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We present a comprehensive dataset of Java vulnerability-fixing commits (VFCs) to advance research in Java vulnerability analysis. Our dataset, derived from thousands of open-source Java projects on GitHub, comprises two variants: JavaVFC and JavaVFC-extended. The dataset was constructed through a rigorous process involving heuristic rules and multiple rounds of manual labeling. We initially used keywords to filter candidate VFCs based on commit messages, then refined this keyword set through iterative manual labeling. The final labeling round achieved a precision score of 0.7 among three annotators. We applied the refined keyword set to 34,321 open-source Java repositories with over 50 GitHub stars, resulting in JavaVFC with 784 manually verified VFCs and JavaVFC-extended with 16,837 automatically identified VFCs. Both variants are presented in a standardized JSONL format for easy access and analysis. This dataset supports various research endeavors, including VFC identification, fine-grained vulnerability detection, and automated vulnerability repair. The JavaVFC and JavaVFC-extended are publicly available at https://zenodo.org/records/13731781.

Embodied AI systems, including AI-powered robots that autonomously interact with the physical world, stand to be significantly advanced by Large Language Models (LLMs), which enable robots to better understand complex language commands and perform advanced tasks with enhanced comprehension and adaptability, highlighting their potential to improve embodied AI capabilities. However, this advancement also introduces safety challenges, particularly in robotic navigation tasks. Improper safety management can lead to failures in complex environments and make the system vulnerable to malicious command injections, resulting in unsafe behaviours such as detours or collisions. To address these issues, we propose \textit{SafeEmbodAI}, a safety framework for integrating mobile robots into embodied AI systems. \textit{SafeEmbodAI} incorporates secure prompting, state management, and safety validation mechanisms to secure and assist LLMs in reasoning through multi-modal data and validating responses. We designed a metric to evaluate mission-oriented exploration, and evaluations in simulated environments demonstrate that our framework effectively mitigates threats from malicious commands and improves performance in various environment settings, ensuring the safety of embodied AI systems. Notably, In complex environments with mixed obstacles, our method demonstrates a significant performance increase of 267\% compared to the baseline in attack scenarios, highlighting its robustness in challenging conditions.

The integration of Large Language Models (LLMs) like GPT-4o into robotic systems represents a significant advancement in embodied artificial intelligence. These models can process multi-modal prompts, enabling them to generate more context-aware responses. However, this integration is not without challenges. One of the primary concerns is the potential security risks associated with using LLMs in robotic navigation tasks. These tasks require precise and reliable responses to ensure safe and effective operation. Multi-modal prompts, while enhancing the robot's understanding, also introduce complexities that can be exploited maliciously. For instance, adversarial inputs designed to mislead the model can lead to incorrect or dangerous navigational decisions. This study investigates the impact of prompt injections on mobile robot performance in LLM-integrated systems and explores secure prompt strategies to mitigate these risks. Our findings demonstrate a substantial overall improvement of approximately 30.8% in both attack detection and system performance with the implementation of robust defence mechanisms, highlighting their critical role in enhancing security and reliability in mission-oriented tasks.

In recent years, Large Language Models (LLMs) have demonstrated remarkable capabilities in understanding and solving mathematical problems, leading to advancements in various fields. We propose an LLM-embodied path planning framework for mobile agents, focusing on solving high-level coverage path planning issues and low-level control. Our proposed multi-layer architecture uses prompted LLMs in the path planning phase and integrates them with the mobile agents' low-level actuators. To evaluate the performance of various LLMs, we propose a coverage-weighted path planning metric to assess the performance of the embodied models. Our experiments show that the proposed framework improves LLMs' spatial inference abilities. We demonstrate that the proposed multi-layer framework significantly enhances the efficiency and accuracy of these tasks by leveraging the natural language understanding and generative capabilities of LLMs. Our experiments show that this framework can improve LLMs' 2D plane reasoning abilities and complete coverage path planning tasks. We also tested three LLM kernels: gpt-4o, gemini-1.5-flash, and claude-3.5-sonnet. The experimental results show that claude-3.5 can complete the coverage planning task in different scenarios, and its indicators are better than those of the other models., Comment: 7 pages, 2 figures, conference

