arXiv subjects

Na Shen

Publications and source records attributed to Na Shen.

7 recordsLinked to original sources

arXiv2026

A 3D foundation model unifying CT interpretation and segmentation

Radiologists interpret computed tomography (CT) scans by jointly determining what a finding represents and where it lies in three-dimensional (3D) anatomy. However, CT models have treated CT interpretation and 3D segmentation as separate tasks, leaving textual findings spatially unverifiable and overlooking potential synergy between clinical understanding and spatial perception. Here we present HoloCT, a generalist 3D foundation model unifying CT interpretation and voxel-level segmentation by jointly modelling whole-volume context and fine-grained anatomical detail, providing 3D masks as evidence. We curated HoloDATA, comprising 195,921 CT scans from 73 public datasets and six clinical cohorts, with 6.2 million instruction dialogues and 2.8 million CT-mask pairs. Across 346 tasks spanning segmentation, lesion screening, visual question answering, and report generation on 61 internal and 12 external datasets, HoloCT outperformed specialist and foundation models. In multicentre validation across 11,455 clinical CT scans from five hospitals, HoloCT outperformed competing models in lesion segmentation and report generation by 18.2 and 15.3 points. It also achieved 85.1% mean accuracy in screening thyroid tumours and colon lesions, exceeding all four participating radiologists in a retrospective reader study. Further analyses revealed bidirectional semantic-spatial synergy: language-guided segmentation delineated unseen anatomical structures and lesions as well as diffuse free-text findings, outperforming the leading approach by 22.1 points, whereas prompting the model to generate corresponding 3D masks alongside its textual outputs significantly improved interpretation performance. HoloCT shows that clinical understanding and spatial perception can be learned together within a single foundation model and offers a path towards more accurate and reliable CT analysis.

cs.CV↗

arXiv2026

Anatomy-aware Fine-grained Multimodal Fusion for Laryngopharyngeal Cancer T-Staging Prediction Using CT and Radiology Report

Accurate T-staging is crucial for guiding personalized treatment strategies for laryngopharyngeal cancer. However, current clinical practice relies on invasive biopsy procedures, whereas CT-based staging remains challenging due to the complex patterns of tumor invasion. Recent computer-aided approaches face two key challenges: 1) Structural relationship modeling: existing methods underrepresent anatomically structured patterns of tumor invasion, as they either process whole CT volumes without tumor-specific anatomical constraints or rely on labor-intensive tumor segmentation. 2) Fine-grained cross-modal alignment: while radiology reports contain organ-specific invasion details, current methods that apply global feature fusion struggle to accurately align individual anatomical structures with their corresponding textual descriptions. To address these issues, we propose an anatomy-aware multimodal framework that integrates organ-level CT context and radiology reports into a unified representation for laryngopharyngeal T-staging. The framework first constructs an Anatomy-Structured Organ Graph (AOG) that captures invasion patterns between primary sites and surrounding organs, then performs Organ-Anchored Cross-Modal Alignment (OCA) so that each organ node aggregates textual evidence from the radiology report, and finally refines this graph representation by injecting organ-specific invasion cues extracted from the report via Report-Enhanced Graph-Refinement (REG), yielding a multimodal organ graph that combines spatial and textual evidence. Extensive experiments demonstrate that the proposed framework achieves superior performance in T-staging of laryngopharyngeal cancer.

cs.CV↗

arXiv2026

Surface Charge Doping for Ion-Pairing Criticality in Confined Electrolytes

Dielectric confinement strengthens Coulomb correlations in quasi-two-dimensional electrolytes and can promote Bjerrum pairing in charge-neutral slits. Here we use a generalized Debye-Huckel-Bjerrum theory to show that weak surface charge changes this picture by stoichiometrically doping the slit with mobile counterions. These counterions maintain a finite screening floor, decouple microscopic pairing from macroscopic ionicity, and shift association-driven criticality to lower temperatures. The critical-temperature suppression collapses onto a single scaled perturbation variable, revealing how surface charge and dielectric confinement jointly control charged nanofluidic slits. Brownian-dynamics tests further show that the same counterions are not always fully bulk-like diffusive: at low intrinsic salt density, explicit wall charge slows in-plane diffusion, whereas at higher intrinsic density the wall-induced diffusion penalty decreases and the mobile-counterion description becomes dynamically accurate. These results identify surface charge as a thermodynamic doping field that tunes both correlated ionic stability and the diffusion mechanism in nanofluidic confinement.

cond-mat.soft↗

arXiv2025

Effective Lymph Nodes Detection in CT Scans Using Location Debiased Query Selection and Contrastive Query Representation in Transformer

Lymph node (LN) assessment is a critical, indispensable yet very challenging task in the routine clinical workflow of radiology and oncology. Accurate LN analysis is essential for cancer diagnosis, staging, and treatment planning. Finding scatteredly distributed, low-contrast clinically relevant LNs in 3D CT is difficult even for experienced physicians under high inter-observer variations. Previous automatic LN detection works typically yield limited recall and high false positives (FPs) due to adjacent anatomies with similar image intensities, shapes, or textures (vessels, muscles, esophagus, etc). In this work, we propose a new LN DEtection TRansformer, named LN-DETR, to achieve more accurate performance. By enhancing the 2D backbone with a multi-scale 2.5D feature fusion to incorporate 3D context explicitly, more importantly, we make two main contributions to improve the representation quality of LN queries. 1) Considering that LN boundaries are often unclear, an IoU prediction head and a location debiased query selection are proposed to select LN queries of higher localization accuracy as the decoder query's initialization. 2) To reduce FPs, query contrastive learning is employed to explicitly reinforce LN queries towards their best-matched ground-truth queries over unmatched query predictions. Trained and tested on 3D CT scans of 1067 patients (with 10,000+ labeled LNs) via combining seven LN datasets from different body parts (neck, chest, and abdomen) and pathologies/cancers, our method significantly improves the performance of previous leading methods by > 4-5% average recall at the same FP rates in both internal and external testing. We further evaluate on the universal lesion detection task using NIH DeepLesion benchmark, and our method achieves the top performance of 88.46% averaged recall across 0.5 to 4 FPs per image, compared with other leading reported results.

