Lung nodule classification on CT scan patches using 3D convolutional neural networks

Lung cancer remains one of the most common and deadliest forms of cancer worldwide. The likelihood of successful treatment depends strongly on the stage at which the disease is diagnosed. Therefore, early detection of lung cancer represents a critical medical challenge. However, this task poses significant difficulties for thoracic radiologists due to the large number of studies to review, the presence of multiple nodules within the lungs, and the small size of many nodules, which complicates visual assessment. Consequently, the development of automated systems that incorporate highly accurate and computationally efficient lung nodule detection and classification modules is essential. This study introduces three methodological improvements for lung nodule classification: (1) an advanced CT scan cropping strategy that focuses the model on the target nodule while reducing computational cost; (2) target filtering techniques for removing noisy labels; (3) novel augmentation methods to improve model robustness. The integration of these techniques enables the development of a robust classification subsystem within a comprehensive Clinical Decision Support System for lung cancer detection, capable of operating across diverse acquisition protocols, scanner types, and upstream models (segmentation or detection). The multiclass model achieved a Macro ROC AUC of 0.9176 and a Macro F1-score of 0.7658, while the binary model reached a Binary ROC AUC of 0.9383 and a Binary F1-score of 0.8668 on the LIDC-IDRI dataset. These results outperform several previously reported approaches and demonstrate state-of-the-art performance for this task.

A Comprehensive Benchmark of Histopathology Foundation Models for Kidney Histopathology

Histopathology foundation models (HFMs), pretrained on large-scale cancer datasets, have advanced computational pathology. However, their applicability to non-cancerous chronic kidney disease remains underexplored, despite coexistence of renal pathology with malignancies such as renal cell and urothelial carcinoma. We systematically evaluate 11 publicly available HFMs across 11 kidney-specific downstream tasks spanning multiple stains (PAS, H&E, PASM, and IHC), spatial scales (tile and slide-level), task types (classification, regression, and copy detection), and clinical objectives, including detection, diagnosis, and prognosis. Tile-level performance is assessed using repeated stratified group cross-validation, while slide-level tasks are evaluated using repeated nested stratified cross-validation. Statistical significance is examined using Friedman test followed by pairwise Wilcoxon signed-rank testing with Holm-Bonferroni correction and compact letter display visualization. To promote reproducibility, we release an open-source Python package, kidney-hfm-eval, available at https://pypi.org/project/kidney-hfm-eval/ , that reproduces the evaluation pipelines. Results show moderate to strong performance on tasks driven by coarse meso-scale renal morphology, including diagnostic classification and detection of prominent structural alterations. In contrast, performance consistently declines for tasks requiring fine-grained microstructural discrimination, complex biological phenotypes, or slide-level prognostic inference, largely independent of stain type. Overall, current HFMs appear to encode predominantly static meso-scale representations and may have limited capacity to capture subtle renal pathology or prognosis-related signals. Our results highlight the need for kidney-specific, multi-stain, and multimodal foundation models to support clinically reliable decision-making in nephrology.

DiffusionXRay: A Diffusion and GAN-Based Approach for Enhancing Digitally Reconstructed Chest Radiographs

Deep learning-based automated diagnosis of lung cancer has emerged as a crucial advancement that enables healthcare professionals to detect and initiate treatment earlier. However, these models require extensive training datasets with diverse case-specific properties. High-quality annotated data is particularly challenging to obtain, especially for cases with subtle pulmonary nodules that are difficult to detect even for experienced radiologists. This scarcity of well-labeled datasets can limit model performance and generalization across different patient populations. Digitally reconstructed radiographs (DRR) using CT-Scan to generate synthetic frontal chest X-rays with artificially inserted lung nodules offers one potential solution. However, this approach suffers from significant image quality degradation, particularly in the form of blurred anatomical features and loss of fine lung field structures. To overcome this, we introduce DiffusionXRay, a novel image restoration pipeline for Chest X-ray images that synergistically leverages denoising diffusion probabilistic models (DDPMs) and generative adversarial networks (GANs). DiffusionXRay incorporates a unique two-stage training process: First, we investigate two independent approaches, DDPM-LQ and GAN-based MUNIT-LQ, to generate low-quality CXRs, addressing the challenge of training data scarcity, posing this as a style transfer problem. Subsequently, we train a DDPM-based model on paired low-quality and high-quality images, enabling it to learn the nuances of X-ray image restoration. Our method demonstrates promising results in enhancing image clarity, contrast, and overall diagnostic value of chest X-rays while preserving subtle yet clinically significant artifacts, validated by both quantitative metrics and expert radiological assessment.