Data augmentation techniques apply transformations to existing texts to generate additional data. The transformations may produce low-quality texts, where the meaning of the text is changed and the text may even be mangled beyond human comprehension. Analyzing the synthetically generated texts and their corresponding labels is slow and demanding. To winnow out texts with incorrect labels, we develop INSPECTOR, a human-in-the-loop data inspection technique. INSPECTOR combines the strengths of provenance tracking techniques with assistive labeling. INSPECTOR allows users to group related texts by their transformation provenance, i.e., the transformations applied to the original text, or feature provenance, the linguistic features of the original text. For assistive labeling, INSPECTOR computes metrics that approximate data quality, and allows users to compare the corresponding label of each text against the predictions of a large language model. In a user study, INSPECTOR increases the number of texts with correct labels identified by 3X on a sentiment analysis task and by 4X on a hate speech detection task. The participants found grouping the synthetically generated texts by their common transformation to be the most useful technique. Surprisingly, grouping texts by common linguistic features was perceived to be unhelpful. Contrary to prior work, our study finds that no single technique obviates the need for human inspection effort. This validates the design of INSPECTOR which combines both analysis of data provenance and assistive labeling to reduce human inspection effort., Comment: NAACL 2024 Findings

Compiler technologies in deep learning and domain-specific hardware acceleration are increasingly adopting extensible compiler frameworks such as Multi-Level Intermediate Representation (MLIR) to facilitate more efficient development. With MLIR, compiler developers can easily define their own custom IRs in the form of MLIR dialects. However, the diversity and rapid evolution of such custom IRs make it impractical to manually write a custom test generator for each dialect. To address this problem, we design a new test generator called SYNTHFUZZ that combines grammar-based fuzzing with custom mutation synthesis. The key essence of SYNTHFUZZ is two fold: (1) It automatically infers parameterized context-dependent custom mutations from existing test cases. (2) It then concretizes the mutation's content depending on the target context and reduces the chance of inserting invalid edits by performing k-ancestor and pre(post)fix matching. SYNTHFUZZ obviates the need to manually define custom mutation operators for each dialect. We compare SYNTHFUZZ to three baselines: Grammarinator, MLIRSmith, and NeuRI. We conduct this comprehensive comparison on four different MLIR projects. Each project defines a new set of MLIR dialects where manually writing a custom test generator would take weeks of effort. Our evaluation shows that SYNTHFUZZ on average improves MLIR dialect pair coverage by 1.75 times, which increases branch coverage by 1.22 times. Further, we show that our context dependent custom mutation increases the proportion of valid tests by up to 1.11 times, indicating that SYNTHFUZZ correctly concretizes its parameterized mutations with respect to the target context. Parameterization of the mutations reduces the fraction of tests violating the base MLIR constraints by 0.57 times, increasing the time spent fuzzing dialect-specific code.

Fluorescence imaging in thick biological tissues is challenging due to sample-induced aberration and scattering, which leads to severe degradation of image quality and resolution. Fluorescence imaging in reflection geometry further exacerbates this issue since the point spread function is distorted in both excitation and emission pathways. Here, we propose a novel approach termed adaptive optics virtual structured illumination microscopy (AO V-SIM) that enables super-resolution multiphoton imaging through a scattering medium in reflection geometry. Our approach exploits the incoherent reflection matrix obtained using a conventional point-scanning fluorescence microscope with an array detector. We introduce V-SIM super-resolution reconstruction algorithm based on the incoherent reflection matrix. Furthermore, we introduce a software adaptive optics correction algorithm, AO V-SIM, which recovers unattenuated and phase-corrected optical transfer function for both excitation and emission pathways. The effectiveness of our proposed method is experimentally validated through sub-diffraction-limited two-photon fluorescence imaging of various samples in the presence of strong aberration.

