to effectively steer the decoding process. To this end, we propose Intent-Amplified Code Generation (IntentCoding), a novel decoding strategy that enhances an LLM's ability to follow user intent. IntentCoding captures the influence of user intent by masking out the intent, and applies a multi-strength ensemble mechanism to amplify the effect of user intent during generation. IntentCoding is model-agnostic, requires no additional training, and integrates seamlessly with existing decoding procedures. To enable systematic evaluation, we also construct CodeConstraints, a benchmark dataset specifically designed to test user intent compliance under varying numbers of constraints. Experiments on our constructed Constraints, as well as popular IFEvalCode, HumanEval and LiveCodeBench datasets, show that our IntentCoding model significantly improves both constraint satisfaction and functional correctness compared to standard decoding approaches. IntentCoding achieves up to 71.0% relative improvement on CodeConstraints, achieves up to 67.3% relative improvement on IFEvalCode and achieves up to 29.3% relative improvement in pass@1 on HumanEval and LiveCodeBench compared with greedy decoding.

cs.SE↗

arXiv2025

GraphLocator: Graph-guided Causal Reasoning for Issue Localization

The issue localization task aims to identify the locations in a software repository that requires modification given a natural language issue description. This task is fundamental yet challenging in automated software engineering due to the semantic gap between issue description and source code implementation. This gap manifests as two mismatches:(1) symptom-to-cause mismatches, where descriptions do not explicitly reveal underlying root causes; (2) one-to-many mismatches, where a single issue corresponds to multiple interdependent code entities. To address these two mismatches, we propose GraphLocator, an approach that mitigates symptom-to-cause mismatches through causal structure discovering and resolves one-to-many mismatches via dynamic issue disentangling. The key artifact is the causal issue graph (CIG), in which vertices represent discovered sub-issues along with their associated code entities, and edges encode the causal dependencies between them. The workflow of GraphLocator consists of two phases: symptom vertices locating and dynamic CIG discovering; it first identifies symptom locations on the repository graph, then dynamically expands the CIG by iteratively reasoning over neighboring vertices. Experiments on three real-world datasets demonstrates the effectiveness of GraphLocator: (1) Compared with baselines, GraphLocator achieves more accurate localization with average improvements of +19.49% in function-level recall and +11.89% in precision. (2) GraphLocator outperforms baselines on both symptom-to-cause and one-to-many mismatch scenarios, achieving recall improvement of +16.44% and +19.18%, precision improvement of +7.78% and +13.23%, respectively. (3) The CIG generated by GraphLocator yields the highest relative improvement, resulting in a 28.74% increase in performance on downstream resolving task.

cs.SE↗

arXiv2025

Gradient as Conditions: Rethinking HOG for All-in-one Image Restoration

All-in-one image restoration (AIR) aims to address diverse degradations within a unified model by leveraging informative degradation conditions to guide the restoration process. However, existing methods often rely on implicitly learned priors, which may entangle feature representations and hinder performance in complex or unseen scenarios. Histogram of Oriented Gradients (HOG) as a classical gradient representation, we observe that it has strong discriminative capability across diverse degradations, making it a powerful and interpretable prior for AIR. Based on this insight, we propose HOGformer, a Transformer-based model that integrates learnable HOG features for degradation-aware restoration. The core of HOGformer is a Dynamic HOG-aware Self-Attention (DHOGSA) mechanism, which adaptively models long-range spatial dependencies conditioned on degradation-specific cues encoded by HOG descriptors. To further adapt the heterogeneity of degradations in AIR, we propose a Dynamic Interaction Feed-Forward (DIFF) module that facilitates channel-spatial interactions, enabling robust feature transformation under diverse degradations. Besides, we propose a HOG loss to explicitly enhance structural fidelity and edge sharpness. Extensive experiments on a variety of benchmarks, including adverse weather and natural degradations, demonstrate that HOGformer achieves state-of-the-art performance and generalizes well to complex real-world scenarios.Code is available at https://github.com/Fire-friend/HOGformer.

cs.CV↗

arXiv2025

Aligning Academia with Industry: An Empirical Study of Industrial Needs and Academic Capabilities in AI-Driven Software Engineering

