Contrasting Low and High-Resolution Features for HER2 Scoring using Deep Learning

Breast cancer, the most common malignancy among women, requires precise detection and classification for effective treatment. Immunohistochemistry (IHC) biomarkers like HER2, ER, and PR are critical for identifying breast cancer subtypes. However, traditional IHC classification relies on pathologists' expertise, making it labor-intensive and subject to significant inter-observer variability. To address these challenges, this study introduces the India Pathology Breast Cancer Dataset (IPD-Breast), comprising of 1,272 IHC slides (HER2, ER, and PR) aimed at automating receptor status classification. The primary focus is on developing predictive models for HER2 3-way classification (0, Low, High) to enhance prognosis. Evaluation of multiple deep learning models revealed that an end-to-end ConvNeXt network utilizing low-resolution IHC images achieved an AUC, F1, and accuracy of 91.79%, 83.52%, and 83.56%, respectively, for 3-way classification, outperforming patch-based methods by over 5.35% in F1 score. This study highlights the potential of simple yet effective deep learning techniques to significantly improve accuracy and reproducibility in breast cancer classification, supporting their integration into clinical workflows for better patient outcomes.

Requirements for Quality Assurance of AI Models for Early Detection of Lung Cancer

Lung cancer is the second most common cancer and the leading cause of cancer-related deaths worldwide. Survival largely depends on tumor stage at diagnosis, and early detection with low-dose CT can significantly reduce mortality in high-risk patients. AI can improve the detection, measurement, and characterization of pulmonary nodules while reducing assessment time. However, the training data, functionality, and performance of available AI systems vary considerably, complicating software selection and regulatory evaluation. Manufacturers must specify intended use and provide test statistics, but they can choose their training and test data, limiting standardization and comparability. Under the EU AI Act, consistent quality assurance is required for AI-based nodule detection, measurement, and characterization. This position paper proposes systematic quality assurance grounded in a validated reference dataset, including real screening cases plus phantom data to verify volume and growth rate measurements. Regular updates shall reflect demographic shifts and technological advances, ensuring ongoing relevance. Consequently, ongoing AI quality assurance is vital. Regulatory challenges are also adressed. While the MDR and the EU AI Act set baseline requirements, they do not adequately address self-learning algorithms or their updates. A standardized, transparent quality assessment - based on sensitivity, specificity, and volumetric accuracy - enables an objective evaluation of each AI solution's strengths and weaknesses. Establishing clear testing criteria and systematically using updated reference data lay the groundwork for comparable performance metrics, informing tenders, guidelines, and recommendations.

Identifying regions of interest in whole slide images of renal cell carcinoma

The histopathological images contain a huge amount of information, which can make diagnosis an extremely timeconsuming and tedious task. In this study, we developed a completely automated system to detect regions of interest (ROIs) in whole slide images (WSI) of renal cell carcinoma (RCC), to reduce time analysis and assist pathologists in making more accurate decisions. The proposed approach is based on an efficient texture descriptor named dominant rotated local binary pattern (DRLBP) and color transformation to reveal and exploit the immense texture variability at the microscopic high magnifications level. Thereby, the DRLBPs retain the structural information and utilize the magnitude values in a local neighborhood for more discriminative power. For the classification of the relevant ROIs, feature extraction of WSIs patches was performed on the color channels separately to form the histograms. Next, we used the most frequently occurring patterns as a feature selection step to discard non-informative features. The performances of different classifiers on a set of 1800 kidney cancer patches originating from 12 whole slide images were compared and evaluated. Furthermore, the small size of the image dataset allows to investigate deep learning approach based on transfer learning for image patches classification by using deep features and fine-tuning methods. High recognition accuracy was obtained and the classifiers are efficient, the best precision result was 99.17% achieved with SVM. Moreover, transfer learning models perform well with comparable performance, and the highest precision using ResNet-50 reached 98.50%. The proposed approach results revealed a very efficient image classification and demonstrated efficacy in identifying ROIs. This study presents an automatic system to detect regions of interest relevant to the diagnosis of kidney cancer in whole slide histopathology images.

An Inclusive Foundation Model for Generalizable Cytogenetics in Precision Oncology

Chromosome analysis is vital for diagnosing genetic disorders and guiding cancer therapy decisions through the identification of somatic clonal aberrations. However, developing an AI model are hindered by the overwhelming complexity and diversity of chromosomal abnormalities, requiring extensive annotation efforts, while automated methods remain task-specific and lack generalizability due to the scarcity of comprehensive datasets spanning diverse resource conditions. Here, we introduce CHROMA, a foundation model for cytogenomics, designed to overcome these challenges by learning generalizable representations of chromosomal abnormalities. Pre-trained on over 84,000 specimens (~4 million chromosomal images) via self-supervised learning, CHROMA outperforms other methods across all types of abnormalities, even when trained on fewer labelled data and more imbalanced datasets. By facilitating comprehensive mapping of instability and clonal leisons across various aberration types, CHROMA offers a scalable and generalizable solution for reliable and automated clinical analysis, reducing the annotation workload for experts and advancing precision oncology through the early detection of rare genomic abnormalities, enabling broad clinical AI applications and making advanced genomic analysis more accessible.

