Unpaired Image-to-Image Translation for Segmentation and Signal Unmixing

This work introduces Ui2i, a novel model for unpaired image-to-image translation, trained on content-wise unpaired datasets to enable style transfer across domains while preserving content. Building on CycleGAN, Ui2i incorporates key modifications to better disentangle content and style features, and preserve content integrity. Specifically, Ui2i employs U-Net-based generators with skip connections to propagate localized shallow features deep into the generator. Ui2i removes feature-based normalization layers from all modules and replaces them with approximate bidirectional spectral normalization -- a parameter-based alternative that enhances training stability. To further support content preservation, channel and spatial attention mechanisms are integrated into the generators. Training is facilitated through image scale augmentation. Evaluation on two biomedical tasks -- domain adaptation for nuclear segmentation in immunohistochemistry (IHC) images and unmixing of biological structures superimposed in single-channel immunofluorescence (IF) images -- demonstrates Ui2i's ability to preserve content fidelity in settings that demand more accurate structural preservation than typical translation tasks. To the best of our knowledge, Ui2i is the first approach capable of separating superimposed signals in IF images using real, unpaired training data.

Geometric GNNs for Charged Particle Tracking at GlueX

Nuclear physics experiments are aimed at uncovering the fundamental building blocks of matter. The experiments involve high-energy collisions that produce complex events with many particle trajectories. Tracking charged particles resulting from collisions in the presence of a strong magnetic field is critical to enable the reconstruction of particle trajectories and precise determination of interactions. It is traditionally achieved through combinatorial approaches that scale worse than linearly as the number of hits grows. Since particle hit data naturally form a 3-dimensional point cloud and can be structured as graphs, Graph Neural Networks (GNNs) emerge as an intuitive and effective choice for this task. In this study, we evaluate the GNN model for track finding on the data from the GlueX experiment at Jefferson Lab. We use simulation data to train the model and test on both simulation and real GlueX measurements. We demonstrate that GNN-based track finding outperforms the currently used traditional method at GlueX in terms of segment-based efficiency at a fixed purity while providing faster inferences. We show that the GNN model can achieve significant speedup by processing multiple events in batches, which exploits the parallel computation capability of Graphical Processing Units (GPUs). Finally, we compare the GNN implementation on GPU and FPGA and describe the trade-off.

Complex System Diagnostics Using a Knowledge Graph-Informed and Large Language Model-Enhanced Framework

In this paper, we present a novel diagnostic framework that integrates Knowledge Graphs (KGs) and Large Language Models (LLMs) to support system diagnostics in high-reliability systems such as nuclear power plants. Traditional diagnostic modeling struggles when systems become too complex, making functional modeling a more attractive approach. Our approach introduces a diagnostic framework grounded in the functional modeling principles of the Dynamic Master Logic (DML) model. It incorporates two coordinated LLM components, including an LLM-based workflow for automated construction of DML logic from system documentation and an LLM agent that facilitates interactive diagnostics. The generated logic is encoded into a structured KG, referred to as KG-DML, which supports hierarchical fault reasoning. Expert knowledge or operational data can also be incorporated to refine the model's precision and diagnostic depth. In the interaction phase, users submit natural language queries, which are interpreted by the LLM agent. The agent selects appropriate tools for structured reasoning, including upward and downward propagation across the KG-DML. Rather than embedding KG content into every prompt, the LLM agent distinguishes between diagnostic and interpretive tasks. For diagnostics, the agent selects and executes external tools that perform structured KG reasoning. For general queries, a Graph-based Retrieval-Augmented Generation (Graph-RAG) approach is used, retrieving relevant KG segments and embedding them into the prompt to generate natural explanations. A case study on an auxiliary feedwater system demonstrated the framework's effectiveness, with over 90% accuracy in key elements and consistent tool and argument extraction, supporting its use in safety-critical diagnostics.

