arXiv subjects

Veronika Cheplygina

Publications and source records attributed to Veronika Cheplygina.

At least 19 recordsLinked to original sources

arXiv2026

Data Annotations as Pedagogical Hints: From Subjective Labels to Critical Thinking

Machine learning courses often use pre-labelled datasets, hiding the subjectivity of human annotation. This produces an overly trusting view of data and AI models in students, at the expense of interpretive diversity and contestability of algorithmic outputs. We investigated whether manual data annotation tasks teach students about subjective labelling. Study Design: An annotation activity was implemented at two universities: Fontys (Netherlands) and IT University Copenhagen (Denmark). Students annotated skin lesion images for hair coverage on a 3-point scale. Surveys were collected from 43 participants, measuring their understanding of annotation ambiguity, data quality, bias, fairness, implementation barriers, and pedagogical effectiveness. Key Findings: Self-reported familiarity with the course content increased substantially across all concepts. Most students recognised that personal interpretation affects annotations. Students rated the activity as more effective than traditional lectures in understanding bias. Participants were motivated to learn more. Main Drawbacks: Emotional discomfort from viewing medical images was the primary issue. Many students still requested clearer guidelines to reduce disagreement, suggesting they had not yet internalised that disagreement arising from different perspectives is a feature, not a bug. Recommendations for Future Iterations: Ensure sufficient interpretive ambiguity in materials. Reduce repetitive annotation workload. Mitigate emotional discomfort from sensitive content. Explicitly frame disagreement as a learning opportunity rather than a problem to solve. Manual data annotations effectively teach students that human judgement shapes model behaviour and that disagreement reflects domain complexity, not just noise.

cs.CY↗

arXiv2026

Medical Imaging AI Competitions Lack Fairness

Benchmarking competitions are central to the development of artificial intelligence (AI) in medical imaging, defining performance standards and shaping methodological progress. However, it remains unclear whether these benchmarks provide data that are sufficiently representative, accessible, and reusable to support clinically meaningful AI. In this work, we assess fairness along two complementary dimensions: (1) whether challenge datasets capture the diversity of real-world clinical data, and (2) whether they are accessible and legally reusable in line with the FAIR principles. To address this question, we conducted a large-scale systematic study of 249 biomedical image analysis challenges comprising 458 tasks across 19 imaging modalities. Our findings reveal limited representation across challenge datasets with respect to geographic location, imaging modalities, and problem types, raising concerns about how well current benchmarks reflect real-world clinical diversity. Despite their widespread influence, challenge datasets were frequently constrained by restrictive or ambiguous access conditions, inconsistent or non-compliant licensing practices, and incomplete documentation, limiting reproducibility and long-term reuse. Together, these shortcomings expose foundational fairness limitations in our benchmarking ecosystem and highlight a disconnect between leaderboard success and clinical relevance.

cs.CV↗

arXiv2026

Look What the Probes Dragged In! Real-World Chest X-ray Shortcuts in MedCLIP

Vision-language models, such as contrastive language-image pre-training (CLIP)-based approaches, have reached state-of-the-art (SOTA) results in medical artificial intelligence. However, recent work reveals that CLIP-based models remain vulnerable to shortcuts. We investigate how real-world shortcuts manifest across different layers of the medical CLIP-based model, MedCLIP, and its vision encoder, a frozen ResNet-50. We attach 17 linear classification probes to the intermediate layers of the ResNet-50 and train them on three different dataset configurations and targets: NIH-CXR14 (pneumothorax) and PadChest (cardiomegaly and pneumothorax). This setup allows us to observe model behaviour during evaluation using subgroup-based calibration and layer-wise confidence curves. We find that the final linear probes achieve a high AUROC but poor calibration in the models. The layer-wise confidence analyses suggest that shortcuts emerge at different depths. Patterns consistent with localised shortcuts, such as drains, appear at later layers, while patterns consistent with diffuse shortcuts, such as scanner-specific noise patterns, emerge earlier, aligning with previous work. Finally, we conduct a manual analysis of the images, which reveals data quality issues in both NIH-CXR14 and PadChest. Our findings underscore that even SOTA models remain vulnerable to shortcuts, and the need for high-quality and well-annotated datasets to draw solid conclusions. Code can be found on our GitHub: https://github.com/nikodice4/MedCLIP_shortcuts.

cs.CV↗

arXiv2026

Robustness of transferability estimation metrics for medical imaging

In transfer learning, the choice of source model largely influences the performance on a target dataset. Still, selecting a fitting source remains a challenging task, especially in medical imaging where one has to decide between models pre-trained on off-the-shelf options, such as ImageNet, and domain specific datasets. Transferability estimation (TE) metrics address this problem by aiming to predict the best performing source model in a computationally cost effective way. However, previous work has reported conflicting TE metric performances due to differences in experimental setups. Moreover, most TE metrics are designed for and evaluated on natural images, while being optimized for accuracy, whereas in medical imaging metrics that are more robust to class imbalance are typically used. We study the impact of varying the target dataset as an isolated factor, by constructing miniature populations of different sample sizes and random seeds. In addition, we investigate the influence of the evaluation metric used to obtain the reference ranking. We find that small modifications to the target dataset change the rankings. Furthermore, we show that the choice of evaluation metric affects the reference rankings and therefore the evaluation of TE metrics. Overall, we observe a low agreement between rankings from TE metrics and reference. The code, model checkpoints and data splits used in this work are available through https://github.com/niclasclassen/robustness-of-transferability-estimation-metrics-for-medical-imaging.