Early and Prediagnostic Detection of Pancreatic Cancer from Computed Tomography

Pancreatic ductal adenocarcinoma (PDAC), one of the deadliest solid malignancies, is often detected at a late and inoperable stage. Retrospective reviews of prediagnostic CT scans, when conducted by expert radiologists aware that the patient later developed PDAC, frequently reveal lesions that were previously overlooked. To help detecting these lesions earlier, we developed an automated system named ePAI (early Pancreatic cancer detection with Artificial Intelligence). It was trained on data from 1,598 patients from a single medical center. In the internal test involving 1,009 patients, ePAI achieved an area under the receiver operating characteristic curve (AUC) of 0.939-0.999, a sensitivity of 95.3%, and a specificity of 98.7% for detecting small PDAC less than 2 cm in diameter, precisely localizing PDAC as small as 2 mm. In an external test involving 7,158 patients across 6 centers, ePAI achieved an AUC of 0.918-0.945, a sensitivity of 91.5%, and a specificity of 88.0%, precisely localizing PDAC as small as 5 mm. Importantly, ePAI detected PDACs on prediagnostic CT scans obtained 3 to 36 months before clinical diagnosis that had originally been overlooked by radiologists. It successfully detected and localized PDACs in 75 of 159 patients, with a median lead time of 347 days before clinical diagnosis. Our multi-reader study showed that ePAI significantly outperformed 30 board-certified radiologists by 50.3% (P < 0.05) in sensitivity while maintaining a comparable specificity of 95.4% in detecting PDACs early and prediagnostic. These findings suggest its potential of ePAI as an assistive tool to improve early detection of pancreatic cancer.

LungCRCT: Causal Representation based Lung CT Processing for Lung Cancer Treatment

Due to silence in early stages, lung cancer has been one of the most leading causes of mortality in cancer patients world-wide. Moreover, major symptoms of lung cancer are hard to differentiate with other respiratory disease symptoms such as COPD, further leading patients to overlook cancer progression in early stages. Thus, to enhance survival rates in lung cancer, early detection from consistent proactive respiratory system monitoring becomes crucial. One of the most prevalent and effective methods for lung cancer monitoring would be low-dose computed tomography(LDCT) chest scans, which led to remarkable enhancements in lung cancer detection or tumor classification tasks under rapid advancements and applications of computer vision based AI models such as EfficientNet or ResNet in image processing. However, though advanced CNN models under transfer learning or ViT based models led to high performing lung cancer detections, due to its intrinsic limitations in terms of correlation dependence and low interpretability due to complexity, expansions of deep learning models to lung cancer treatment analysis or causal intervention analysis simulations are still limited. Therefore, this research introduced LungCRCT: a latent causal representation learning based lung cancer analysis framework that retrieves causal representations of factors within the physical causal mechanism of lung cancer progression. With the use of advanced graph autoencoder based causal discovery algorithms with distance Correlation disentanglement and entropy-based image reconstruction refinement, LungCRCT not only enables causal intervention analysis for lung cancer treatments, but also leads to robust, yet extremely light downstream models in malignant tumor classification tasks with an AUC score of 93.91%.

Synthetic-Powered Multiple Testing with FDR Control

Multiple hypothesis testing with false discovery rate (FDR) control is a fundamental problem in statistical inference, with broad applications in genomics, drug screening, and outlier detection. In many such settings, researchers may have access not only to real experimental observations but also to auxiliary or synthetic data -- from past, related experiments or generated by generative models -- that can provide additional evidence about the hypotheses of interest. We introduce SynthBH, a synthetic-powered multiple testing procedure that safely leverages such synthetic data. We prove that SynthBH guarantees finite-sample, distribution-free FDR control under a mild PRDS-type positive dependence condition, without requiring the pooled-data p-values to be valid under the null. The proposed method adapts to the (unknown) quality of the synthetic data: it enhances the sample efficiency and may boost the power when synthetic data are of high quality, while controlling the FDR at a user-specified level regardless of their quality. We demonstrate the empirical performance of SynthBH on tabular outlier detection benchmarks and on genomic analyses of drug-cancer sensitivity associations, and further study its properties through controlled experiments on simulated data.

