arXiv subjects

Zhengyang Xu

Publications and source records attributed to Zhengyang Xu.

6 recordsLinked to original sources

arXiv2026

Policy-Driven CT-Agent: Modeling Phase-Aware Diagnostic Control for Clinically Consistent CT Reasoning

Computed Tomography (CT) diagnosis often relies on dynamic selection of imaging phases, such as non-contrast, arterial, or venous phases, based on preliminary findings, clinical suspicion, and diagnostic guidelines. This phase-wise decision process is critical for reducing unnecessary radiation exposure while supporting timely staging and treatment planning. However, phase-selection protocols can vary across hospitals, regions, and guidelines, while most existing CT-based AI methods assume that all phases are available and focus on static tasks under a fixed imaging phase, failing to model whether additional phases are required. This limitation stems from heterogeneous multi-phase representations, the need for knowledge-guided phase control beyond visual cues, and the lack of supervision for phase-sufficiency decisions in existing datasets. To address these challenges, we propose Policy-Driven CT-Agent (PD-CTAgent) for clinically consistent CT phase selection and diagnostic reasoning. PD-CTAgent introduces a Clinical Structure Abstraction Module (CSAM) to harmonize heterogeneous CT phases into a unified, phase-aware evidence representation. Based on this representation, a Knowledge-Guided Diagnostic Control Model (KDCM) evaluates phase sufficiency and iteratively requests additional phases when necessary. The policy-driven agent design further allows PD-CTAgent to flexibly follow different institutional, regional, or guideline-specific diagnostic protocols. Together, PD-CTAgent bridges static CT analysis and real-world clinical workflows. Experiments on two public datasets, LIDC and MCT-LTDiag, and one private dataset demonstrate its effectiveness and clinical consistency. Code will be made public upon acceptance.

cs.LG↗

arXiv2026

Paired Uterine Whole-Slide Images and Pathology Reports for Multimodal Computational Pathology

Uterine diseases represent an important category of gynecologic pathology and require accurate histopathological assessment for diagnosis and treatment planning. Whole-slide images (WSI) have enabled the digital transformation of pathology workflows and provided new opportunities for artificial intelligence (AI) in computational pathology. In particular, multimodal models that jointly analyze histopathology images and pathology reports have shown promising potential for automated pathology report generation and AI-assisted diagnosis. However, the development of such systems remains limited by the scarcity of datasets that pair whole-slide images with clinically meaningful pathology reports. Instead, existing pathology datasets focus on patch- or slide-level annotations of a single endpoint (e.g., disease class), which do not fully capture the rich information in full clinical diagnostic workflow reports. Here, we introduce TUM-Uteria, a uterine pathology dataset comprising WSIs paired with diagnostic pathology reports at both the case and slide levels, collected from a tertiary medical center. The dataset contains 216 clinical cases, comprising 455 slide-level WSI-report pairs. The dataset underwent a structured multi-stage validation procedure involving board-certified pathologists to ensure reliable annotations. TUM-Uteria supports research in computational pathology, including whole-slide image analysis, multimodal learning, and automated pathology report generation.

cs.CV↗

arXiv2026

MMNavAgent: Multi-Magnification WSI Navigation Agent for Clinically Consistent Whole-Slide Analysis

Recent AI navigation approaches aim to improve Whole-Slide Image (WSI) diagnosis by modeling spatial exploration and selecting diagnostically relevant regions, yet most operate at a single fixed magnification or rely on predefined magnification traversal. In clinical practice, pathologists examine slides across multiple magnifications and selectively inspect only necessary scales, dynamically integrating global and cellular evidence in a sequential manner. This mismatch prevents existing methods from modeling cross-magnification interactions and adaptive magnification selection inherent to real diagnostic workflows. To these, we propose a clinically consistent Multi-Magnification WSI Navigation Agent (MMNavAgent) that explicitly models multi magnification interaction and adaptive magnification selection. Specifically, we introduce a Cross-Magnification navigation Tool (CMT) that aggregates contextual information from adjacent magnifications to enhance discriminative representations along the navigation path. We further introduce a Magnification Selection Tool (MST) that leverages memory-driven reasoning within the agent framework to enable interactive and adaptive magnification selection, mimicking the sequential decision process of pathologists. Extensive experiments on a public dataset demonstrate improved diagnostic performance, with 1.45% gain of AUC and 2.93% gain of BACC over a non-agent baseline. Code will be public upon acceptance.

