Peng Zhang, Yang Wang, Xutong Liu, Yanhui Li, Yibao Yang, Ziyuan Wang, Xiaoyu Zhou, Lin Chen, Yuming Zhou
Background. Many mutation reduction strategies, which aim to reduce the number of mutants, have been proposed. Problem. It is important to measure the ability of a mutation reduction strategy to maintain test suite effectiveness evaluation. However, existing evaluation indicators are unable to measure the "order-preserving ability". Objective. We aim to propose evaluation indicators to measure the "order-preserving ability" of a mutation reduction strategy, which is important but missing in our community. Method. Given a test suite on a Software Under Test (SUT) with a set of original mutants, we leverage the test suite to generate a group of test suites that have a partial order relationship in fault detecting potential. When evaluating a reduction strategy, we first construct two partial order relationships among the generated test suites in terms of mutation score, one with the original mutants and another with the reduced mutants. Then, we measure the extent to which the two partial order relationships are consistent. The more consistent the two partial order relationships are, the stronger the Order Preservation (OP) of the mutation reduction strategy is, and the more effective the reduction strategy is. Furthermore, we propose Effort-aware Relative Order Preservation (EROP) to measure how much gain a mutation reduction strategy can provide compared with a random reduction strategy. Result. The experimental results show that OP and EROP are able to efficiently measure the "order-preserving ability" of a mutation reduction strategy. As a result, they have a better ability to distinguish various mutation reduction strategies compared with the existing evaluation indicators. Conclusion. We suggest, for the researchers, that OP and EROP should be used to measure the effectiveness of a mutant reduction strategy.
Shiran Liu, Zhaoqiang Guo, Yanhui Li, Chuanqi Wang, Lin Chen, Zhongbin Sun, Yuming Zhou
The label quality of defect data sets has a direct influence on the reliability of defect prediction models. In this study, for multi-version-project defect data sets, we propose an approach to automatically detecting instances with inconsistent labels (i.e. the phenomena of instances having the same source code but different labels over multiple versions of a software project) and understand their influence on the evaluation and interpretation of defect prediction models. Based on five multi-version-project defect data sets (either widely used or the most up-to-date in the literature) collected by diverse approaches, we find that: (1) most versions in the investigated defect data sets contain inconsistent labels with varying degrees; (2) the existence of inconsistent labels in a training data set may considerably change the prediction performance of a defect prediction model as well as can lead to the identification of substantially different true defective modules; and (3) the importance ranking of independent variables in a defect prediction model can be substantially shifted due to the existence of inconsistent labels. The above findings reveal that inconsistent labels in defect data sets can profoundly change the prediction ability and interpretation of a defect prediction model. Therefore, we strongly suggest that practitioners should detect and exclude inconsistent labels in defect data sets to avoid their potential negative influence on defect prediction models. What is more, it is necessary for researchers to improve existing defect label collection approaches to reduce inconsistent labels. Furthermore, there is a need to re-examine the experimental conclusions of previous studies using multi-version-project defect data sets with a high ratio of inconsistent labels.
Zhaoqiang Guo, Shiran Liu, Jinping Liu, Yanhui Li, Lin Chen, Hongmin Lu, Yuming Zhou, Baowen Xu
In the process of software evolution, developers often sacrifice the long-term code quality to satisfy the short-term goals due to specific reasons, which is called technical debt. In particular, self-admitted technical debt (SATD) refers to those that were intentionally introduced and remarked by code comments. Those technical debts reduce the quality of software and increase the cost of subsequent software maintenance. Therefore, it is necessary to find out and resolve these debts in time. Recently, many approaches have been proposed to identify SATD. However, those approaches either have a low accuracy or are complex to implementation in practice. In this paper, we propose a simple unsupervised baseline approach that fuzzily matches task annotation tags (MAT) to identify SATD. MAT does not need any training data to build a prediction model. Instead, MAT only examines whether any of four task tags (i.e. TODO, FIXME, XXX, and HACK) appears in the comments of a target project to identify SATD. In this sense, MAT is a natural baseline approach, which has a good understandability, in SATD identification. In order to evaluate the usefulness of MAT, we use 10 open-source projects to conduct the experiment. The experimental results reveal that MAT has a surprisingly excellent performance for SATD identification compared with the state-of-the-art approaches. As such, we suggest that, in the future SATD identification studies, MAT should be considered as an easy-to-implement baseline to which any new approach should be compared against to demonstrate its usefulness.