In this paper, we define the spectral Einstein functional associated with the sub-Dirac operator for manifolds with boundary. A proof of the Dabrowski-Sitarz-Zalecki type theorem for spectral Einstein functions associated with the sub-Dirac operator on four-dimensional manifolds with boundary is also given., Comment: arXiv admin note: text overlap with arXiv:2308.00833, arXiv:2312.00838

Our paper provides empirical comparisons between recent IDSs to provide an objective comparison between them to help users choose the most appropriate solution based on their requirements. Our results show that no one solution is the best, but is dependent on external variables such as the types of attacks, complexity, and network environment in the dataset. For example, BoT_IoT and Stratosphere IoT datasets both capture IoT-related attacks, but the deep neural network performed the best when tested using the BoT_IoT dataset while HELAD performed the best when tested using the Stratosphere IoT dataset. So although we found that a deep neural network solution had the highest average F1 scores on tested datasets, it is not always the best-performing one. We further discuss difficulties in using IDS from literature and project repositories, which complicated drawing definitive conclusions regarding IDS selection., Comment: 10 pages

The 2019 edition of Stack Overflow developer survey highlights that, for the first time, Python outperformed Java in terms of popularity. The gap between Python and Java further widened in the 2020 edition of the survey. Unfortunately, despite the rapid increase in Python's popularity, there are not many testing and debugging tools that are designed for Python. This is in stark contrast with the abundance of testing and debugging tools for Java. Thus, there is a need to push research on tools that can help Python developers. One factor that contributed to the rapid growth of Java testing and debugging tools is the availability of benchmarks. A popular benchmark is the Defects4J benchmark; its initial version contained 357 real bugs from 5 real-world Java programs. Each bug comes with a test suite that can expose the bug. Defects4J has been used by hundreds of testing and debugging studies and has helped to push the frontier of research in these directions. In this project, inspired by Defects4J, we create another benchmark database and tool that contain 493 real bugs from 17 real-world Python programs. We hope our benchmark can help catalyze future work on testing and debugging tools that work on Python programs.

Large language models of code have shown remarkable effectiveness across various software engineering tasks. Despite the availability of many cloud services built upon these powerful models, there remain several scenarios where developers cannot take full advantage of them, stemming from factors such as restricted or unreliable internet access, institutional privacy policies that prohibit external transmission of code to third-party vendors, and more. Therefore, developing a compact, efficient, and yet energy-saving model for deployment on developers' devices becomes essential. To this aim, we propose Avatar, a novel approach that crafts a deployable model from a large language model of code by optimizing it in terms of model size, inference latency, energy consumption, and carbon footprint while maintaining a comparable level of effectiveness. The key idea of Avatar is to formulate the optimization of language models as a multi-objective configuration tuning problem and solve it with the help of a Satisfiability Modulo Theories (SMT) solver and a tailored optimization algorithm. The SMT solver is used to form an appropriate configuration space, while the optimization algorithm identifies the Pareto-optimal set of configurations for training the optimized models using knowledge distillation. We evaluate Avatar with two popular language models of code, i.e., CodeBERT and GraphCodeBERT, on two popular tasks, i.e., vulnerability prediction and clone detection. We use Avatar to produce optimized models with a small size (3 MB), which is 160$\times$ smaller than the original large models. On the two tasks, the optimized models significantly reduce the energy consumption (up to 184$\times$ less), carbon footprint (up to 157$\times$ less), and inference latency (up to 76$\times$ faster), with only a negligible loss in effectiveness (1.67\% on average)., Comment: Accepted by Software Engineering in Society Track of the 46th IEEE/ACM International Conference on Software Engineering (ICSE '24)

