We present a comprehensive study on fully automated pollen recognition across both conventional optical and digital in-line holographic microscopy (DIHM) images of sample slides. Visually recognizing pollen in unreconstructed holographic images remains challenging due to speckle noise, twin-image artifacts and substantial divergence from bright-field appearances. We establish the performance baseline by training YOLOv8s for object detection and MobileNetV3L for classification on a dual-modality dataset of automatically annotated optical and affinely aligned DIHM images. On optical data, detection mAP50 reaches 91.3% and classification accuracy reaches 97%, whereas on DIHM data, we achieve only 8.15% for detection mAP50 and 50% for classification accuracy. Expanding the bounding boxes of pollens in DIHM images over those acquired in aligned optical images achieves 13.3% for detection mAP50 and 54% for classification accuracy. To improve object detection in DIHM images, we employ a Wasserstein GAN with spectral normalization (WGAN-SN) to create synthetic DIHM images, yielding an FID score of 58.246. Mixing real-world and synthetic data at the 1.0 : 1.5 ratio for DIHM images improves object detection up to 15.4%. These results demonstrate that GAN-based augmentation can reduce the performance divide, bringing fully automated DIHM workflows for veterinary imaging a small but important step closer to practice.

Biomedical image segmentation is critical for precise structure delineation and downstream analysis. Traditional methods often struggle with noisy data, while deep learning models such as U-Net have set new benchmarks in segmentation performance. nnU-Net further automates model configuration, making it adaptable across datasets without extensive tuning. However, it requires a substantial amount of annotated data for cross-validation, posing a challenge when only raw images but no labels are available. Large foundation models offer zero-shot generalizability, but may underperform on specific datasets with unique characteristics, limiting their direct use for analysis. This work addresses these bottlenecks by proposing a data-centric AI workflow that leverages active learning and pseudo-labeling to combine the strengths of traditional neural networks and large foundation models while minimizing human intervention. The pipeline starts by generating pseudo-labels from a foundation model, which are then used for nnU-Net's self-configuration. Subsequently, a representative core-set is selected for minimal manual annotation, enabling effective fine-tuning of the nnU-Net model. This approach significantly reduces the need for manual annotations while maintaining competitive performance, providing an accessible solution for biomedical researchers to apply state-of-the-art AI techniques in their segmentation tasks. The code is available at https://github.com/MMV-Lab/AL_BioMed_img_seg.

Purpose: This study introduces a novel Deep Learning (DL) - based q uality a sses s ment (QA) approach specifically designed for evaluating auto - generated contours (auto - contour s) in auto - segmentation for radiotherapy, with a focus on Online Adaptive Radiotherapy (OART). The proposed method leverages Bayesian Ordinal Classification (BOC), combined with cali brated thresholds derived from uncertainty quantification, to deliver confident QA predictions . This approach address es key challenges in clinical auto - segmentation QA workflows such as the absence of ground truth contours, limited availability of manually labeled data, and inherent uncertainty in AI model predictions . Methods: We developed a BOC model to classify the quality of auto - contour s and quantify uncertainty. To enhance predictive reliability, we implemented a calibration step to determine optimal uncertainty thresholds that meet specific clinical accuracy requirements . The method was validated under three distinct data availability scenarios: absence of manual labels, limited manual labeling, and extensive manual labeling. We specifically tested our method for auto - segmented rectum contours in prostate cancer radiotherapy. Geometric surrogate labels were employed in the absence of manual labels, transfer learning was applied when manual labels were limited, and direct use of manual labels was perf ormed when extensive labeling was available. Results: The BOC model demonstrated robust performance across all data availability scenarios for confident predictions, with significant accuracy gains when pre - trained with surrogate labels and fine - tuned with limited manual ly label ed data . Specifically, fine - tuning the pretrained model with just 30 manually labeled cases and calibrating with 34 subjects achieved over an accuracy of over 90% against manual labels in the test dataset .

In large-scale supervised learning, penalized logistic regression (PLR) effectively addresses the overfitting problem by introducing regularization terms yet its performance still depends on efficient variable selection strategies. This paper theoretically demonstrates that label noise stemming from manual labeling, which is solely related to classification difficulty, represents a type of beneficial noise for variable selection in PLR. This benefit is reflected in a more accurate estimation of the selected non-zero coefficients when compared with the case where only truth labels are used. Under large-scale settings, the sample size for PLR can become very large, making it infeasible to store on a single machine. In such cases, distributed computing methods are required to handle PLR model with manual labeling. This paper presents a partition-insensitive parallel algorithm founded on the ADMM (alternating direction method of multipliers) algorithm to address PLR by incorporating manual labeling. The partition insensitivity of the proposed algorithm refers to the fact that the solutions obtained by the algorithm will not change with the distributed storage of data. In addition, the algorithm has global convergence and a sublinear convergence rate. Experimental results indicate that, as compared with traditional variable selection classification techniques, the PLR with manually-labeled noisy data achieves higher estimation and classification accuracy across multiple large-scale datasets.

