Search

Your search keyword '"Xie, Yuanyuan"' showing total 1,411 results
Start Over Author "Xie, Yuanyuan"
1,411 results on '"Xie, Yuanyuan"'

1. Augmenting LLMs to Repair Obsolete Test Cases with Static Collector and Neural Reranker

Author

Liu, Jun, Yan, Jiwei, Xie, Yuanyuan, Yan, Jun, and Zhang, Jian

Subjects
Computer Science - Software Engineering
Abstract

During software evolution, it is advocated that test code should co-evolve with production code. In real development scenarios, test updating may lag behind production code changing, which may cause the project to fail to compile or bring other troubles. Existing techniques based on pre-trained language models can be adopted to repair obsolete tests caused by such unsynchronized code changes, especially syntactic-related ones. However, the lack of target-oriented contextual information affects repair accuracy on large-scale projects. Starting from an obsoleted test, the key challenging task is precisely identifying and constructing Test-Repair-Oriented Contexts (TROCtx) from the whole repository within a limited token size. In this paper, we propose SynBCIATR (Syntactic-Breaking-Change-Induced Automated Test Repair), a novel approach to automatically repair obsolete test cases via precise and concise TROCtx construction. Inspired by developers' programming practices of the task, we design three types of TROCtx: class contexts, usage contexts, and environment contexts. For every type of TROCtx, SynBCIATR automatically collects the changed-token-related code information through static analysis techniques. Then it generates reranking queries to identify the most relevant TROCtxs, which will be taken as the repair-required key context and be input to the Large Language Model for the final test repair. To evaluate the effectiveness of SynBCIATR, we construct a benchmark dataset that contains diverse syntactic breaking changes. The experimental results show that SynBCIATR outperforms baseline approaches both on textual- and intent-matching metrics. With the augmentation of TROCtx constructed by SynBCIATR, hallucinations are reduced by 57.1%.

Published
2024

6. Re-imagining the Future of Forest Management -- An Age-Dependent Approach towards Harvesting

Author

Bian, Shuyang, Xie, Yuanyuan, and Zhang, Flora

Subjects
Quantitative Biology - Other Quantitative Biology
Abstract

Facing the drastic climate changes, current strategies for enhancing carbon dioxide stocks need to be thoroughly honed. To address the problem, we first built a carbon sequestration growth model driven by growth rate dependency (GRDM). We abstracted the carbon cycling system into the process of photosynthesis, the humidity fluctuation, and the original storage of carbon in the trees. In the photosynthesis model, we considered various factors, including transition rate of absorption and organic matter production. We also designed an Economic Return Evaluation Model (EREM) to estimate the optimal distribution of trees in the forest based on the utility function. Maximizing the utility brought by the amount of carbon storage, we derived the equation for profit optimization with the constraints of total economic expenses allowed. To assess its performance, we took an object-oriented approach, simulated an ideal forest by placing instances of trees and plotted a time-dependent forest composition graph. After proper normalization of climate and economic data, we also make predictions for 169 worldwide forest-covered countries. Our model further suggests high sensitivity and robustness with a similar trend of overall utility when environmental aridity or proportion of harvested woods are varied. Finally, we apply the model to Georgia temperate deciduous forest, and we evaluate the carbon storage ability to adjust the Red Spruce based on available biological literature research. We recognize that while the model is preliminary in its failure to identify a diverse array of variables, it has encapsulated key features of idealized forests.

Published
2023

20. Semilinear heat equations and parabolic variational inequalities on graphs

Author

Lin, Yong and Xie, Yuanyuan

Subjects
Mathematics - Analysis of PDEs
Abstract

Let $G=(V,E)$ be a locally finite connected weighted graph, and $\Omega$ be an unbounded subset of $V$. Using Rothe's method, we study the existence of solutions for the semilinear heat equation $\partial_tu+|u|^{p-1}\cdot u=\Delta u~(p\ge1)$ and the parabolic variational inequality \begin{eqnarray*} \int_{\Omega^\circ} \partial_tu\cdot(v-u)\,d\mu\ge \int_{\Omega^\circ}(\Delta u+f)\cdot(v-u)\,d\mu \qquad\mbox{for any }v\in \mathcal{H}, \end{eqnarray*} where $\mathcal{H}=\{u\in W^{1,2}(V):u=0\mbox{ on }V\backslash\Omega^\circ\}$.

Published
2021

21. Application of Rothe's method to a nonlinear wave equation on graphs

Author

Lin, Yong and Xie, Yuanyuan

Subjects
Mathematics - Analysis of PDEs
Abstract

We study a nonlinear wave equation on finite connected weighted graphs. Using Rothe's and energy methods, we prove the existence and uniqueness of solution under certain assumption. For linear wave equation on graphs, Lin and Xie \cite{Lin-Xie} obtained the existence and uniqueness of solution. The main novelty of this paper is that the wave equation we considered has the nonlinear damping term $|u_t|^{p-1}\cdot u_t$ ($p>1$).