Quantum-inspired Machine Learning (QiML) is a burgeoning field, receiving global attention from researchers for its potential to leverage principles of quantum mechanics within classical computational frameworks. However, current review literature often presents a superficial exploration of QiML, focusing instead on the broader Quantum Machine Learning (QML) field. In response to this gap, this survey provides an integrated and comprehensive examination of QiML, exploring QiML's diverse research domains including tensor network simulations, dequantized algorithms, and others, showcasing recent advancements, practical applications, and illuminating potential future research avenues. Further, a concrete definition of QiML is established by analyzing various prior interpretations of the term and their inherent ambiguities. As QiML continues to evolve, we anticipate a wealth of future developments drawing from quantum mechanics, quantum computing, and classical machine learning, enriching the field further. This survey serves as a guide for researchers and practitioners alike, providing a holistic understanding of QiML's current landscape and future directions., Comment: 59 pages, 13 figures, 9 tables. - Edited for spelling, grammar, and corrected minor typos in formulas - Adjusted wording in places for better clarity - Corrected contact info - Added Table 1 to clarify variables used in dequantized algs. - Added subsections in QVAS discussing QCBMs and TN-based VQC models - Included additional references as requested by authors to ensure a more exhaustive survey

The SZZ algorithm is used to connect bug-fixing commits to the earlier commits that introduced bugs. This algorithm has many applications and many variants have been devised. However, there are some types of commits that cannot be traced by the SZZ algorithm, referred to as "ghost commits". The evaluation of how these ghost commits impact the SZZ algorithm remains limited. Moreover, these algorithms have been evaluated on datasets created by software engineering researchers from information in bug trackers and version controlled histories. Since Oct 2013, the Linux kernel developers have started labelling bug-fixing patches with the commit identifiers of the corresponding bug-inducing commit(s) as a standard practice. As of v6.1-rc5, 76,046 pairs of bug-fixing patches and bug-inducing commits are available. This provides a unique opportunity to evaluate the SZZ algorithm on a large dataset that has been created and reviewed by project developers, entirely independently of the biases of software engineering researchers. In this paper, we apply six SZZ algorithms to 76,046 pairs of bug-fixing patches and bug-introducing commits from the Linux kernel. Our findings reveal that SZZ algorithms experience a more significant decline in recall on our dataset (13.8%) as compared to prior findings reported by Rosa et al., and the disparities between the individual SZZ algorithms diminish. Moreover, we find that 17.47% of bug-fixing commits are ghost commits. Finally, we propose Tracing-Commit SZZ (TC-SZZ), that traces all commits in the change history of lines modified or deleted in bug-fixing commits. Applying TC-SZZ to all failure cases, excluding ghost commits, we found that TC-SZZ could identify 17.7% of them. Our further analysis found that 34.6% of bug-inducing commits were in the function history, 27.5% in the file history (but not in the function history), and..., Comment: This article has been accepted for publication in IEEE Transactions on Software Engineering

With the increasing reliance on Open Source Software, users are exposed to third-party library vulnerabilities. Software Composition Analysis (SCA) tools have been created to alert users of such vulnerabilities. SCA requires the identification of vulnerability-fixing commits. Prior works have proposed methods that can automatically identify such vulnerability-fixing commits. However, identifying such commits is highly challenging, as only a very small minority of commits are vulnerability fixing. Moreover, code changes can be noisy and difficult to analyze. We observe that noise can occur at different levels of detail, making it challenging to detect vulnerability fixes accurately. To address these challenges and boost the effectiveness of prior works, we propose MiDas (Multi-Granularity Detector for Vulnerability Fixes). Unique from prior works, Midas constructs different neural networks for each level of code change granularity, corresponding to commit-level, file-level, hunk-level, and line-level, following their natural organization. It then utilizes an ensemble model that combines all base models to generate the final prediction. This design allows MiDas to better handle the noisy and highly imbalanced nature of vulnerability-fixing commit data. Additionally, to reduce the human effort required to inspect code changes, we have designed an effort-aware adjustment for Midas's outputs based on commit length. The evaluation results demonstrate that MiDas outperforms the current state-of-the-art baseline in terms of AUC by 4.9% and 13.7% on Java and Python-based datasets, respectively. Furthermore, in terms of two effort-aware metrics, EffortCost@L and Popt@L, MiDas also outperforms the state-of-the-art baseline, achieving improvements of up to 28.2% and 15.9% on Java, and 60% and 51.4% on Python, respectively.