APSeg: Auto-Prompt Model with Acquired and Injected Knowledge for Nuclear Instance Segmentation and Classification

Nuclear instance segmentation and classification provide critical quantitative foundations for digital pathology diagnosis. With the advent of the foundational Segment Anything Model (SAM), the accuracy and efficiency of nuclear segmentation have improved significantly. However, SAM imposes a strong reliance on precise prompts, and its class-agnostic design renders its classification results entirely dependent on the provided prompts. Therefore, we focus on generating prompts with more accurate localization and classification and propose \textbf{APSeg}, \textbf{A}uto-\textbf{P}rompt model with acquired and injected knowledge for nuclear instance \textbf{Seg}mentation and classification. APSeg incorporates two knowledge-aware modules: (1) Distribution-Guided Proposal Offset Module (\textbf{DG-POM}), which learns distribution knowledge through density map guided, and (2) Category Knowledge Semantic Injection Module (\textbf{CK-SIM}), which injects morphological knowledge derived from category descriptions. We conducted extensive experiments on the PanNuke and CoNSeP datasets, demonstrating the effectiveness of our approach. The code will be released upon acceptance.

Instance Migration Diffusion for Nuclear Instance Segmentation in Pathology

Nuclear instance segmentation plays a vital role in disease diagnosis within digital pathology. However, limited labeled data in pathological images restricts the overall performance of nuclear instance segmentation. To tackle this challenge, we propose a novel data augmentation framework Instance Migration Diffusion Model (IM-Diffusion), IM-Diffusion designed to generate more varied pathological images by constructing diverse nuclear layouts and internuclear spatial relationships. In detail, we introduce a Nuclear Migration Module (NMM) which constructs diverse nuclear layouts by simulating the process of nuclear migration. Building on this, we further present an Internuclear-regions Inpainting Module (IIM) to generate diverse internuclear spatial relationships by structure-aware inpainting. On the basis of the above, IM-Diffusion generates more diverse pathological images with different layouts and internuclear spatial relationships, thereby facilitating downstream tasks. Evaluation on the CoNSeP and GLySAC datasets demonstrate that the images generated by IM-Diffusion effectively enhance overall instance segmentation performance. Code will be made public later.

An Explainable Neural Radiomic Sequence Model with Spatiotemporal Continuity for Quantifying 4DCT-based Pulmonary Ventilation

Accurate evaluation of regional lung ventilation is essential for the management and treatment of lung cancer patients, supporting assessments of pulmonary function, optimization of therapeutic strategies, and monitoring of treatment response. Currently, ventilation scintigraphy using nuclear medicine techniques is widely employed in clinical practice; however, it is often time-consuming, costly, and entails additional radiation exposure. In this study, we propose an explainable neural radiomic sequence model to identify regions of compromised pulmonary ventilation based on four-dimensional computed tomography (4DCT). A cohort of 45 lung cancer patients from the VAMPIRE dataset was analyzed. For each patient, lung volumes were segmented from 4DCT, and voxel-wise radiomic features (56-dimensional) were extracted across the respiratory cycle to capture local intensity and texture dynamics, forming temporal radiomic sequences. Ground truth ventilation defects were delineated voxel-wise using Galligas-PET and DTPA-SPECT. To identify compromised regions, we developed a temporal saliency-enhanced explainable long short-term memory (LSTM) network trained on the radiomic sequences. Temporal saliency maps were generated to highlight key features contributing to the model's predictions. The proposed model demonstrated robust performance, achieving average (range) Dice similarity coefficients of 0.78 (0.74-0.79) for 25 PET cases and 0.78 (0.74-0.82) for 20 SPECT cases. The temporal saliency map explained three key radiomic sequences in ventilation quantification: during lung exhalation, compromised pulmonary function region typically exhibits (1) an increasing trend of intensity and (2) a decreasing trend of homogeneity, in contrast to healthy lung tissue.

Are nuclear masks all you need for improved out-of-domain generalisation? A closer look at cancer classification in histopathology

Domain generalisation in computational histopathology is challenging because the images are substantially affected by differences among hospitals due to factors like fixation and staining of tissue and imaging equipment. We hypothesise that focusing on nuclei can improve the out-of-domain (OOD) generalisation in cancer detection. We propose a simple approach to improve OOD generalisation for cancer detection by focusing on nuclear morphology and organisation, as these are domain-invariant features critical in cancer detection. Our approach integrates original images with nuclear segmentation masks during training, encouraging the model to prioritise nuclei and their spatial arrangement. Going beyond mere data augmentation, we introduce a regularisation technique that aligns the representations of masks and original images. We show, using multiple datasets, that our method improves OOD generalisation and also leads to increased robustness to image corruptions and adversarial attacks. The source code is available at https://github.com/undercutspiky/SFL/