Xutong Liu, Yufei Zhou, Yutian Tang, Junyan Qian, Yuming Zhou
Online Just-In-Time Software Defect Prediction (O-JIT-SDP) uses an online model to predict whether a new software change will introduce a bug or not. However, existing studies neglect the interaction of Software Quality Assurance (SQA) staff with the model, which may miss the opportunity to improve the prediction accuracy through the feedback from SQA staff. To tackle this problem, we propose Human-In-The-Loop (HITL) O-JIT-SDP that integrates feedback from SQA staff to enhance the prediction process. Furthermore, we introduce a performance evaluation framework that utilizes a k-fold distributed bootstrap method along with the Wilcoxon signed-rank test. This framework facilitates thorough pairwise comparisons of alternative classification algorithms using a prequential evaluation approach. Our proposal enables continuous statistical testing throughout the prequential process, empowering developers to make real-time decisions based on robust statistical evidence. Through experimentation across 10 GitHub projects, we demonstrate that our evaluation framework enhances the credibility of model evaluation, and the incorporation of HITL feedback elevates the prediction performance of online JIT-SDP models. These advancements hold the potential to significantly enhance the value of O-JIT-SDP for industrial applications.
Shiran Liu, Zhaoqiang Guo, Yanhui Li, Hongmin Lu, Lin Chen, Lei Xu, Yuming Zhou, Baowen Xu
Code documentations are essential for software quality assurance, but due to time or economic pressures, code developers are often unable to write documents for all modules in a project. Recently, a supervised artificial neural network (ANN) approach is proposed to prioritize important modules for documentation effort. However, as a supervised approach, there is a need to use labeled training data to train the prediction model, which may not be easy to obtain in practice. Furthermore, it is unclear whether the ANN approach is generalizable, as it is only evaluated on several small data sets. In this paper, we propose an unsupervised approach based on PageRank to prioritize documentation effort. This approach identifies "important" modules only based on the dependence relationships between modules in a project. As a result, the PageRank approach does not need any training data to build the prediction model. In order to evaluate the effectiveness of the PageRank approach, we use six additional large data sets to conduct the experiments in addition to the same data sets collected from open-source projects as used in prior studies. The experimental results show that the PageRank approach is superior to the state-of-the-art ANN approach in prioritizing important modules for documentation effort. In particular, due to the simplicity and effectiveness, we advocate that the PageRank approach should be used as an easy-to-implement baseline in future research on documentation effort prioritization, and any new approach should be compared with it to demonstrate its effectiveness.
Xutong Liu, Shiran Liu, Zhaoqiang Guo, Peng Zhag, Yibiao Yang, Huihui Liu, Hongmin Lu, Yanhui Li, Lin Chen, Yuming Zhou
In defect prediction community, many defect prediction models have been proposed and indeed more new models are continuously being developed. However, there is no consensus on how to evaluate the performance of a newly proposed model. In this paper, we aim to propose MATTER, a fraMework towArd a consisTenT pErformance compaRison, which makes model performance directly comparable across different studies. We take three actions to build a consistent evaluation framework for defect prediction models. First, we propose a simple and easy-to-use unsupervised baseline model ONE (glObal baseliNe modEl) to provide "a single point of comparison". Second, we propose using the SQA-effort-aligned threshold setting to make a fair comparison. Third, we suggest reporting the evaluation results in a unified way and provide a set of core performance indicators for this purpose, thus enabling an across-study comparison to attain real progress. The experimental results show that MATTER can serve as an effective framework to support a consistent performance evaluation for defect prediction models and hence can help determine whether a newly proposed defect prediction model is practically useful for practitioners and inform the real progress in the road of defect prediction. Furthermore, when applying MATTER to evaluate the representative defect prediction models proposed in recent years, we find that most of them (if not all) are not superior to the simple baseline model ONE in terms of the SQA-effort awareness prediction performance. This reveals that the real progress in defect prediction has been overestimated. We hence recommend that, in future studies, when any new defect prediction model is proposed, MATTER should be used to evaluate its actual usefulness (on the same benchmark test data sets) to advance scientific progress in defect prediction.