The rapid advancement of large language models (LLMs) is fundamentally reshaping software engineering (SE), driving a paradigm shift in both academic research and industrial practice. While top-tier SE venues continue to show sustained or emerging focus on areas like automated testing and program repair, with researchers worldwide reporting continuous performance gains, the alignment of these academic advances with real industrial needs remains unclear. To bridge this gap, we first conduct a systematic analysis of 1,367 papers published in FSE, ASE, and ICSE between 2022 and 2025, identifying key research topics, commonly used benchmarks, industrial relevance, and open-source availability. We then carry out an empirical survey across 17 organizations, collecting 282 responses on six prominent topics, i.e., program analysis, automated testing, code generation/completion, issue resolution, pre-trained code models, and dependency management, through structured questionnaires. By contrasting academic capabilities with industrial feedback, we derive seven critical implications, highlighting under-addressed challenges in software requirements and architecture, the reliability and explainability of intelligent SE approaches, input assumptions in academic research, practical evaluation tensions, and ethical considerations. This study aims to refocus academic attention on these important yet under-explored problems and to guide future SE research toward greater industrial impact.

cs.SE↗

arXiv2025

UCRBench: Benchmarking LLMs on Use Case Recovery

Use cases are widely employed to specify functional requirements, yet existing benchmarks are scarce and face the risk of being misaligned with actual system behavior, similarly limiting the rigorous evaluation of large language models (LLMs) in generating use cases from source code. We address this gap by introducing code-aligned use case benchmarks, constructed through manual validation of both user-goal and subfunction use cases across nine real-world software projects. Using this benchmark, we conduct the first systematic study of LLMs and propose a hierarchical evaluation protocol that assesses actor correctness, name accuracy, path fidelity, and behavioral coverage. The results show that while LLMs can partially reconstruct system functionality, their performance varies significantly across projects, with particularly noticeable shortcomings in domain-specific and multi-module systems. The models also exhibit high omission rates and struggle to maintain consistent abstraction when aggregating subfunctions into user-goal use cases, highlighting both the potential and current limitations of LLM-based use case reverse engineering.

cs.SE↗

arXiv2025

Bidirectional Representations Augmented Autoregressive Biological Sequence Generation

Autoregressive (AR) models, common in sequence generation, are limited in many biological tasks such as de novo peptide sequencing and protein modeling by their unidirectional nature, failing to capture crucial global bidirectional token dependencies. Non-Autoregressive (NAR) models offer holistic, bidirectional representations but face challenges with generative coherence and scalability. To transcend this, we propose a hybrid framework enhancing AR generation by dynamically integrating rich contextual information from non-autoregressive mechanisms. Our approach couples a shared input encoder with two decoders: a non-autoregressive one learning latent bidirectional biological features, and an AR decoder synthesizing the biological sequence by leveraging these bidirectional features. A novel cross-decoder attention module enables the AR decoder to iteratively query and integrate these bidirectional features, enriching its predictions. This synergy is cultivated via a tailored training strategy with importance annealing for balanced objectives and cross-decoder gradient blocking for stable, focused learning. Evaluations on a demanding nine-species benchmark of de novo peptide sequencing show that our model substantially surpasses AR and NAR baselines. It uniquely harmonizes AR stability with NAR contextual awareness, delivering robust, superior performance on diverse downstream data. This research advances biological sequence modeling techniques and contributes a novel architectural paradigm for augmenting AR models with enhanced bidirectional understanding for complex sequence generation. Code is available at https://github.com/BEAM-Labs/denovo.

cs.LG↗

arXiv2025

Generative AI for Self-Adaptive Systems: State of the Art and Research Roadmap

Self-adaptive systems (SASs) are designed to handle changes and uncertainties through a feedback loop with four core functionalities: monitoring, analyzing, planning, and execution. Recently, generative artificial intelligence (GenAI), especially the area of large language models, has shown impressive performance in data comprehension and logical reasoning. These capabilities are highly aligned with the functionalities required in SASs, suggesting a strong potential to employ GenAI to enhance SASs. However, the specific benefits and challenges of employing GenAI in SASs remain unclear. Yet, providing a comprehensive understanding of these benefits and challenges is complex due to several reasons: limited publications in the SAS field, the technological and application diversity within SASs, and the rapid evolution of GenAI technologies. To that end, this paper aims to provide researchers and practitioners a comprehensive snapshot that outlines the potential benefits and challenges of employing GenAI's within SAS. Specifically, we gather, filter, and analyze literature from four distinct research fields and organize them into two main categories to potential benefits: (i) enhancements to the autonomy of SASs centered around the specific functions of the MAPE-K feedback loop, and (ii) improvements in the interaction between humans and SASs within human-on-the-loop settings. From our study, we outline a research roadmap that highlights the challenges of integrating GenAI into SASs. The roadmap starts with outlining key research challenges that need to be tackled to exploit the potential for applying GenAI in the field of SAS. The roadmap concludes with a practical reflection, elaborating on current shortcomings of GenAI and proposing possible mitigation strategies.