Effective connectivity can describe the causal patterns among brain regions. These patterns have the potential to reveal the pathological mechanism and promote early diagnosis and effective drug development for cognitive disease. However, the current methods utilize software toolkits to extract empirical features from brain imaging to estimate effective connectivity. These methods heavily rely on manual parameter settings and may result in large errors during effective connectivity estimation. In this paper, a novel brain imaging-to-graph generation (BIGG) framework is proposed to map functional magnetic resonance imaging (fMRI) into effective connectivity for mild cognitive impairment (MCI) analysis. To be specific, the proposed BIGG framework is based on the diffusion denoising probabilistic models (DDPM), where each denoising step is modeled as a generative adversarial network (GAN) to progressively translate the noise and conditional fMRI to effective connectivity. The hierarchical transformers in the generator are designed to estimate the noise at multiple scales. Each scale concentrates on both spatial and temporal information between brain regions, enabling good quality in noise removal and better inference of causal relations. Meanwhile, the transformer-based discriminator constrains the generator to further capture global and local patterns for improving high-quality and diversity generation. By introducing the diffusive factor, the denoising inference with a large sampling step size is more efficient and can maintain high-quality results for effective connectivity generation. Evaluations of the ADNI dataset demonstrate the feasibility and efficacy of the proposed model. The proposed model not only achieves superior prediction performance compared with other competing methods but also predicts MCI-related causal connections that are consistent with clinical studies., Comment: 10 pages, 12 figures

Deutsch's algorithm is the first quantum algorithm to show the advantage over the classical algorithm. Here we generalize Deutsch's problem to $n$ functions and propose a new quantum algorithm with indefinite causal order to solve this problem. The new algorithm not only reduces the number of queries to the black-box by half over the classical algorithm, but also significantly reduces the number of required quantum gates over the Deutsch's algorithm. We experimentally demonstrate the algorithm in a stable Sagnac loop interferometer with common path, which overcomes the obstacles of both phase instability and low fidelity of Mach-Zehnder interferometer. The experimental results have shown both an ultra-high and robust success probability $\sim 99.7\%$. Our work opens up a new path towards solving the practical problems with indefinite casual order quantum circuits.

Second-harmonic generation (SHG) microscopy provides label-free imaging of biological tissues with unique contrast mechanisms, but its resolution is limited by the diffraction limit. Here, we present the first experimental demonstration of super-resolution quantitative phase imaging of the SHG field based on synthetic aperture Fourier holographic microscopy. We discuss the mathematical model of synthetic-aperture imaging of SHG fields, as well as the computational adaptive optics technique for correcting sample-induced aberration. We demonstrate proof-of-concept experiments where SHG targets are embedded within a thick scattering medium to validate the performance of the proposed imaging technique. It is shown to be able to overcome the conventional Abbe diffraction limit even in the complex aberrations and strong multiple scattering. We also demonstrate SHG-based super-resolution deep-tissue phase imaging of ex-vivo zebrafish muscle tissue.

Multiple light scattering hampers imaging objects in complex scattering media. Approaches used in real practices mainly aim to filter out multiple scattering obscuring the ballistic waves that travel straight through the scattering medium. Here, we propose a method that makes the deterministic use of multiple scattering for microscopic imaging of an object embedded deep within scattering media. The proposed method finds a stack of multiple complex phase plates that generate similar light trajectories as the original scattering medium. By implementing the inverse scattering using the identified phase plates, our method rectifies multiple scattering and amplifies ballistic waves by almost 600 times, which leads to a substantial increase in imaging depth. Our study marks an important milestone in solving the longstanding high-order inverse scattering problems.

