arXiv subjects

Xingyuan Wei

Publications and source records attributed to Xingyuan Wei.

6 recordsLinked to original sources

arXiv2026

ProtRLSearch: A Multi-Round Multimodal Protein Search Agent with Large Language Models Trained via Reinforcement Learning

Protein analysis tasks arising in healthcare settings often require accurate reasoning under protein sequence constraints, involving tasks such as functional interpretation of disease-related variants, protein-level analysis for clinical research, and similar scenarios. To address such tasks, search agents are introduced to search protein-related information, providing support for disease-related variant analysis and protein function reasoning in protein-centric inference. However, such search agents are mostly limited to single-round, text-only modality search, which prevents the protein sequence modality from being incorporated as a multimodal input into the search decision-making process. Meanwhile, their reliance on reinforcement learning (RL) supervision that focuses solely on the final answer results in a lack of search process constraints, making deviations in keyword selection and reasoning directions difficult to identify and correct in a timely manner. To address these limitations, we propose ProtRLSearch, a multi-round protein search agent trained with multi-dimensional reward based RL, which jointly leverages protein sequence and text as multimodal inputs during real-time search to produce high quality reports. To evaluate the ability of models to integrate protein sequence information and text-based multimodal inputs in realistic protein query settings, we construct ProtMCQs, a benchmark of 3,000 multiple choice questions (MCQs) organized into three difficulty levels. The benchmark evaluates protein query tasks that range from sequence constrained reasoning about protein function and phenotype changes to comprehensive protein reasoning that integrates multi-dimensional sequence features with signal pathways and regulatory networks.

cs.AI↗

arXiv2025

Mitigating the Impact of Malware Evolution on API Sequence-based Windows Malware Detector

In dynamic Windows malware detection, deep learning models are extensively deployed to analyze API sequences. Methods based on API sequences play a crucial role in malware prevention. However, due to the continuous updates of APIs and the changes in API sequence calls leading to the constant evolution of malware variants, the detection capability of API sequence-based malware detection models significantly diminishes over time. We observe that the API sequences of malware samples before and after evolution usually have similar malicious semantics. Specifically, compared to the original samples, evolved malware samples often use the API sequences of the pre-evolution samples to achieve similar malicious behaviors. For instance, they access similar sensitive system resources and extend new malicious functions based on the original functionalities. In this paper, we propose a framework MME(Mitigating the impact of Malware Evolution), a framework that can enhance existing API sequence-based malware detectors and mitigate the adverse effects of malware evolution. To help detection models capture the similar semantics of these post-evolution API sequences, our framework represents API sequences using API knowledge graphs and system resource encodings and applies contrastive learning to enhance the model's encoder. Results indicate that, compared to regular Text-CNN, our framework can significantly reduce the false positive rate by 13.10% and improve the F1-Score by 8.47% on five years of data, achieving the best experimental results. Additionally, evaluations show that our framework can save on the human costs required for model maintenance. We only need 1% of the budget per month to reduce the false positive rate by 11.16% and improve the F1-Score by 6.44%.

cs.CR↗

arXiv2025

BioMedSearch: A Multi-Source Biomedical Retrieval Framework Based on LLMs

Biomedical queries often rely on a deep understanding of specialized knowledge such as gene regulatory mechanisms and pathological processes of diseases. They require detailed analysis of complex physiological processes and effective integration of information from multiple data sources to support accurate retrieval and reasoning. Although large language models (LLMs) perform well in general reasoning tasks, their generated biomedical content often lacks scientific rigor due to the inability to access authoritative biomedical databases and frequently fabricates protein functions, interactions, and structural details that deviate from authentic information. Therefore, we present BioMedSearch, a multi-source biomedical information retrieval framework based on LLMs. The method integrates literature retrieval, protein database and web search access to support accurate and efficient handling of complex biomedical queries. Through sub-queries decomposition, keywords extraction, task graph construction, and multi-source information filtering, BioMedSearch generates high-quality question-answering results. To evaluate the accuracy of question answering, we constructed a multi-level dataset, BioMedMCQs, consisting of 3,000 questions. The dataset covers three levels of reasoning: mechanistic identification, non-adjacent semantic integration, and temporal causal reasoning, and is used to assess the performance of BioMedSearch and other methods on complex QA tasks. Experimental results demonstrate that BioMedSearch consistently improves accuracy over all baseline models across all levels. Specifically, at Level 1, the average accuracy increases from 59.1% to 91.9%; at Level 2, it rises from 47.0% to 81.0%; and at the most challenging Level 3, the average accuracy improves from 36.3% to 73.4%. The code and BioMedMCQs are available at: https://github.com/CyL-ucas/BioMed_Search