In medical imaging, the primary challenge is collecting large-scale labeled data due to privacy concerns, logistics, and high labeling costs. In this work, we present the UK Biobank Organs and Bones (UKBOB), the largest labeled dataset of body organs, comprising 51,761 MRI 3D samples (equivalent to 17.9 million 2D images) and more than 1.37 billion 2D segmentation masks of 72 organs, all based on the UK Biobank MRI dataset. We utilize automatic labeling, introduce an automated label cleaning pipeline with organ-specific filters, and manually annotate a subset of 300 MRIs with 11 abdominal classes to validate the quality (referred to as UKBOB-manual). This approach allows for scaling up the dataset collection while maintaining confidence in the labels. We further confirm the validity of the labels by demonstrating zero-shot generalization of trained models on the filtered UKBOB to other small labeled datasets from similar domains (e.g., abdominal MRI). To further mitigate the effect of noisy labels, we propose a novel method called Entropy Test-time Adaptation (ETTA) to refine the segmentation output. We use UKBOB to train a foundation model, Swin-BOB, for 3D medical image segmentation based on the Swin-UNetr architecture, achieving state-of-the-art results in several benchmarks in 3D medical imaging, including the BRATS brain MRI tumor challenge (with a 0.4% improvement) and the BTCV abdominal CT scan benchmark (with a 1.3% improvement). The pre-trained models and the code are available at https://emmanuelleb985.github.io/ukbob , and the filtered labels will be made available with the UK Biobank.

The extraction of relevant data from Electronic Health Records (EHRs) is crucial to identifying symptoms and automating epidemiological surveillance processes. By harnessing the vast amount of unstructured text in EHRs, we can detect patterns that indicate the onset of disease outbreaks, enabling faster, more targeted public health responses. Our proposed framework provides a flexible and efficient solution for mining data from unstructured texts, significantly reducing the need for extensive manual labeling by specialists. Experiments show that our framework achieving strong performance with as few as 200 manually labeled texts, even for complex classification problems. Additionally, our approach can function with simple lightweight models, achieving competitive and occasionally even better results compared to more resource-intensive deep learning models. This capability not only accelerates processing times but also preserves patient privacy, as the data can be processed on weaker on-site hardware rather than being transferred to external systems. Our methodology, therefore, offers a practical, scalable, and privacy-conscious approach to real-time epidemiological monitoring, equipping health institutions to respond rapidly and effectively to emerging health threats.

The increasing availability of biomedical data is helping to design more robust deep learning (DL) algorithms to analyze biomedical samples. Currently, one of the main limitations to train DL algorithms to perform a specific task is the need for medical experts to label data. Automatic methods to label data exist, however automatic labels can be noisy and it is not completely clear when automatic labels can be adopted to train DL models. This paper aims to investigate under which circumstances automatic labels can be adopted to train a DL model on the classification of Whole Slide Images (WSI). The analysis involves multiple architectures, such as Convolutional Neural Networks (CNN) and Vision Transformer (ViT), and over 10000 WSIs, collected from three use cases: celiac disease, lung cancer and colon cancer, which one including respectively binary, multiclass and multilabel data. The results allow identifying 10% as the percentage of noisy labels that lead to train competitive models for the classification of WSIs. Therefore, an algorithm generating automatic labels needs to fit this criterion to be adopted. The application of the Semantic Knowledge Extractor Tool (SKET) algorithm to generate automatic labels leads to performance comparable to the one obtained with manual labels, since it generates a percentage of noisy labels between 2-5%. Automatic labels are as effective as manual ones, reaching solid performance comparable to the one obtained training models with manual labels.

The goal of our work is to develop a Screening Tool, software that would automatically evaluate all brain MRI scans In clinical practice, we often see significant delays between in a given hospital, and which would produce pre-diagnostic MRI scans and the diagnosis made by radiologists, even for reports for radiologists. Based on such reports, radiologists severe cases. In some cases, this may be caused by the lack could easily decide which examinations need to be processed of additional information and clues, so even the severe cases sooner and with higher priority, or, they might decide to process need to wait in the queue for diagnosis. This can be avoided if the "easy cases" first (i.e., cases that can be completed there is an automatic software tool, which would supplement quickly and easily), to increase diagnostic throughput. The additional information, alerting radiologists that the particular ultimate goal is to help decrease the waiting time between the patient may be a severe case. We are presenting an automatic scan and the diagnosis, especially for severe cases, by assisting brain MRI Screening Tool and we are demonstrating its capabilities radiologists to work more efficiently with better prioritization.

Like many team sports, basketball involves two groups of players who engage in collaborative and adversarial activities to win a game. Players and teams are executing various complex strategies to gain an advantage over their opponents. Defining, identifying, and analyzing different types of activities is an important task in sports analytics, as it can lead to better strategies and decisions by the players and coaching staff. The objective of this paper is to automatically recognize basketball group activities from tracking data representing locations of players and the ball during a game. We propose a novel deep learning approach for group activity recognition (GAR) in team sports called NETS. To efficiently model the player relations in team sports, we combined a Transformer-based architecture with LSTM embedding, and a team-wise pooling layer to recognize the group activity. Training such a neural network generally requires a large amount of annotated data, which incurs high labeling cost. To address scarcity of manual labels, we generate weak-labels and pretrain the neural network on a self-supervised trajectory prediction task. We used a large tracking data set from 632 NBA games to evaluate our approach. The results show that NETS is capable of learning group activities with high accuracy, and that self- and weak-supervised training in NETS have a positive impact on GAR accuracy.

"Just Accepted" papers have undergone full peer review and have been accepted for publication in Radiology: Artificial Intelligence. This article will undergo copyediting, layout, and proof review before it is published in its final version. Please note that during production of the final copyedited article, errors may be discovered which could affect the content. To develop a convolutional neural network (CNN) solution for landmark detection in cardiac MRI. This retrospective study included cine, late-gadolinium enhancement (LGE), and T1 mapping scans from two hospitals.