Peng Zhang, Yang Wang, Xutong Liu, Yibiao Yang, Yanhui Li, Lin Chen, Ziyuan Wang, Chang-ai Sun, Yuming Zhou
Comparing test suite effectiveness metrics has always been a research hotspot. However, prior studies have different conclusions or even contradict each other for comparing different test suite effectiveness metrics. The problem we found most troubling to our community is that researchers tend to oversimplify the description of the ground truth they use. For example, a common expression is that "we studied the correlation between real faults and the metric to evaluate (MTE)". However, the meaning of "real faults" is not clear-cut. As a result, there is a need to scrutinize the meaning of "real faults". Without this, it will be half-knowledgeable with the conclusions. To tackle this challenge, we propose a framework ASSENT (evAluating teSt Suite EffectiveNess meTrics) to guide the follow-up research. In nature, ASSENT consists of three fundamental components: ground truth, benchmark test suites, and agreement indicator. First, materialize the ground truth for determining the real order in effectiveness among test suites. Second, generate a set of benchmark test suites and derive their ground truth order in effectiveness. Third, for the benchmark test suites, generate the MTE order in effectiveness by the metric to evaluate (MTE). Finally, calculate the agreement indicator between the two orders. Under ASSENT, we are able to compare the accuracy of different test suite effectiveness metrics. We apply ASSENT to evaluate representative test suite effectiveness metrics, including mutation score metrics and code coverage metrics. Our results show that, based on the real faults, mutation score and subsuming mutation score are the best metrics to quantify test suite effectiveness. Meanwhile, by using mutants instead of real faults, MTEs will be overestimated by more than 20% in values.
Mingke Yang, Yuming Zhou, Bixin Li, Yutian Tang
Jupyter Notebook is a popular tool among data analysts and scientists for working with data. It provides a way to combine code, documentation, and visualizations in a single, interactive environment, facilitating code reuse. While code reuse can improve programming efficiency, it can also decrease readability, security, and overall performance. We conduct a large-scale exploratory study of code reuse practices in the Jupyter Notebook development community on the Stack Overflow platform to understand the potential negative impacts of code reuse. Our findings identified 1,097,470 Jupyter Notebook clone pairs that reuse Stack Overflow code snippets, and the average code snippet has 7.91 code quality violations. Through our research, we gain insight into the reasons behind Jupyter Notebook developers' decision to reuse code and the potential drawbacks of this practice.