eess.IV↗

arXiv2026

Effect of Demographic Bias on Skin Lesion Classification

In this study, we evaluate the performance of skin lesion classification using ResNet-based convolutional models, focusing on the impact of demographic bias in training data, particularly variations in patient sex and age. We use linear programming to generate datasets with controlled demographic characteristics, allowing systematic investigation of bias effects. Three learning strategies are evaluated: a single-task model, a reinforcing multi-task model, and an adversarial learning scheme. Our sex-based analysis indicates that sex-specific training datasets optimise model performance. Notably, including male patients in the training data improved performance for the male subgroup, even in female-majority cases. Reinforcing and adversarial learning schemes narrowed or eliminated bias gaps in balanced and female-majority datasets. However, these strategies proved less effective in male-majority settings, where models continued to perform better for males than females. The two learning schemes showed marginal bias reduction compared to the baseline model in predominantly male patient populations. Age-based analysis demonstrates comparable baseline performance across the three model approaches, with performance declining across age categories. Younger groups consistently achieve the highest performance, regardless of training data distribution. Although balanced training yields optimal results for the youngest age category, performance decreases in older categories. We find that sex biases arise mainly from data imbalances, while age biases consistently favour younger groups regardless of distribution. These distinct mechanisms require targeted mitigation strategies. Additionally, cross-dataset validation on two external datasets revealed that domain shifts notably affect performance and patterns of demographic bias.

cs.AI↗

arXiv2026

Intuitions of Machine Learning Researchers about Transfer Learning for Medical Image Classification

Transfer learning is crucial for medical imaging, yet the selection of source datasets often relies on researchers' intuition rather than systematic principles, which can impact the generalizability of algorithms and, thus, patient outcomes. This study investigates these decisions through a task-based survey with machine learning practitioners. Unlike prior work that benchmarks models and experimental setups, we take a human-computer interaction (HCI) perspective on how practitioners select source datasets. Our findings indicate that choices are task-dependent and influenced by community practices, dataset properties, and computational (data embedding), or perceived visual or semantic similarity. However, similarity ratings and expected performance are not always aligned, challenging a traditional "more similar is better" view. Moreover, ethical and fairness considerations remain largely absent from source dataset sections. Participants often used ambiguous terminology, which suggests a need for clearer definitions and tools to make them explicit and usable. By clarifying these heuristics and introducing a conceptual framework of transfer learning factors, this work provides practical insights for more systematic source selection in transfer learning.

cs.CV↗

arXiv2026

Dataset Diversity Metrics and Impact on Classification Models

The diversity of training datasets is usually perceived as an important aspect to obtain a robust model. However, the definition of diversity is often not defined or differs across papers, and while some metrics exist, the quantification of this diversity is often overlooked when developing new algorithms. In this work, we study the behaviour of multiple dataset diversity metrics for image, text and metadata using MorphoMNIST, a toy dataset with controlled perturbations, and PadChest, a publicly available chest X-ray dataset. We evaluate whether these metrics correlate with each other but also with the intuition of a clinical expert. We also assess whether they correlate with downstream-task performance and how they impact the training dynamic of the models. We find limited correlations between the AUC and image or metadata reference-free diversity metrics, but higher correlations with the FID and the semantic diversity metrics. Finally, the clinical expert indicates that scanners are the main source of diversity in practice. However, we find that the addition of another scanner to the training set leads to shortcut learning. The code used in this study is available at https://github.com/TheoSourget/dataset_diversity_evaluation

cs.CV↗

arXiv2025

Robustness and sex differences in skin cancer detection: logistic regression vs CNNs

Deep learning has been reported to achieve high performances in the detection of skin cancer, yet many challenges regarding the reproducibility of results and biases remain. This study is a replication (different data, same analysis) of a previous study on Alzheimer's disease detection, which studied the robustness of logistic regression (LR) and convolutional neural networks (CNN) across patient sexes. We explore sex bias in skin cancer detection, using the PAD-UFES-20 dataset with LR trained on handcrafted features reflecting dermatological guidelines (ABCDE and the 7-point checklist), and a pre-trained ResNet-50 model. We evaluate these models in alignment with the replicated study: across multiple training datasets with varied sex composition to determine their robustness. Our results show that both the LR and the CNN were robust to the sex distribution, but the results also revealed that the CNN had a significantly higher accuracy (ACC) and area under the receiver operating characteristics (AUROC) for male patients compared to female patients. The data and relevant scripts to reproduce our results are publicly available (https://github.com/ nikodice4/Skin-cancer-detection-sex-bias).

