Zhang, Xinrui
Biological Sequence with Language Model Prompting: A Survey
Jiang, Jiyue, Wang, Zikang, Shan, Yuheng, Chai, Heyan, Li, Jiayi, Ma, Zixian, Zhang, Xinrui, Li, Yu
Large Language models (LLMs) have emerged as powerful tools for addressing challenges across diverse domains. Notably, recent studies have demonstrated that large language models significantly enhance the efficiency of biomolecular analysis and synthesis, attracting widespread attention from academics and medicine. In this paper, we systematically investigate the application of prompt-based methods with LLMs to biological sequences, including DNA, RNA, proteins, and drug discovery tasks. Specifically, we focus on how prompt engineering enables LLMs to tackle domain-specific problems, such as promoter sequence prediction, protein structure modeling, and drug-target binding affinity prediction, often with limited labeled data. Furthermore, our discussion highlights the transformative potential of prompting in bioinformatics while addressing key challenges such as data scarcity, multimodal fusion, and computational resource limitations. Our aim is for this paper to function both as a foundational primer for newcomers and a catalyst for continued innovation within this dynamic field of study.
Real-world Troublemaker: A 5G Cloud-controlled Track Testing Framework for Automated Driving Systems in Safety-critical Interaction Scenarios
Zhang, Xinrui, Xiong, Lu, Zhang, Peizhi, Huang, Junpeng, Ma, Yining
--Track testing plays a critical role in the safety evaluation of autonomous driving systems (ADS), as it provides a real-world interaction environment. However, the inflexibility in motion control of object targets and the absence of intelligent interactive testing methods often result in pre-fixed and limited testing scenarios. T o address these limitations, we propose a novel 5G cloud-controlled track testing framework, Real-world Troublemaker . This framework overcomes the rigidity of traditional pre-programmed control by leveraging 5G cloud-controlled object targets integrated with the Internet of Things (IoT) and vehicle teleoperation technologies. Unlike conventional testing methods that rely on pre-set conditions, we propose a dynamic game strategy based on a quadratic risk interaction utility function, facilitating intelligent interactions with the vehicle under test (VUT) and creating a more realistic and dynamic interaction environment. The proposed framework has been successfully implemented at the T ongji University Intelligent Connected V ehicle Evaluation Base. Field test results demonstrate that Troublemaker can perform dynamic interactive testing of ADS accurately and effectively. Compared to traditional methods, Troublemaker improves scenario reproduction accuracy by 65.2%, increases the diversity of interaction strategies by approximately 9.2 times, and enhances exposure frequency of safety-critical scenarios by 3.5 times in unprotected left-turn scenarios. Index T erms --Automated driving systems, track testing, 5G, cloud-controlled object targets, interaction scenarios. HE safety of automated driving systems (ADS) must be ensured prior to their practical implementation, which requires a well-established testing framework [1]. Existing test standards, such as ISO 26262 [2], UN R157 [3], and UN R171 [4], are not sufficient to comprehensively evaluate ADS. According to the driving automation levels defined by SAE J3016 from SAE International, a high-level ADS (i.e., Level 3 or higher) is expected to perform driving tasks independently and autonomously, with the driver no longer retaining continuous control over vehicle movement [5]. While ADS has already been deployed in various countries and regions, numerous ADS traffic incidents highlight that safety testing for high-level ADS remains a critical technical challenge. In comparison to traditional vehicles and advanced driver assistance systems (ADAS), high-level ADS testing faces significant transformations and challenges, particularly in terms of both test subjects and requirements.
SGA: A Graph Augmentation Method for Signed Graph Neural Networks
Zhang, Zeyu, Wan, Shuyan, Wang, Sijie, Zheng, Xianda, Zhang, Xinrui, Zhao, Kaiqi, Liu, Jiamou, Hao, Dong
Signed Graph Neural Networks (SGNNs) are vital for analyzing complex patterns in real-world signed graphs containing positive and negative links. However, three key challenges hinder current SGNN-based signed graph representation learning: sparsity in signed graphs leaves latent structures undiscovered, unbalanced triangles pose representation difficulties for SGNN models, and real-world signed graph datasets often lack supplementary information like node labels and features. These constraints limit the potential of SGNN-based representation learning. We address these issues with data augmentation techniques. Despite many graph data augmentation methods existing for unsigned graphs, none are tailored for signed graphs. Our paper introduces the novel Signed Graph Augmentation framework (SGA), comprising three main components. First, we employ the SGNN model to encode the signed graph, extracting latent structural information for candidate augmentation structures. Second, we evaluate these candidate samples (edges) and select the most beneficial ones for modifying the original training set. Third, we propose a novel augmentation perspective that assigns varying training difficulty to training samples, enabling the design of a new training strategy. Extensive experiments on six real-world datasets (Bitcoin-alpha, Bitcoin-otc, Epinions, Slashdot, Wiki-elec, and Wiki-RfA) demonstrate that SGA significantly improves performance across multiple benchmarks. Our method outperforms baselines by up to 22.2% in AUC for SGCN on Wiki-RfA, 33.3% in F1-binary, 48.8% in F1-micro, and 36.3% in F1-macro for GAT on Bitcoin-alpha in link sign prediction.