Published
2021

26. SENP5 deteriorates traumatic brain injury via SUMO2-dependent suppression of E2F1 SUMOylation

Author

Ding Yanfu, Chen Feifei, Yang Weitao, Fu Xiaobin, and Xie Yuanyuan

Subjects
traumatic brain injury, SENP5, E2F1, SUMOylation, p53 signaling pathway, Biochemistry, QD415-436, Genetics, QH426-470
Abstract

Traumatic brain injury (TBI) represents a main public health concern during the past decade, attracting considerable interest because of its rising prevalence, wide-ranging risk factors and lifelong familial and societal influence. SUMO2 can conjugate to substrates upon various cellular stresses. Nevertheless, whether and how SUMO2-specific proteases partake in TBI is less understood. The aim of this study is to dissect the effects of SUMO-specific peptidase 5 (SENP5) on accentuating TBI in rats in an effort to unveil its underlying mechanism. SENP5 is overexpressed in hippocampal tissues of TBI rats, and inhibition of SENP5 reduces neurological function scores, decreases brain water content, inhibits apoptosis in hippocampal tissues, and attenuates brain injury caused in rats. Moreover, SENP5 inhibits the SUMOylation level of E2F transcription factor 1 (E2F1) and increases the protein expression of E2F1. Silencing of E2F1 blocks the p53 signaling pathway. Overexpression of E2F1 partially reverses the protective effect of sh-SENP5 on TBI in rats. These findings reveal an essential role of SENP5 and the SUMOylation status of E2F1 in the TBI development.

Published
2023
Full Text
View/download PDF

35. Novel rare genetic variants of familial and sporadic pulmonary atresia identified by whole-exome sequencing

Author

Xing Junyue, Wang Hongdan, Xie Yuanyuan, Fan Taibing, Cui Cunying, Li Yanan, Wang Shuai, Gu Weiyue, Wang Chengzeng, Tang Hao, and Liu Lin

Subjects
pulmonary atresia, whole-exome sequencing, rare variants, genetics, Biology (General), QH301-705.5
Abstract

Pulmonary atresia (PA) is a severe cyanotic congenital heart disease. Although some genetic mutations have been described to be associated with PA, the knowledge of pathogenesis is insufficient. The aim of this research was to use whole-exome sequencing (WES) to determine novel rare genetic variants in PA patients. We performed WES in 33 patients (27 patient–parent trios and 6 single probands) and 300 healthy control individuals. By applying an enhanced analytical framework to incorporate de novo and case–control rare variation, we identified 176 risk genes (100 de novo variants and 87 rare variants). Protein‒protein interaction (PPI) analysis and Genotype-Tissue Expression analysis revealed that 35 putative candidate genes had PPIs with known PA genes with high expression in the human heart. Expression quantitative trait loci analysis revealed that 27 genes that were identified as novel PA genes that could be affected by the surrounding single nucleotide polymorphism were screened. Furthermore, we screened rare damaging variants with a threshold of minor allele frequency at 0.5% in the ExAC_EAS and GnomAD_exome_EAS databases, and the deleteriousness was predicted by bioinformatics tools. For the first time, 18 rare variants in 11 new candidate genes have been identified that may play a role in the pathogenesis of PA. Our research provides new insights into the pathogenesis of PA and helps to identify the critical genes for PA.

Published
2023
Full Text
View/download PDF

46. The existence of the solution of the wave equation on graphs

Author

Lin, Yong and Xie, Yuanyuan

Subjects
Mathematics - Analysis of PDEs
Abstract

Let $G=(V, E)$ be a finite weighted graph, and $\Omega\subseteq V$ be a domain such that $\Omega^\circ\neq\emptyset$. In this paper, we study the following initial boundary problem for the non-homogenous wave equation \begin{equation*} \left\{ \begin{aligned} &\partial_t^2 u(t,x)-\Delta_\Omega u(t,x)=f(t,x),\qquad&&(t,x)\in[0,\infty)\times \Omega^\circ,\\ &u(0,x)=g(x),\qquad&& x\in\Omega^\circ,\\ &\partial_tu(0,x)=h(x),\qquad&& x\in\Omega^\circ,\\ &u(t,x)=0,\qquad&&(t,x)\in[0,\infty)\times\partial \Omega, \end{aligned} \right. \end{equation*} where $\Delta_\Omega$ denotes the Dirichlet Laplacian on $\Omega^\circ$. Using Rothe's method, we prove that the above wave equation has a unique solution.

Published
2019

Catalog

Books, media, physical & digital resources
See catalog results