Haoyang Li, Sheng Lin, Fangcheng Fu, Yuming Zhou, Xiaodong Ji, Yanfeng Zhao, Lefeng Wang, Jie Jiang, Bin Cui
Reinforcement learning (RL) post-training has become pivotal for enhancing the capabilities of modern large models. A recent trend is to develop RL systems with a fully disaggregated architecture, which decouples the three RL phases (rollout, reward, and training) onto separate resources and executes them asynchronously. However, two critical data-level concerns arise: (1) asynchronous execution leads to data staleness in trajectories (the data generated by rollout) as the model parameters used in rollout may not be up to date, which impairs RL convergence; and (2) the length variation of trajectories introduces severe data skewness, leading to workload imbalance and degraded system performance. Existing systems fail to address these two concerns in a unified manner. Techniques that tightly control data staleness often constrain effective data skewness mitigation, while aggressive data skewness mitigation tends to exacerbate data staleness. As a result, systems are forced to trade off convergence for performance, or vice versa. To address this, we propose StaleFlow, an RL post-training system that jointly tackles data staleness and skewness. First, to control staleness, StaleFlow introduces a global consistency protocol that tracks the full lifecycle of each trajectory and constrains staleness. Second, to mitigate skewness, StaleFlow re-designs the RL system architecture by constructing data servers for trajectories and parameters to achieve flexible rollout coordination. Subsequently, we develop a suite of staleness-aware, throughput-oriented strategies to enhance system performance. Evaluations show that StaleFlow achieves up to 1.42-2.68$\times$ (1.17-2.01$\times$ on average) higher throughput than state-of-the-art systems, without compromising convergence.
Zhijie Liu, Yutian Tang, Xiapu Luo, Yuming Zhou, Liang Feng Zhang
Large language models (LLMs) have demonstrated impressive capabilities across various NLP tasks. Additionally, LLMs are also highly valuable in supporting software engineering tasks, particularly in the field of code generation. Automatic code generation is a process of automatically generating source code or executable code based on given specifications or requirements, improving developer productivity. In this study, we perform a systematic empirical assessment to the quality of code generation using ChatGPT. We leverage 728 algorithm problems in five languages (i.e., C, C++, Java, Python, and JavaScript) and 18 CWEs with 54 code scenarios for the code generation task. Our evaluation encompasses a comprehensive analysis of code snippets generated by ChatGPT, focusing on three critical aspects: correctness, complexity, and security. We also specifically investigate ChatGPT's ability to engage in multi-round fixing process (i.e., ChatGPT's dialog ability) of facilitating code generation. By delving into the generated code and examining the experimental results, this work provides valuable insights into the performance of ChatGPT in tackling code generation tasks over the three critical aspects. Overall, our findings uncover potential issues and limitations that arise in the ChatGPT-based code generation and lay the groundwork for improving AI and LLM-based code generation techniques.
Pengfei Lan, Yuming Zhou, Adrian N. Pfeiffer, Qingbin Zhang, Peixiang Lu, Katsumi Midorikawa Lu
The experimental observations of sequential double ionization (SDI) of Ar [A. N. Pfeiffer {\it et al.}, Nature Phys. {\bf 7}, 428 (2011)], such as the four-peak momentum distribution and the ionization time of the first and second electrons, are investigated and reproduced with a quantum model by including and excluding the $e$-$e$ correlation effect. Based on the comparison of experiment and simulation, the role of $e$-$e$ correlation in SDI is discussed. It is shown that the inclusion of $e$-$e$ correlation is necessary to reproduce the momentum distribution of electrons.
Yibiao Yang, Qingyang Li, Maolin Sun, Jiangchang Wu, Yuming Zhou
Background: Compilers are fundamental to software development, translating high-level source code into executable software systems. Faults in compilers can have severe consequences and thus effective localization and resolution of compiler bugs are crucial. Problem: In practice, developers often examine version history to identify and investigate bug-inducing commit (BIC) for fixing bugs. However, while numerous sophisticated Spectrum-Based Fault Localization (SBFL) techniques have been proposed for compiler fault isolation, their effectiveness has not been evaluated against the BIC-based strategies widely adopted in practice. Objective: This study aims to bridge this gap by directly comparing a BIC-based strategy, Basic, with representative SBFL techniques in the context of compiler fault localization. The BIC-based strategy closely aligns with common developer practices, as it directly identifies the BIC and treats the files modified in that commit as faulty candidates. Method: The Basic identifies the most recent good release and earliest bad release, and then employs a binary search to pinpoint the bug-inducing commit. All files modified in the identified commit are flagged as potentially faulty. We rigorously compare Basic against SBFL-based techniques using a benchmark consisting of 60 GCC bugs and 60 LLVM bugs. Result: Our analysis reveals that Basic performs comparably to, and in many cases outperforms, state-of-the-art SBFL-based techniques, particularly on the critical Top-1 and Top-5 ranking metrics. Conclusion: This study provides new insights into the practical effectiveness of SBFL-based techniques in real-world compiler debugging scenarios. We recommend that future research adopt Basic as a baseline when developing and evaluating new compiler fault isolation methods.