cs.SE↗

arXiv2025

Large Language Model Unlearning for Source Code

While Large Language Models (LLMs) excel at code generation, their inherent tendency toward verbatim memorization of training data introduces critical risks like copyright infringement, insecure emission, and deprecated API utilization, etc. A straightforward yet promising defense is unlearning, ie., erasing or down-weighting the offending snippets through post-training. However, we find its application to source code often tends to spill over, damaging the basic knowledge of programming languages learned by the LLM and degrading the overall capability. To ease this challenge, we propose PROD for precise source code unlearning. PROD surgically zeroes out the prediction probability of the prohibited tokens, and renormalizes the remaining distribution so that the generated code stays correct. By excising only the targeted snippets, PROD achieves precise forgetting without much degradation of the LLM's overall capability. To facilitate in-depth evaluation against PROD, we establish an unlearning benchmark consisting of three downstream tasks (ie., unlearning of copyrighted code, insecure code, and deprecated APIs), and introduce Pareto Dominance Ratio (PDR) metric, which indicates both the forget quality and the LLM utility. Our comprehensive evaluation demonstrates that PROD achieves superior overall performance between forget quality and model utility compared to existing unlearning approaches across three downstream tasks, while consistently exhibiting improvements when applied to LLMs of varying series. PROD also exhibits superior robustness against adversarial attacks without generating or exposing the data to be forgotten. These results underscore that our approach not only successfully extends the application boundary of unlearning techniques to source code, but also holds significant implications for advancing reliable code generation.

cs.SE↗

arXiv2025

A Viable Paradigm of Software Automation: Iterative End-to-End Automated Software Development

Software development automation is a long-term goal in software engineering. With the development of artificial intelligence (AI), more and more researchers are exploring approaches to software automation. They view AI systems as tools or assistants in software development, still requiring significant human involvement. Another initiative is ``vibe coding'', where AI systems write and repeatedly revise most (or even all) of the code. We foresee these two development paths will converge towards the same destination: AI systems participate in throughout the software development lifecycle, expanding boundaries of full-stack software development. In this paper, we present a vision of an iterative end-to-end automated software development paradigm AutoSW. It operates in an analyze-plan-implement-deliver loop, where AI systems as human partners become first-class actors, translating human intentions expressed in natural language into executable software. We explore a lightweight prototype across the paradigm and initially execute various representative cases. The results indicate that AutoSW can successfully deliver executable software, providing a feasible direction for truly end-to-end automated software development.

cs.SE↗

arXiv2025

A Needle in a Haystack: Intent-driven Reusable Artifacts Recommendation with LLMs

In open source software development, the reuse of existing artifacts has been widely adopted to avoid redundant implementation work. Reusable artifacts are considered more efficient and reliable than developing software components from scratch. However, when faced with a large number of reusable artifacts, developers often struggle to find artifacts that can meet their expected needs. To reduce this burden, retrieval-based and learning-based techniques have been proposed to automate artifact recommendations. Recently, Large Language Models (LLMs) have shown the potential to understand intentions, perform semantic alignment, and recommend usable artifacts. Nevertheless, their effectiveness has not been thoroughly explored. To fill this gap, we construct an intent-driven artifact recommendation benchmark named IntentRecBench, covering three representative open source ecosystems. Using IntentRecBench, we conduct a comprehensive comparative study of five popular LLMs and six traditional approaches in terms of precision and efficiency. Our results show that although LLMs outperform traditional methods, they still suffer from low precision and high inference cost due to the large candidate space. Inspired by the ontology-based semantic organization in software engineering, we propose TreeRec, a feature tree-guided recommendation framework to mitigate these issues. TreeRec leverages LLM-based semantic abstraction to organize artifacts into a hierarchical semantic tree, enabling intent and function alignment and reducing reasoning time. Extensive experiments demonstrate that TreeRec consistently improves the performance of diverse LLMs across ecosystems, highlighting its generalizability and potential for practical deployment.

cs.SE↗