arXiv subjects

Simeng Zhu

Publications and source records attributed to Simeng Zhu.

10 recordsLinked to original sources

arXiv2026

RADIANT-PET: Reasoning-Augmented PET/CT Lesion Segmentation with Large Language Models and Reinforcement Learning

Accurate lesion segmentation in PET/CT is critical for oncology, yet remains challenging because physiologic tracer uptake and artifacts can mimic malignant signal. We present RADIANT-PET, a reasoning-augmented framework that couples a high-sensitivity voxel-level segmentation model with lesion-level large language model (LLM) adjudication. Candidate uptake regions are generated with a deliberately permissive segmentation stage, then converted into structured textual descriptions that summarize uptake intensity, morphology, and regional and global anatomical context. An LLM classifies each candidate as true lesion vs. false positive, optionally leveraging the radiology report as additional clinical context. To strengthen lesion-level reasoning, we further optimize a local LLM via reinforcement learning using Group Relative Policy Optimization, rewarding correct lesion classification and anatomically concordant site assignment. Across AutoPET and an OSU test cohort, RADIANT-PET consistently outperforms strong image-only baselines, with the largest improvements observed when radiology reports are provided. Overall, these results demonstrate that LLM-based lesion-level reasoning adds a novel reasoning layer beyond conventional segmentation, suppressing physiologic false positives and aligning voxel-level predictions with clinical interpretation. The project repository is available at: https://github.com/jwang-580/RADIANT-PET.

cs.CV↗

arXiv2025

Atlas is Your Perfect Context: One-Shot Customization for Generalizable Foundational Medical Image Segmentation

Accurate segmentation of anatomical structures in medical images is essential for diagnosis and treatment planning. While recent interactive segmentation foundation models enhance generalization through large-scale multimodal pretraining, they still depend on precise prompts and can fail in underrepresented clinical contexts (e.g., small organs-at-risk). We present AtlasSegFM, an atlas-guided framework that customizes off-the-shelf foundation models to new clinical contexts with a single annotated example. AtlasSegFM 1) performs atlas-query registration to generate context-aware prompts, 2) refines the segmentation with a frozen foundation model, and 3) applies a lightweight adaptive fusion module to combine atlas priors with foundation-model inputs and predictions. Extensive experiments on six public and in-house datasets across radiotherapy and vascular scenarios show consistent gains, with the largest improvements on small and delicate structures. AtlasSegFM provides a lightweight, deployable solution for one-shot customization of segmentation foundation models in real-world clinical workflows.

cs.CV↗

arXiv2025

Second-order spatial analysis of shapes of tumor cell nuclei

Intra-tumor heterogeneity driving disease progression is characterized by distinct growth and spatial proliferation patterns of cells and their nuclei within tumor and non-tumor tissues. A widely accepted hypothesis is that these spatial patterns are correlated with morphology of the cells and their nuclei. Nevertheless, tools to quantify the correlation, with uncertainty, are scarce, and the state-of-the-art is based on low-dimensional numerical summaries of the shapes that are inadequate to fully encode shape information. To this end, we propose a marked point process framework to assess spatial correlation among shapes of planar closed curves, which represent cell or nuclei outlines. With shapes of curves as marks, the framework is based on a mark-weighted $K$ function, a second-order spatial statistic that accounts for the marks' variation by using test functions that capture only the shapes of cells and their nuclei. We then develop local and global hypothesis tests for spatial dependence between the marks using the $K$ function. The framework is brought to bear on the cell nuclei extracted from histopathology images of breast cancer, where we uncover distinct correlation patterns that are consistent with clinical expectations.

stat.AP↗

arXiv2025

Modality-AGnostic Image Cascade (MAGIC) for Multi-Modality Cardiac Substructure Segmentation

