TransST: Transfer Learning Embedded Spatial Factor Modeling of Spatial Transcriptomics Data

Background: Spatial transcriptomics have emerged as a powerful tool in biomedical research because of its ability to capture both the spatial contexts and abundance of the complete RNA transcript profile in organs of interest. However, limitations of the technology such as the relatively low resolution and comparatively insufficient sequencing depth make it difficult to reliably extract real biological signals from these data. To alleviate this challenge, we propose a novel transfer learning framework, referred to as TransST, to adaptively leverage the cell-labeled information from external sources in inferring cell-level heterogeneity of a target spatial transcriptomics data. Results: Applications in several real studies as well as a number of simulation settings show that our approach significantly improves existing techniques. For example, in the breast cancer study, TransST successfully identifies five biologically meaningful cell clusters, including the two subgroups of cancer in situ and invasive cancer; in addition, only TransST is able to separate the adipose tissues from the connective issues among all the studied methods. Conclusions: In summary, the proposed method TransST is both effective and robust in identifying cell subclusters and detecting corresponding driving biomarkers in spatial transcriptomics data.

The impact of tissue detection on diagnostic artificial intelligence algorithms in digital pathology

Tissue detection is a crucial first step in most digital pathology applications. Details of the segmentation algorithm are rarely reported, and there is a lack of studies investigating the downstream effects of a poor segmentation algorithm. Disregarding tissue detection quality could create a bottleneck for downstream performance and jeopardize patient safety if diagnostically relevant parts of the specimen are excluded from analysis in clinical applications. This study aims to determine whether performance of downstream tasks is sensitive to the tissue detection method, and to compare performance of classical and AI-based tissue detection. To this end, we trained an AI model for Gleason grading of prostate cancer in whole slide images (WSIs) using two different tissue detection algorithms: thresholding (classical) and UNet++ (AI). A total of 33,823 WSIs scanned on five digital pathology scanners were used to train the tissue detection AI model. The downstream Gleason grading algorithm was trained and tested using 70,524 WSIs from 13 clinical sites scanned on 13 different scanners. There was a decrease from 116 (0.43%) to 22 (0.08%) fully undetected tissue samples when switching from thresholding-based tissue detection to AI-based, suggesting an AI model may be more reliable than a classical model for avoiding total failures on slides with unusual appearance. On the slides where tissue could be detected by both algorithms, no significant difference in overall Gleason grading performance was observed. However, tissue detection dependent clinically significant variations in AI grading were observed in 3.5% of malignant slides, highlighting the importance of robust tissue detection for optimal clinical performance of diagnostic AI.

Universal Lymph Node Detection in Multiparametric MRI with Selective Augmentation

Robust localization of lymph nodes (LNs) in multiparametric MRI (mpMRI) is critical for the assessment of lymphadenopathy. Radiologists routinely measure the size of LN to distinguish benign from malignant nodes, which would require subsequent cancer staging. Sizing is a cumbersome task compounded by the diverse appearances of LNs in mpMRI, which renders their measurement difficult. Furthermore, smaller and potentially metastatic LNs could be missed during a busy clinical day. To alleviate these imaging and workflow problems, we propose a pipeline to universally detect both benign and metastatic nodes in the body for their ensuing measurement. The recently proposed VFNet neural network was employed to identify LN in T2 fat suppressed and diffusion weighted imaging (DWI) sequences acquired by various scanners with a variety of exam protocols. We also use a selective augmentation technique known as Intra-Label LISA (ILL) to diversify the input data samples the model sees during training, such that it improves its robustness during the evaluation phase. We achieved a sensitivity of $\sim$83\% with ILL vs. $\sim$80\% without ILL at 4 FP/vol. Compared with current LN detection approaches evaluated on mpMRI, we show a sensitivity improvement of $\sim$9\% at 4 FP/vol.

PS3C: An Ensemble-Based Two-Step Framework for Classification of Pep Smear Cell Images

Early detection of cervical cancer is crucial for improving patient outcomes and reducing mortality by identifying precancerous lesions as soon as possible. As a result, the use of pap smear screening has significantly increased, leading to a growing demand for automated tools that can assist cytologists managing their rising workload. To address this, the Pep Smear Cell Classification Challenge (PS3C) has been organized in association with ISBI in 2025. This project aims to promote the development of automated tools for pep smear images classification. The analyzed images are grouped into four categories: healthy, unhealthy, both, and rubbish images which are considered as unsuitable for diagnosis. In this work, we propose a two-stage ensemble approach: first, a neural network determines whether an image is rubbish or not. If not, a second neural network classifies the image as containing a healthy cell, an unhealthy cell, or both.

Distributed U-net model and Image Segmentation for Lung Cancer Detection

Until now, in the wake of the COVID-19 pandemic in 2019, lung diseases, especially diseases such as lung cancer and chronic obstructive pulmonary disease (COPD), have become an urgent global health issue. In order to mitigate the goal problem, early detection and accurate diagnosis of these conditions are critical for effective treatment and improved patient outcomes. To further research and reduce the error rate of hospital diagnoses, this comprehensive study explored the potential of computer-aided design (CAD) systems, especially utilizing advanced deep learning models such as U-Net. And compared with the literature content of other authors, this study explores the capabilities of U-Net in detail, and enhances the ability to simulate CAD systems through the VGG16 algorithm. An extensive dataset consisting of lung CT images and corresponding segmentation masks, curated collaboratively by multiple academic institutions, serves as the basis for empirical validation. In this paper, the efficiency of U-Net model is evaluated rigorously and precisely under multiple hardware configurations, such as single CPU, single GPU, distributed GPU and federated learning, and the effectiveness and development of the method in the segmentation task of lung disease are demonstrated. Empirical results clearly affirm the robust performance of the U-Net model, most effectively utilizing four GPUs for distributed learning, and these results highlight the potential of U-Net-based CAD systems for accurate and timely lung disease detection and diagnosis huge potential.