Linghan Meng, Yanhui Li, Lin Chen, Zhi Wang, Di Wu, Yuming Zhou, Baowen Xu
The boom of DL technology leads to massive DL models built and shared, which facilitates the acquisition and reuse of DL models. For a given task, we encounter multiple DL models available with the same functionality, which are considered as candidates to achieve this task. Testers are expected to compare multiple DL models and select the more suitable ones w.r.t. the whole testing context. Due to the limitation of labeling effort, testers aim to select an efficient subset of samples to make an as precise rank estimation as possible for these models. To tackle this problem, we propose Sample Discrimination based Selection (SDS) to select efficient samples that could discriminate multiple models, i.e., the prediction behaviors (right/wrong) of these samples would be helpful to indicate the trend of model performance. To evaluate SDS, we conduct an extensive empirical study with three widely-used image datasets and 80 real world DL models. The experimental results show that, compared with state-of-the-art baseline methods, SDS is an effective and efficient sample selection method to rank multiple DL models.
Xiangping Chen, Xing Hu, Yuan Huang, He Jiang, Weixing Ji, Yanjie Jiang, Yanyan Jiang, Bo Liu, Hui Liu, Xiaochen Li, Xiaoli Lian, Guozhu Meng, Xin Peng, Hailong Sun, Lin Shi, Bo Wang, Chong Wang, Jiayi Wang, Tiantian Wang, Jifeng Xuan, Xin Xia, Yibiao Yang, Yixin Yang, Li Zhang, Yuming Zhou, Lu Zhang
Researchers have recently achieved significant advances in deep learning techniques, which in turn has substantially advanced other research disciplines, such as natural language processing, image processing, speech recognition, and software engineering. Various deep learning techniques have been successfully employed to facilitate software engineering tasks, including code generation, software refactoring, and fault localization. Many papers have also been presented in top conferences and journals, demonstrating the applications of deep learning techniques in resolving various software engineering tasks. However, although several surveys have provided overall pictures of the application of deep learning techniques in software engineering, they focus more on learning techniques, that is, what kind of deep learning techniques are employed and how deep models are trained or fine-tuned for software engineering tasks. We still lack surveys explaining the advances of subareas in software engineering driven by deep learning techniques, as well as challenges and opportunities in each subarea. To this end, in this paper, we present the first task-oriented survey on deep learning-based software engineering. It covers twelve major software engineering subareas significantly impacted by deep learning techniques. Such subareas spread out the through the whole lifecycle of software development and maintenance, including requirements engineering, software development, testing, maintenance, and developer collaboration. As we believe that deep learning may provide an opportunity to revolutionize the whole discipline of software engineering, providing one survey covering as many subareas as possible in software engineering can help future research push forward the frontier of deep learning-based software engineering more systematically.