Multimodal system for skin cancer detection

Melanoma detection is vital for early diagnosis and effective treatment. While deep learning models on dermoscopic images have shown promise, they require specialized equipment, limiting their use in broader clinical settings. This study introduces a multi-modal melanoma detection system using conventional photo images, making it more accessible and versatile. Our system integrates image data with tabular metadata, such as patient demographics and lesion characteristics, to improve detection accuracy. It employs a multi-modal neural network combining image and metadata processing and supports a two-step model for cases with or without metadata. A three-stage pipeline further refines predictions by boosting algorithms and enhancing performance. To address the challenges of a highly imbalanced dataset, specific techniques were implemented to ensure robust training. An ablation study evaluated recent vision architectures, boosting algorithms, and loss functions, achieving a peak Partial ROC AUC of 0.18068 (0.2 maximum) and top-15 retrieval sensitivity of 0.78371. Results demonstrate that integrating photo images with metadata in a structured, multi-stage pipeline yields significant performance improvements. This system advances melanoma detection by providing a scalable, equipment-independent solution suitable for diverse healthcare environments, bridging the gap between specialized and general clinical practices.

An Innovative Framework for Breast Cancer Detection Using Pyramid Adaptive Atrous Convolution, Transformer Integration, and Multi-Scale Feature Fusion

Breast cancer is one of the most common cancers among women worldwide, and its accurate and timely diagnosis plays a critical role in improving treatment outcomes. This thesis presents an innovative framework for detecting malignant masses in mammographic images by integrating the Pyramid Adaptive Atrous Convolution (PAAC) and Transformer architectures. The proposed approach utilizes Multi-Scale Feature Fusion to enhance the extraction of features from benign and malignant tissues and combines Dice Loss and Focal Loss functions to improve the model's learning process, effectively reducing errors in binary breast cancer classification and achieving high accuracy and efficiency. In this study, a comprehensive dataset of breast cancer images from INbreast, MIAS, and DDSM was preprocessed through data augmentation and contrast enhancement and resized to 227x227 pixels for model training. Leveraging the Transformer's ability to manage long-range dependencies with Self-Attention mechanisms, the proposed model achieved high accuracy in detecting cancerous masses, outperforming foundational models such as BreastNet, DeepMammo, Multi-Scale CNN, Swin-Unet, and SegFormer. The final evaluation results for the proposed model include an accuracy of 98.5\%, sensitivity of 97.8\%, specificity of 96.3\%, F1-score of 98.2\%, and overall precision of 97.9\%. These metrics demonstrate a significant improvement over traditional methods and confirm the model's effectiveness in identifying cancerous masses in complex scenarios and large datasets. This model shows potential as a reliable and efficient tool for breast cancer diagnosis and can be effectively integrated into medical diagnostic systems.

Learning with Geometric Priors in U-Net Variants for Polyp Segmentation

Accurate and robust polyp segmentation is essential for early colorectal cancer detection and for computer-aided diagnosis. While convolutional neural network-, Transformer-, and Mamba-based U-Net variants have achieved strong performance, they still struggle to capture geometric and structural cues, especially in low-contrast or cluttered colonoscopy scenes. To address this challenge, we propose a novel Geometric Prior-guided Module (GPM) that injects explicit geometric priors into U-Net-based architectures for polyp segmentation. Specifically, we fine-tune the Visual Geometry Grounded Transformer (VGGT) on a simulated ColonDepth dataset to estimate depth maps of polyp images tailored to the endoscopic domain. These depth maps are then processed by GPM to encode geometric priors into the encoder's feature maps, where they are further refined using spatial and channel attention mechanisms that emphasize both local spatial and global channel information. GPM is plug-and-play and can be seamlessly integrated into diverse U-Net variants. Extensive experiments on five public polyp segmentation datasets demonstrate consistent gains over three strong baselines. Code and the generated depth maps are available at: https://github.com/fvazqu/GPM-PolypSeg

Enabling Real-Time Colonoscopic Polyp Segmentation on Commodity CPUs via Ultra-Lightweight Architecture

Early detection of colorectal cancer hinges on real-time, accurate polyp identification and resection. Yet current high-precision segmentation models rely on GPUs, making them impractical to deploy in primary hospitals, mobile endoscopy units, or capsule robots. To bridge this gap, we present the UltraSeg family, operating in an extreme-compression regime (<0.3 M parameters). UltraSeg-108K (0.108 M parameters) is optimized for single-center data, while UltraSeg-130K (0.13 M parameters) generalizes to multi-center, multi-modal images. By jointly optimizing encoder-decoder widths, incorporating constrained dilated convolutions to enlarge receptive fields, and integrating a cross-layer lightweight fusion module, the models achieve 90 FPS on a single CPU core without sacrificing accuracy. Evaluated on seven public datasets, UltraSeg retains >94% of the Dice score of a 31 M-parameter U-Net while utilizing only 0.4% of its parameters, establishing a strong, clinically viable baseline for the extreme-compression domain and offering an immediately deployable solution for resource-constrained settings. This work provides not only a CPU-native solution for colonoscopy but also a reproducible blueprint for broader minimally invasive surgical vision applications. Source code is publicly available to ensure reproducibility and facilitate future benchmarking.