cs.CV↗

arXiv2025

A Continual Learning-driven Model for Accurate and Generalizable Segmentation of Clinically Comprehensive and Fine-grained Whole-body Anatomies in CT

Precision medicine in the quantitative management of chronic diseases and oncology would be greatly improved if the Computed Tomography (CT) scan of any patient could be segmented, parsed and analyzed in a precise and detailed way. However, there is no such fully annotated CT dataset with all anatomies delineated for training because of the exceptionally high manual cost, the need for specialized clinical expertise, and the time required to finish the task. To this end, we proposed a novel continual learning-driven CT model that can segment complete anatomies presented using dozens of previously partially labeled datasets, dynamically expanding its capacity to segment new ones without compromising previously learned organ knowledge. Existing multi-dataset approaches are not able to dynamically segment new anatomies without catastrophic forgetting and would encounter optimization difficulty or infeasibility when segmenting hundreds of anatomies across the whole range of body regions. Our single unified CT segmentation model, CL-Net, can highly accurately segment a clinically comprehensive set of 235 fine-grained whole-body anatomies. Composed of a universal encoder, multiple optimized and pruned decoders, CL-Net is developed using 13,952 CT scans from 20 public and 16 private high-quality partially labeled CT datasets of various vendors, different contrast phases, and pathologies. Extensive evaluation demonstrates that CL-Net consistently outperforms the upper limit of an ensemble of 36 specialist nnUNets trained per dataset with the complexity of 5% model size and significantly surpasses the segmentation accuracy of recent leading Segment Anything-style medical image foundation models by large margins. Our continual learning-driven CL-Net model would lay a solid foundation to facilitate many downstream tasks of oncology and chronic diseases using the most widely adopted CT imaging.

eess.IV↗

arXiv2025

From Slices to Sequences: Autoregressive Tracking Transformer for Cohesive and Consistent 3D Lymph Node Detection in CT Scans

Lymph node (LN) assessment is an essential task in the routine radiology workflow, providing valuable insights for cancer staging, treatment planning and beyond. Identifying scatteredly-distributed and low-contrast LNs in 3D CT scans is highly challenging, even for experienced clinicians. Previous lesion and LN detection methods demonstrate effectiveness of 2.5D approaches (i.e, using 2D network with multi-slice inputs), leveraging pretrained 2D model weights and showing improved accuracy as compared to separate 2D or 3D detectors. However, slice-based 2.5D detectors do not explicitly model inter-slice consistency for LN as a 3D object, requiring heuristic post-merging steps to generate final 3D LN instances, which can involve tuning a set of parameters for each dataset. In this work, we formulate 3D LN detection as a tracking task and propose LN-Tracker, a novel LN tracking transformer, for joint end-to-end detection and 3D instance association. Built upon DETR-based detector, LN-Tracker decouples transformer decoder's query into the track and detection groups, where the track query autoregressively follows previously tracked LN instances along the z-axis of a CT scan. We design a new transformer decoder with masked attention module to align track query's content to the context of current slice, meanwhile preserving detection query's high accuracy in current slice. An inter-slice similarity loss is introduced to encourage cohesive LN association between slices. Extensive evaluation on four lymph node datasets shows LN-Tracker's superior performance, with at least 2.7% gain in average sensitivity when compared to other top 3D/2.5D detectors. Further validation on public lung nodule and prostate tumor detection tasks confirms the generalizability of LN-Tracker as it achieves top performance on both tasks.

cs.CV↗

arXiv2023

Anatomy-Aware Lymph Node Detection in Chest CT using Implicit Station Stratification

Finding abnormal lymph nodes in radiological images is highly important for various medical tasks such as cancer metastasis staging and radiotherapy planning. Lymph nodes (LNs) are small glands scattered throughout the body. They are grouped or defined to various LN stations according to their anatomical locations. The CT imaging appearance and context of LNs in different stations vary significantly, posing challenges for automated detection, especially for pathological LNs. Motivated by this observation, we propose a novel end-to-end framework to improve LN detection performance by leveraging their station information. We design a multi-head detector and make each head focus on differentiating the LN and non-LN structures of certain stations. Pseudo station labels are generated by an LN station classifier as a form of multi-task learning during training, so we do not need another explicit LN station prediction model during inference. Our algorithm is evaluated on 82 patients with lung cancer and 91 patients with esophageal cancer. The proposed implicit station stratification method improves the detection sensitivity of thoracic lymph nodes from 65.1% to 71.4% and from 80.3% to 85.5% at 2 false positives per patient on the two datasets, respectively, which significantly outperforms various existing state-of-the-art baseline techniques such as nnUNet, nnDetection and LENS.

cs.CV↗