cs.CV↗

arXiv2025

Towards Cellular-Scale Interpretability in Pathology Foundation Models for Biomarker Assessment

Molecular biomarker testing in pathology is often costly and tissue-consuming, limiting scalable clinical deployment. Artificial intelligence applied to hematoxylin and eosin (HE)-stained histology could enable rapid biomarker screening, but clinical translation requires models that are both accurate and interpretable. Here we introduce Hireca, a biomarker-focused pathology foundation model pretrained on more than 80,000 whole-slide images spanning 38 organ types from three medical centers, together with CytoMap, an interpretability module that localizes cellular-scale evidence underlying predictions. Across 10 biomarker tasks encompassing morphological, molecular, genetic, and spatial-transcriptomic-proxy readouts, Hireca ranked first in five tasks and outperformed comparable models overall. In evaluation by eight pathologists from two countries, CytoMap was consistently preferred over alternative visualization approaches and revealed error patterns in difficult cases. These results position Hireca and CytoMap as a transparent framework for clinically reviewable biomarker assessment directly from routine HE histology.

cs.CV↗

arXiv2025

You Only Train Once: A Flexible Training Framework for Code Vulnerability Detection Driven by Vul-Vector

With the pervasive integration of computer applications across industries, the presence of vulnerabilities within code bases poses significant risks. The diversity of software ecosystems coupled with the intricate nature of modern software engineering has led to a shift from manual code vulnerability identification towards the adoption of automated tools. Among these, deep learning-based approaches have risen to prominence due to their superior accuracy; however, these methodologies encounter several obstacles. Primarily, they necessitate extensive labeled datasets and prolonged training periods, and given the rapid emergence of new vulnerabilities, the frequent retraining of models becomes a resource-intensive endeavor, thereby limiting their applicability in cutting-edge scenarios. To mitigate these challenges, this paper introduces the \underline{\textbf{YOTO}}--\underline{\textbf{Y}}ou \underline{\textbf{O}}nly \underline{\textbf{T}}rain \underline{\textbf{O}}nce framework. This innovative approach facilitates the integration of multiple types of vulnerability detection models via parameter fusion, eliminating the need for joint training. Consequently, YOTO enables swift adaptation to newly discovered vulnerabilities, significantly reducing both the time and computational resources required for model updates.

cs.SE↗

arXiv2024

StaPep: an open-source tool for the structure prediction and feature extraction of hydrocarbon-stapled peptides

Many tools exist for extracting structural and physiochemical descriptors from linear peptides to predict their properties, but similar tools for hydrocarbon-stapled peptides are lacking.Here, we present StaPep, a Python-based toolkit designed for generating 2D/3D structures and calculating 21 distinct features for hydrocarbon-stapled peptides.The current version supports hydrocarbon-stapled peptides containing 2 non-standard amino acids (norleucine and 2-aminoisobutyric acid) and 6 nonnatural anchoring residues (S3, S5, S8, R3, R5 and R8).Then we established a hand-curated dataset of 201 hydrocarbon-stapled peptides and 384 linear peptides with sequence information and experimental membrane permeability, to showcase StaPep's application in artificial intelligence projects.A machine learning-based predictor utilizing above calculated features was developed with AUC of 0.85, for identifying cell-penetrating hydrocarbon-stapled peptides.StaPep's pipeline spans data retrieval, cleaning, structure generation, molecular feature calculation, and machine learning model construction for hydrocarbon-stapled peptides.The source codes and dataset are freely available on Github: https://github.com/dahuilangda/stapep_package.

q-bio.BM↗