Cardiac substructure delineation is emerging in treatment planning to minimize the risk of radiation-induced heart disease. Deep learning offers efficient methods to reduce contouring burden but currently lacks generalizability across different modalities and overlapping structures. This work introduces and validates a Modality-AGnostic Image Cascade (MAGIC) deep-learning pipeline for comprehensive and multi-modal cardiac substructure segmentation. MAGIC is implemented through replicated encoding and decoding branches of an nnU-Net backbone to handle multi-modality inputs and overlapping labels. First benchmarked on the multi-modality whole-heart segmentation (MMWHS) dataset including cardiac CT-angiography (CCTA) and MR modalities, twenty cardiac substructures (heart, chambers, great vessels (GVs), valves, coronary arteries (CAs), and conduction nodes) from clinical simulation CT (Sim-CT), low-field MR-Linac, and cardiac CT-angiography (CCTA) modalities were delineated to train semi-supervised (n=151), validate (n=15), and test (n=30) MAGIC. For comparison, fourteen single-modality comparison models (two MMWHS modalities and four subgroups across three clinical modalities) were trained. Methods were evaluated for efficiency and against reference contours through the Dice similarity coefficient (DSC) and two-tailed Wilcoxon Signed-Rank test (p<0.05). Average MMWHS DSC scores across CCTA and MR inputs were 0.88(0.08) and 0.87(0.04) respectively with significant improvement over unimodal baselines. Average 20-structure DSC scores were 0.75(0.16) for Sim-CT, 0.68(0.21) for MR-Linac, and 0.80(0.16) for CCTA. Furthermore, >80% and >70% reductions in training time and parameters were achieved, respectively. MAGIC offers an efficient, lightweight solution capable of segmenting multiple image modalities and overlapping structures in a single model without compromising segmentation accuracy.

physics.med-ph↗

arXiv2025

WAFBOOSTER: Automatic Boosting of WAF Security Against Mutated Malicious Payloads

Web application firewall (WAF) examines malicious traffic to and from a web application via a set of security rules. It plays a significant role in securing Web applications against web attacks. However, as web attacks grow in sophistication, it is becoming increasingly difficult for WAFs to block the mutated malicious payloads designed to bypass their defenses. In response to this critical security issue, we have developed a novel learning-based framework called WAFBOOSTER, designed to unveil potential bypasses in WAF detections and suggest rules to fortify their security. Using a combination of shadow models and payload generation techniques, we can identify malicious payloads and remove or modify them as needed. WAFBOOSTER generates signatures for these malicious payloads using advanced clustering and regular expression matching techniques to repair any security gaps we uncover. In our comprehensive evaluation of eight real-world WAFs, WAFBOOSTER improved the true rejection rate of mutated malicious payloads from 21% to 96%, with no false rejections. WAFBOOSTER achieves a false acceptance rate 3X lower than state-of-the-art methods for generating malicious payloads. With WAFBOOSTER, we have taken a step forward in securing web applications against the ever-evolving threats.

cs.CR↗

arXiv2024

Widely Tunable Photonic Filter Based on Equivalent Chirped Four-Phase-Shifted Sampled Bragg Gratings

We have developed an integrated dual-band photonic filter (PF) utilizing equivalent chirped four-phase-shifted sidewall-sampled Bragg gratings (4PS-SBG) on a silicon-on-insulator (SOI) platform. Using the reconstruction equivalent-chirp technique, we designed linearly chirped 4PS Bragg gratings with two {\pi}-phase shifts ({\pi}-PS) positioned at 1/3 and 2/3 of the grating cavity, introducing two passbands in the +1st order channel. Leveraging the significant thermo-optic effect of silicon, dual-band tuning is achieved through integrated micro-heaters (MHs) on the chip surface. By varying the injection currents from 0 to 85 mA into the MHs, the device demonstrates continuous and wide-range optical frequency division (OFD) performance, with the frequency interval between the two passbands adjustable from 52.1 GHz to 439.5 GHz. Four notable frequency division setups at 100 GHz, 200 GHz, 300 GHz, and 400 GHz were demonstrated using a 100 GHz, 1535 nm semiconductor passive mode-locked laser as the light source.