PolypSegTrack: Unified Foundation Model for Colonoscopy Video Analysis

Early detection, accurate segmentation, classification and tracking of polyps during colonoscopy are critical for preventing colorectal cancer. Many existing deep-learning-based methods for analyzing colonoscopic videos either require task-specific fine-tuning, lack tracking capabilities, or rely on domain-specific pre-training. In this paper, we introduce \textit{PolypSegTrack}, a novel foundation model that jointly addresses polyp detection, segmentation, classification and unsupervised tracking in colonoscopic videos. Our approach leverages a novel conditional mask loss, enabling flexible training across datasets with either pixel-level segmentation masks or bounding box annotations, allowing us to bypass task-specific fine-tuning. Our unsupervised tracking module reliably associates polyp instances across frames using object queries, without relying on any heuristics. We leverage a robust vision foundation model backbone that is pre-trained unsupervisedly on natural images, thereby removing the need for domain-specific pre-training. Extensive experiments on multiple polyp benchmarks demonstrate that our method significantly outperforms existing state-of-the-art approaches in detection, segmentation, classification, and tracking.

Opportunistic Screening for Pancreatic Cancer using Computed Tomography Imaging and Radiology Reports

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer, with most cases diagnosed at stage IV and a five-year overall survival rate below 5%. Early detection and prognosis modeling are crucial for improving patient outcomes and guiding early intervention strategies. In this study, we developed and evaluated a deep learning fusion model that integrates radiology reports and CT imaging to predict PDAC risk. The model achieved a concordance index (C-index) of 0.6750 (95% CI: 0.6429, 0.7121) and 0.6435 (95% CI: 0.6055, 0.6789) on the internal and external dataset, respectively, for 5-year survival risk estimation. Kaplan-Meier analysis demonstrated significant separation (p<0.0001) between the low and high risk groups predicted by the fusion model. These findings highlight the potential of deep learning-based survival models in leveraging clinical and imaging data for pancreatic cancer.

An Efficient Approach to Detecting Lung Nodules Using Swin Transformer

Lung cancer has the highest rate of cancer-caused deaths, and early-stage diagnosis could increase the survival rate. Lung nodules are common indicators of lung cancer, making their detection crucial. Various lung nodule detection models exist, but many lack efficiency. Hence, we propose a more efficient approach by leveraging 2D CT slices, reducing computational load and complexity in training and inference. We employ the tiny version of Swin Transformer to benefit from Vision Transformers (ViT) while maintaining low computational cost. A Feature Pyramid Network is added to enhance detection, particularly for small nodules. Additionally, Transfer Learning is used to accelerate training. Our experimental results show that the proposed model outperforms state-of-the-art methods, achieving higher mAP and mAR for small nodules by 1.3% and 1.6%, respectively. Overall, our model achieves the highest mAP of 94.7% and mAR of 94.9%.

GS-TransUNet: Integrated 2D Gaussian Splatting and Transformer UNet for Accurate Skin Lesion Analysis

We can achieve fast and consistent early skin cancer detection with recent developments in computer vision and deep learning techniques. However, the existing skin lesion segmentation and classification prediction models run independently, thus missing potential efficiencies from their integrated execution. To unify skin lesion analysis, our paper presents the Gaussian Splatting - Transformer UNet (GS-TransUNet), a novel approach that synergistically combines 2D Gaussian splatting with the Transformer UNet architecture for automated skin cancer diagnosis. Our unified deep learning model efficiently delivers dual-function skin lesion classification and segmentation for clinical diagnosis. Evaluated on ISIC-2017 and PH2 datasets, our network demonstrates superior performance compared to existing state-of-the-art models across multiple metrics through 5-fold cross-validation. Our findings illustrate significant advancements in the precision of segmentation and classification. This integration sets new benchmarks in the field and highlights the potential for further research into multi-task medical image analysis methodologies, promising enhancements in automated diagnostic systems.

Optimized Pap Smear Image Enhancement: Hybrid PMD Filter-CLAHE Using Spider Monkey Optimization

Pap smear image quality is crucial for cervical cancer detection. This study introduces an optimized hybrid approach that combines the Perona-Malik Diffusion (PMD) filter with contrast-limited adaptive histogram equalization (CLAHE) to enhance Pap smear image quality. The PMD filter reduces the image noise, whereas CLAHE improves the image contrast. The hybrid method was optimized using spider monkey optimization (SMO PMD-CLAHE). BRISQUE and CEIQ are the new objective functions for the PMD filter and CLAHE optimization, respectively. The simulations were conducted using the SIPaKMeD dataset. The results indicate that SMO outperforms state-of-the-art methods in optimizing the PMD filter and CLAHE. The proposed method achieved an average effective measure of enhancement (EME) of 5.45, root mean square (RMS) contrast of 60.45, Michelson's contrast (MC) of 0.995, and entropy of 6.80. This approach offers a new perspective for improving Pap smear image quality.