cs.CL↗

arXiv2025

Hybrid Multi-stage Decoding for Few-shot NER with Entity-aware Contrastive Learning

Few-shot named entity recognition can identify new types of named entities based on a few labeled examples. Previous methods employing token-level or span-level metric learning suffer from the computational burden and a large number of negative sample spans. In this paper, we propose the Hybrid Multi-stage Decoding for Few-shot NER with Entity-aware Contrastive Learning (MsFNER), which splits the general NER into two stages: entity-span detection and entity classification. There are 3 processes for introducing MsFNER: training, finetuning, and inference. In the training process, we train and get the best entity-span detection model and the entity classification model separately on the source domain using meta-learning, where we create a contrastive learning module to enhance entity representations for entity classification. During finetuning, we finetune the both models on the support dataset of target domain. In the inference process, for the unlabeled data, we first detect the entity-spans, then the entity-spans are jointly determined by the entity classification model and the KNN. We conduct experiments on the open FewNERD dataset and the results demonstrate the advance of MsFNER.

cs.CL↗

arXiv2025

DWFS-Obfuscation: Dynamic Weighted Feature Selection for Robust Malware Familial Classification under Obfuscation

Due to its open-source nature, the Android operating system has consistently been a primary target for attackers. Learning-based methods have made significant progress in the field of Android malware detection. However, traditional detection methods based on static features struggle to identify obfuscated malicious code, while methods relying on dynamic analysis suffer from low efficiency. To address this, we propose a dynamic weighted feature selection method that analyzes the importance and stability of features, calculates scores to filter out the most robust features, and combines these selected features with the program's structural information. We then utilize graph neural networks for classification, thereby improving the robustness and accuracy of the detection system. We analyzed 8,664 malware samples from eight malware families and tested a total of 44,940 malware variants generated using seven obfuscation strategies. Experiments demonstrate that our proposed method achieves an F1-score of 95.56% on the unobfuscated dataset and 92.28% on the obfuscated dataset, indicating that the model can effectively detect obfuscated malware.

cs.CR↗

arXiv2024

PromptSAM+: Malware Detection based on Prompt Segment Anything Model

Machine learning and deep learning (ML/DL) have been extensively applied in malware detection, and some existing methods demonstrate robust performance. However, several issues persist in the field of malware detection: (1) Existing work often overemphasizes accuracy at the expense of practicality, rarely considering false positive and false negative rates as important metrics. (2) Considering the evolution of malware, the performance of classifiers significantly declines over time, greatly reducing the practicality of malware detectors. (3) Prior ML/DL-based efforts heavily rely on ample labeled data for model training, largely dependent on feature engineering or domain knowledge to build feature databases, making them vulnerable if correct labels are scarce. With the development of computer vision, vision-based malware detection technology has also rapidly evolved. In this paper, we propose a visual malware general enhancement classification framework, `PromptSAM+', based on a large visual network segmentation model, the Prompt Segment Anything Model(named PromptSAM+). Our experimental results indicate that 'PromptSAM+' is effective and efficient in malware detection and classification, achieving high accuracy and low rates of false positives and negatives. The proposed method outperforms the most advanced image-based malware detection technologies on several datasets. 'PromptSAM+' can mitigate aging in existing image-based malware classifiers, reducing the considerable manpower needed for labeling new malware samples through active learning. We conducted experiments on datasets for both Windows and Android platforms, achieving favorable outcomes. Additionally, our ablation experiments on several datasets demonstrate that our model identifies effective modules within the large visual network.

cs.CR↗