Zeyu Lu, Peng Zhang, Chun Yong Chong, Shan Gao, Yibiao Yang, Yanhui Li, Lin Chen, Yuming Zhou
Existing fine-grained predictive mutation testing studies predominantly rely on deep learning, which faces two critical limitations in practice: (1) Exorbitant computational costs. The deep learning models adopted in these studies demand significant computational resources for training and inference acceleration. This introduces high costs and undermines the cost-reduction goal of predictive mutation testing. (2) Constrained applicability. Although modern mutation testing tools generate mutants both inside and outside methods, current fine-grained predictive mutation testing approaches handle only inside-method mutants. As a result, they cannot predict outside-method mutants, limiting their applicability in real-world scenarios. We propose WITNESS, a new fine-grained predictive mutation testing approach. WITNESS adopts a twofold design: (1) With collected features from both inside-method and outside-method mutants, WITNESS is suitable for all generated mutants. (2) Instead of using computationally expensive deep learning, WITNESS employs lightweight classical machine learning models for training and prediction. This makes it more cost-effective and enabling straightforward explanations of the decision-making processes behind the adopted models. Evaluations on Defects4J projects show that WITNESS consistently achieves state-of-the-art predictive performance across different scenarios. Additionally, WITNESS significantly enhances the efficiency of kill matrix prediction. Post-hoc analysis reveals that features incorporating information from before and after the mutation are the most important among those used in WITNESS. Test case prioritization based on the predicted kill matrix shows that WITNESS delivers results much closer to those obtained by using the actual kill matrix, outperforming baseline approaches.
Qingyang Li, Yibiao Yang, Maolin Sun, Jiangchang Wu, Qingkai Shi, Yuming Zhou
Compilers are fundamental to modern software development, making the effective identification and resolution of compiler faults essential. However, localizing these faults to specific source files remains highly challenging due to the complexity and scale of modern compiler infrastructures. In this study, we propose MultiConf, a novel approach that automatically isolates compiler faults by constructing multiple pairs of adversarial compilation configurations. Each adversarial compilation configuration pair consists of a failing configuration and its corresponding passing configuration, which differ in only a small number of fine-grained options. MultiConf generates failing configurations through a lightweight construction process and derives the corresponding passing configurations by selectively disabling bug-related fine-grained options. We then employ a Spectrum-Based Fault Localization (SBFL) formula to rank the suspiciousness of compiler source files. Each adversarial configuration pair independently produces a ranking, which is subsequently aggregated using a weighted voting scheme to derive a final suspiciousness ranking, enabling more accurate and robust fault localization. We evaluate MultiConf on a benchmark of 60 real-world GCC compiler bugs. The results demonstrate that MultiConf significantly outperforms existing compiler fault localization techniques in both effectiveness and efficiency. In particular, MultiConf successfully localizes 27 out of 60 bugs at the Top-1 file level, representing improvements of 35.0% and 28.6% over the two state-of-the-art approaches, Odfl(20) and Basic(21), respectively.
Maolin Sun, Yibiao Yang, Yuming Zhou
Satisfiability Modulo Theory (SMT) solvers are foundational to modern systems and programming languages research, providing the foundation for tasks like symbolic execution and automated verification. Because these solvers sit on the critical path, their correctness is essential, and high-quality test formulas are key to uncovering bugs. However, while prior testing techniques performed well on earlier solver versions, they struggle to keep pace with rapidly evolving features. Recent approaches based on Large Language Models (LLMs) show promise in exploring advanced solver capabilities, but two obstacles remain: nearly half of the generated formulas are syntactically invalid, and iterative interactions with LLMs introduce substantial computational overhead. In this study, we present Once4All, a novel LLM-assisted fuzzing framework that addresses both issues by shifting from direct formula generation to the synthesis of generators for reusable terms (i.e., logical expressions). Specifically, Once4All uses LLMs to (1) automatically extract context-free grammars (CFGs) for SMT theories, including solver-specific extensions, from documentation, and (2) synthesize composable Boolean term generators that adhere to these grammars. During fuzzing, Once4All populates structural skeletons derived from existing formulas with the terms iteratively produced by the LLM-synthesized generators. This design ensures syntactic validity while promoting semantic diversity. Notably, Once4All requires only one-time LLM interaction investment, dramatically reducing runtime cost. We evaluated Once4All on two leading SMT solvers: Z3 and cvc5. Our experiments show that Once4All has identified 43 confirmed bugs, 40 of which have already been fixed by developers.