Tools that alert developers about library vulnerabilities depend on accurate, up-to-date vulnerability databases which are maintained by security researchers. These databases record the libraries related to each vulnerability. However, the vulnerability reports may not explicitly list every library and human analysis is required to determine all the relevant libraries. Human analysis may be slow and expensive, which motivates the need for automated approaches. Researchers and practitioners have proposed to automatically identify libraries from vulnerability reports using extreme multi-label learning (XML). While state-of-the-art XML techniques showed promising performance, their experiment settings do not practically fit what happens in reality. Previous studies randomly split the vulnerability reports data for training and testing their models without considering the chronological order of the reports. This may unduly train the models on chronologically newer reports while testing the models on chronologically older ones. However, in practice, one often receives chronologically new reports, which may be related to previously unseen libraries. Under this practical setting, we observe that the performance of current XML techniques declines substantially, e.g., F1 decreased from 0.7 to 0.28 under experiments without and with consideration of chronological order of vulnerability reports. We propose a practical library identification approach, namely CHRONOS, based on zero-shot learning. The novelty of CHRONOS is three-fold. First, CHRONOS fits into the practical pipeline by considering the chronological order of vulnerability reports. Second, CHRONOS enriches the data of the vulnerability descriptions and labels using a carefully designed data enhancement step. Third, CHRONOS exploits the temporal ordering of the vulnerability reports using a cache to prioritize prediction of..., Comment: Accepted to the Technical Track of ICSE 2023

Code models, such as CodeBERT and CodeT5, offer general-purpose representations of code and play a vital role in supporting downstream automated software engineering tasks. Most recently, code models were revealed to be vulnerable to backdoor attacks. A code model that is backdoor-attacked can behave normally on clean examples but will produce pre-defined malicious outputs on examples injected with triggers that activate the backdoors. Existing backdoor attacks on code models use unstealthy and easy-to-detect triggers. This paper aims to investigate the vulnerability of code models with stealthy backdoor attacks. To this end, we propose AFRAIDOOR (Adversarial Feature as Adaptive Backdoor). AFRAIDOOR achieves stealthiness by leveraging adversarial perturbations to inject adaptive triggers into different inputs. We evaluate AFRAIDOOR on three widely adopted code models (CodeBERT, PLBART and CodeT5) and two downstream tasks (code summarization and method name prediction). We find that around 85% of adaptive triggers in AFRAIDOOR bypass the detection in the defense process. By contrast, only less than 12% of the triggers from previous work bypass the defense. When the defense method is not applied, both AFRAIDOOR and baselines have almost perfect attack success rates. However, once a defense is applied, the success rates of baselines decrease dramatically to 10.47% and 12.06%, while the success rate of AFRAIDOOR are 77.05% and 92.98% on the two tasks. Our finding exposes security weaknesses in code models under stealthy backdoor attacks and shows that the state-of-the-art defense method cannot provide sufficient protection. We call for more research efforts in understanding security threats to code models and developing more effective countermeasures., Comment: 18 pages, Under review of IEEE Transactions on Software Engineering

Many modern software systems are enabled by deep learning libraries such as TensorFlow and PyTorch. As deep learning is now prevalent, the security of deep learning libraries is a key concern. Fuzzing deep learning libraries presents two challenges. Firstly, to reach the functionality of the libraries, fuzzers have to use inputs from the valid input domain of each API function, which may be unknown. Secondly, many inputs are redundant. Randomly sampled invalid inputs are likely not to trigger new behaviors. While existing approaches partially address the first challenge, they overlook the second challenge. We propose SkipFuzz, an approach for fuzzing deep learning libraries. To generate valid inputs, SkipFuzz learns the input constraints of each API function using active learning. By using information gained during fuzzing, SkipFuzz infers a model of the input constraints, and, thus, generate valid inputs. SkipFuzz comprises an active learner which queries a test executor to obtain feedback for inference. After constructing hypotheses, the active learner poses queries and refines the hypotheses using the feedback from the test executor, which indicates if the library accepts or rejects an input, i.e., if it satisfies the input constraints or not. Inputs from different categories are used to invoke the library to check if a set of inputs satisfies a function's input constraints. Inputs in one category are distinguished from other categories by possible input constraints they would satisfy, e.g. they are tensors of a certain shape. As such, SkipFuzz is able to refine its hypothesis by eliminating possible candidates of the input constraints. This active learning-based approach addresses the challenge of redundant inputs. Using SkipFuzz, we have found and reported 43 crashes. 28 of them have been confirmed, with 13 unique CVEs assigned., Comment: 13 pages