Laparoscopic Scene Analysis for Intraoperative Visualisation of Gamma Probe Signals in Minimally Invasive Cancer Surgery

Cancer remains a significant health challenge worldwide, with a new diagnosis occurring every two minutes in the UK. Surgery is one of the main treatment options for cancer. However, surgeons rely on the sense of touch and naked eye with limited use of pre-operative image data to directly guide the excision of cancerous tissues and metastases due to the lack of reliable intraoperative visualisation tools. This leads to increased costs and harm to the patient where the cancer is removed with positive margins, or where other critical structures are unintentionally impacted. There is therefore a pressing need for more reliable and accurate intraoperative visualisation tools for minimally invasive surgery to improve surgical outcomes and enhance patient care. A recent miniaturised cancer detection probe (i.e., SENSEI developed by Lightpoint Medical Ltd.) leverages the cancer-targeting ability of nuclear agents to more accurately identify cancer intra-operatively using the emitted gamma signal. However, the use of this probe presents a visualisation challenge as the probe is non-imaging and is air-gapped from the tissue, making it challenging for the surgeon to locate the probe-sensing area on the tissue surface. Geometrically, the sensing area is defined as the intersection point between the gamma probe axis and the tissue surface in 3D space but projected onto the 2D laparoscopic image. Hence, in this thesis, tool tracking, pose estimation, and segmentation tools were developed first, followed by laparoscope image depth estimation algorithms and 3D reconstruction methods.

MSEG-VCUQ: Multimodal SEGmentation with Enhanced Vision Foundation Models, Convolutional Neural Networks, and Uncertainty Quantification for High-Speed Video Phase Detection Data

Purpose: High-speed video (HSV) phase detection (PD) segmentation is vital in nuclear reactors, chemical processing, and electronics cooling for detecting vapor, liquid, and microlayer phases. Traditional segmentation models face pixel-level accuracy and generalization issues in multimodal data. MSEG-VCUQ introduces VideoSAM, a hybrid framework leveraging convolutional neural networks (CNNs) and transformer-based vision models to enhance segmentation accuracy and generalizability across complex multimodal PD tasks. Methods: VideoSAM combines U-Net CNN and the Segment Anything Model (SAM) for advanced feature extraction and segmentation across diverse HSV PD modalities, spanning fluids like water, FC-72, nitrogen, and argon under varied heat flux conditions. The framework also incorporates uncertainty quantification (UQ) to assess pixel-based discretization errors, delivering reliable metrics such as contact line density and dry area fraction under experimental conditions. Results: VideoSAM outperforms SAM and modality-specific CNN models in segmentation accuracy, excelling in environments with complex phase boundaries, overlapping bubbles, and dynamic liquid-vapor interactions. Its hybrid architecture supports cross-dataset generalization, adapting effectively to varying modalities. The UQ module provides accurate error estimates, enhancing the reliability of segmentation outputs for advanced HSV PD research. Conclusion: MSEG-VCUQ, via VideoSAM, offers a robust solution for HSV PD segmentation, addressing previous limitations with advanced deep learning and UQ techniques. The open-source datasets and tools introduced enable scalable, precise, and adaptable segmentation for multimodal PD datasets, supporting advancements in HSV analysis and autonomous experimentation. The codes and data used for this paper are publicly available at: \url{https://github.com/chikap421/mseg_vcuq}

Irregular Tensor Low-Rank Representation for Hyperspectral Image Representation

Spectral variation is a common problem for hyperspectral image (HSI) representation. Low-rank tensor representation is an important approach to alleviate spectral variations. However, the spatial distribution of the HSI is always irregular, while the previous tensor low-rank representation methods can only be applied to the regular data cubes, which limits the performance. To remedy this issue, in this paper we propose a novel irregular tensor low-rank representation model. We first segment the HSI data into several irregular homogeneous regions. Then, we propose a novel irregular tensor low-rank representation method that can efficiently model the irregular 3D cubes. We further use a non-convex nuclear norm to pursue the low-rankness and introduce a negative global low-rank term that improves global consistency. This proposed model is finally formulated as a convex-concave optimization problem and solved by alternative augmented Lagrangian method. Through experiments on four public datasets, the proposed method outperforms the existing low-rank based HSI methods significantly. Code is available at: https://github.com/hb-studying/ITLRR.