Automated Quality Evaluation of Cervical Cytopathology Whole Slide Images Based on Content Analysis

The ThinPrep Cytologic Test (TCT) is the most widely used method for cervical cancer screening, and the sample quality directly impacts the accuracy of the diagnosis. Traditional manual evaluation methods rely on the observation of pathologist under microscopes. These methods exhibit high subjectivity, high cost, long duration, and low reliability. With the development of computer-aided diagnosis (CAD), an automated quality assessment system that performs at the level of a professional pathologist is necessary. To address this need, we propose a fully automated quality assessment method for Cervical Cytopathology Whole Slide Images (WSIs) based on The Bethesda System (TBS) diagnostic standards, artificial intelligence algorithms, and the characteristics of clinical data. The method analysis the context of WSIs to quantify quality evaluation metrics which are focused by TBS such as staining quality, cell counts and cell mass proportion through multiple models including object detection, classification and segmentation. Subsequently, the XGBoost model is used to mine the attention paid by pathologists to different quality evaluation metrics when evaluating samples, thereby obtaining a comprehensive WSI sample score calculation model. Experimental results on 100 WSIs demonstrate that the proposed evaluation method has significant advantages in terms of speed and consistency.

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.

Automatic Prostate Volume Estimation in Transabdominal Ultrasound Images

Prostate cancer is a leading health concern among men, requiring accurate and accessible methods for early detection and risk stratification. Prostate volume (PV) is a key parameter in multivariate risk stratification for early prostate cancer detection, commonly estimated using transrectal ultrasound (TRUS). While TRUS provides precise prostate volume measurements, its invasive nature often compromises patient comfort. Transabdominal ultrasound (TAUS) provides a non-invasive alternative but faces challenges such as lower image quality, complex interpretation, and reliance on operator expertise. This study introduces a new deep-learning-based framework for automatic PV estimation using TAUS, emphasizing its potential to enable accurate and non-invasive prostate cancer risk stratification. A dataset of TAUS videos from 100 individual patients was curated, with manually delineated prostate boundaries and calculated diameters by an expert clinician as ground truth. The introduced framework integrates deep-learning models for prostate segmentation in both axial and sagittal planes, automatic prostate diameter estimation, and PV calculation. Segmentation performance was evaluated using Dice correlation coefficient (%) and Hausdorff distance (mm). Framework's volume estimation capabilities were evaluated on volumetric error (mL). The framework demonstrates that it can estimate PV from TAUS videos with a mean volumetric error of -5.5 mL, which results in an average relative error between 5 and 15%. The introduced framework for automatic PV estimation from TAUS images, utilizing deep learning models for prostate segmentation, shows promising results. It effectively segments the prostate and estimates its volume, offering potential for reliable, non-invasive risk stratification for early prostate detection.

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.

Hybrid CNN with Chebyshev Polynomial Expansion for Medical Image Analysis

Lung cancer remains one of the leading causes of cancer-related mortality worldwide, with early and accurate diagnosis playing a pivotal role in improving patient outcomes. Automated detection of pulmonary nodules in computed tomography (CT) scans is a challenging task due to variability in nodule size, shape, texture, and location. Traditional Convolutional Neural Networks (CNNs) have shown considerable promise in medical image analysis; however, their limited ability to capture fine-grained spatial-spectral variations restricts their performance in complex diagnostic scenarios. In this study, we propose a novel hybrid deep learning architecture that incorporates Chebyshev polynomial expansions into CNN layers to enhance expressive power and improve the representation of underlying anatomical structures. The proposed Chebyshev-CNN leverages the orthogonality and recursive properties of Chebyshev polynomials to extract high-frequency features and approximate complex nonlinear functions with greater fidelity. The model is trained and evaluated on benchmark lung cancer imaging datasets, including LUNA16 and LIDC-IDRI, achieving superior performance in classifying pulmonary nodules as benign or malignant. Quantitative results demonstrate significant improvements in accuracy, sensitivity, and specificity compared to traditional CNN-based approaches. This integration of polynomial-based spectral approximation within deep learning provides a robust framework for enhancing automated medical diagnostics and holds potential for broader applications in clinical decision support systems.

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.