physics.optics↗

arXiv2024

Continuous Phase Modulation Technology Based on Grating Period Interval for High Grating Coupling Efficiency and Precise Wavelength Control

A novel grating modulation technique for laser arrays is proposed and demonstrated. This method modifies the initial phase within each grating period, applying a total phase shift that increments in an arithmetic progression, ensuring equal channel spacing across the array. Despite the varying phase shifts, the device maintains coupling efficiency comparable to traditional uniform grating structures. Furthermore, the continuous phase modulation enhances the stability of the lasing wavelength of the primary mode, reducing sensitivity to fabrication errors. This improved tolerance to manufacturing inaccuracies represents a significant technological advancement, making this approach highly promising for applications requiring precise and stable wavelength control.

physics.optics↗

arXiv2024

Narrow Linewidth Distributed Feedback Lasers Utilizing Distributed Phase Shift

This study proposes and experimentally demonstrates a distributed feedback (DFB) laser with a distributed phase shift (DPS) region at the center of the DFB cavity. By modeling the field intensity distribution in the cavity and the output spectrum, the DPS region length and phase shift values have been optimized. Experimental comparisons with lasers using traditional {\pi}-phase shifts confirm that DFB lasers with optimized DPS lengths and larger phase shifts (up to 15{\pi}) achieve stable single longitudinal mode operation over a broader current range, with lower threshold current, higher power slope efficiency, and a higher side mode suppression ratio (SMSR). Furthermore, the minimum optical linewidth is reduced significantly, from 1.3 MHz to 220 kHz.

physics.optics↗

arXiv2022

Prostate Cancer Malignancy Detection and localization from mpMRI using auto-Deep Learning: One Step Closer to Clinical Utilization

Automatic diagnosis of malignant prostate cancer patients from mpMRI has been studied heavily in the past years. Model interpretation and domain drift have been the main road blocks for clinical utilization. As an extension from our previous work where we trained a customized convolutional neural network on a public cohort with 201 patients and the cropped 2D patches around the region of interest were used as the input, the cropped 2.5D slices of the prostate glands were used as the input, and the optimal model were searched in the model space using autoKeras. Something different was peripheral zone (PZ) and central gland (CG) were trained and tested separately, the PZ detector and CG detector were demonstrated effectively in highlighting the most suspicious slices out of a sequence, hopefully to greatly ease the workload for the physicians.

eess.IV↗

arXiv2022

OpenKBP-Opt: An international and reproducible evaluation of 76 knowledge-based planning pipelines

We establish an open framework for developing plan optimization models for knowledge-based planning (KBP) in radiotherapy. Our framework includes reference plans for 100 patients with head-and-neck cancer and high-quality dose predictions from 19 KBP models that were developed by different research groups during the OpenKBP Grand Challenge. The dose predictions were input to four optimization models to form 76 unique KBP pipelines that generated 7600 plans. The predictions and plans were compared to the reference plans via: dose score, which is the average mean absolute voxel-by-voxel difference in dose a model achieved; the deviation in dose-volume histogram (DVH) criterion; and the frequency of clinical planning criteria satisfaction. We also performed a theoretical investigation to justify our dose mimicking models. The range in rank order correlation of the dose score between predictions and their KBP pipelines was 0.50 to 0.62, which indicates that the quality of the predictions is generally positively correlated with the quality of the plans. Additionally, compared to the input predictions, the KBP-generated plans performed significantly better (P<0.05; one-sided Wilcoxon test) on 18 of 23 DVH criteria. Similarly, each optimization model generated plans that satisfied a higher percentage of criteria than the reference plans. Lastly, our theoretical investigation demonstrated that the dose mimicking models generated plans that are also optimal for a conventional planning model. This was the largest international effort to date for evaluating the combination of KBP prediction and optimization models. In the interest of reproducibility, our data and code is freely available at https://github.com/ababier/open-kbp-opt.

physics.med-ph↗