Maolin Sun, Yibiao Yang, Xuanlin Liu, Yuming Zhou, Baowen Xu
Patching severe security flaws in complex software remains a major challenge. While automated tools like fuzzers efficiently discover bugs, fixing deep-rooted low-level faults (e.g., use-after-free and memory corruption) still requires labor-intensive manual analysis by experts. Emerging Large Language Model (LLM) agents attempt to automate this pipeline, but they typically treat bug fixing as a purely static code-generation task. Relying solely on static artifacts, these methods miss the dynamic execution context strictly necessary for diagnosing intricate memory safety violations. To overcome these limitations, we introduce DebugHarness, an autonomous LLM-powered debugging agent harness that resolves complex vulnerabilities by emulating the interactive debugging practices of human systems engineers. Instead of merely examining static code, DebugHarness actively queries the live runtime environment. Driven by a reproducible crash, it utilizes a pattern-guided investigation strategy to formulate hypotheses, interactively probes program memory states and execution paths, and synthesizes patches via a closed-loop validation cycle. We evaluate DebugHarness on SEC-bench, a rigorous dataset of real-world C/C++ security vulnerabilities. DebugHarness successfully patches approximately 90% of the evaluated bugs. This yields a relative improvement of over 30% compared to state-of-the-art baselines, demonstrating that dynamic debugging significantly enhances LLM diagnostic capabilities. Overall, DebugHarness establishes a novel paradigm for automated program repair, bridging the gap between static LLM reasoning and the dynamic intricacies of low-level systems programming.
Zhichao Zhou, Yuming Zhou, Chunrong Fang, Zhenyu Chen, Yutian Tang
Unit testing is a critical part of software development process, ensuring the correctness of basic programming units in a program (e.g., a method). Search-based software testing (SBST) is an automated approach to generating test cases. SBST generates test cases with genetic algorithms by specifying the coverage criterion (e.g., branch coverage). However, a good test suite must have different properties, which cannot be captured by using an individual coverage criterion. Therefore, the state-of-the-art approach combines multiple criteria to generate test cases. As combining multiple coverage criteria brings multiple objectives for optimization, it hurts the test suites' coverage for certain criteria compared with using the single criterion. To cope with this problem, we propose a novel approach named \textbf{smart selection}. Based on the coverage correlations among criteria and the coverage goals' subsumption relationships, smart selection selects a subset of coverage goals to reduce the number of optimization objectives and avoid missing any properties of all criteria. We conduct experiments to evaluate smart selection on $400$ Java classes with three state-of-the-art genetic algorithms. On average, smart selection outperforms combining all goals on $65.1\%$ of the classes having significant differences between the two approaches.
Yigang Chen, Xiang Ji, Ziyue Zhang, Yuming Zhou, Yang-Chi-Dung Lin, Hsi-Yuan Huang, Tao Zhang, Yi Lai, Ke Chen, Chang Su, Xingqiao Lin, Zihao Zhu, Yanggyi Zhang, Kangping Wei, Jiehui Fu, Yixian Huang, Shidong Cui, Shih-Chung Yen, Ariel Warshel, Hsien-Da Huang
Deep learning-based drug-target interaction (DTI) prediction methods have demonstrated strong performance; however, real-world applicability remains constrained by limited data diversity and modeling complexity. To address these challenges, we propose SCOPE-DTI, a unified framework combining a large-scale, balanced semi-inductive human DTI dataset with advanced deep learning modeling. Constructed from 13 public repositories, the SCOPE dataset expands data volume by up to 100-fold compared to common benchmarks such as the Human dataset. The SCOPE model integrates three-dimensional protein and compound representations, graph neural networks, and bilinear attention mechanisms to effectively capture cross domain interaction patterns, significantly outperforming state-of-the-art methods across various DTI prediction tasks. Additionally, SCOPE-DTI provides a user-friendly interface and database. We further validate its effectiveness by experimentally identifying anticancer targets of Ginsenoside Rh1. By offering comprehensive data, advanced modeling, and accessible tools, SCOPE-DTI accelerates drug discovery research.