cs.CV↗

arXiv2025

Learning to Harmonize Cross-vendor X-ray Images by Non-linear Image Dynamics Correction

In this paper, we explore how conventional image enhancement can improve model robustness in medical image analysis. By applying commonly used normalization methods to images from various vendors and studying their influence on model generalization in transfer learning, we show that the nonlinear characteristics of domain-specific image dynamics cannot be addressed by simple linear transforms. To tackle this issue, we reformulate the image harmonization task as an exposure correction problem and propose a method termed Global Deep Curve Estimation (GDCE) to reduce domain-specific exposure mismatch. GDCE performs enhancement via a pre-defined polynomial function and is trained with a "domain discriminator", aiming to improve model transparency in downstream tasks compared to existing black-box methods.

cs.CV↗

arXiv2025

False Promises in Medical Imaging AI? Assessing Validity of Outperformance Claims

Performance comparisons are fundamental in medical imaging Artificial Intelligence (AI) research, often driving claims of superiority based on relative improvements in common performance metrics. However, such claims frequently rely solely on empirical mean performance. In this paper, we investigate whether newly proposed methods genuinely outperform the state of the art by analyzing a representative cohort of medical imaging papers. We quantify the probability of false claims based on a Bayesian approach that leverages reported results alongside empirically estimated model congruence to estimate whether the relative ranking of methods is likely to have occurred by chance. According to our results, the majority (>80%) of papers claims outperformance when introducing a new method. Our analysis further revealed a high probability (>5%) of false outperformance claims in 86% of classification papers and 53% of segmentation papers. These findings highlight a critical flaw in current benchmarking practices: claims of outperformance in medical imaging AI are frequently unsubstantiated, posing a risk of misdirecting future research efforts.

cs.CV↗

arXiv2025

In the Picture: Medical Imaging Datasets, Artifacts, and their Living Review

Datasets play a critical role in medical imaging research, yet issues such as label quality, shortcuts, and metadata are often overlooked. This lack of attention may harm the generalizability of algorithms and, consequently, negatively impact patient outcomes. While existing medical imaging literature reviews mostly focus on machine learning (ML) methods, with only a few focusing on datasets for specific applications, these reviews remain static -- they are published once and not updated thereafter. This fails to account for emerging evidence, such as biases, shortcuts, and additional annotations that other researchers may contribute after the dataset is published. We refer to these newly discovered findings of datasets as research artifacts. To address this gap, we propose a living review that continuously tracks public datasets and their associated research artifacts across multiple medical imaging applications. Our approach includes a framework for the living review to monitor data documentation artifacts, and an SQL database to visualize the citation relationships between research artifact and dataset. Lastly, we discuss key considerations for creating medical imaging datasets, review best practices for data annotation, discuss the significance of shortcuts and demographic diversity, and emphasize the importance of managing datasets throughout their entire lifecycle. Our demo is publicly available at http://inthepicture.itu.dk/.

cs.CV↗

arXiv2025

Mask of truth: model sensitivity to unexpected regions of medical images

The development of larger models for medical image analysis has led to increased performance. However, it also affected our ability to explain and validate model decisions. Models can use non-relevant parts of images, also called spurious correlations or shortcuts, to obtain high performance on benchmark datasets but fail in real-world scenarios. In this work, we challenge the capacity of convolutional neural networks (CNN) to classify chest X-rays and eye fundus images while masking out clinically relevant parts of the image. We show that all models trained on the PadChest dataset, irrespective of the masking strategy, are able to obtain an Area Under the Curve (AUC) above random. Moreover, the models trained on full images obtain good performance on images without the region of interest (ROI), even superior to the one obtained on images only containing the ROI. We also reveal a possible spurious correlation in the Chaksu dataset while the performances are more aligned with the expectation of an unbiased model. We go beyond the performance analysis with the usage of the explainability method SHAP and the analysis of embeddings. We asked a radiology resident to interpret chest X-rays under different masking to complement our findings with clinical knowledge. Our code is available at https://github.com/TheoSourget/MMC_Masking and https://github.com/TheoSourget/MMC_Masking_EyeFundus

cs.CV↗

arXiv2025

Augmenting Chest X-ray Datasets with Non-Expert Annotations

The advancement of machine learning algorithms in medical image analysis requires the expansion of training datasets. A popular and cost-effective approach is automated annotation extraction from free-text medical reports, primarily due to the high costs associated with expert clinicians annotating medical images, such as chest X-rays. However, it has been shown that the resulting datasets are susceptible to biases and shortcuts. Another strategy to increase the size of a dataset is crowdsourcing, a widely adopted practice in general computer vision with some success in medical image analysis. In a similar vein to crowdsourcing, we enhance two publicly available chest X-ray datasets by incorporating non-expert annotations. However, instead of using diagnostic labels, we annotate shortcuts in the form of tubes. We collect 3.5k chest drain annotations for NIH-CXR14, and 1k annotations for four different tube types in PadChest, and create the Non-Expert Annotations of Tubes in X-rays (NEATX) dataset. We train a chest drain detector with the non-expert annotations that generalizes well to expert labels. Moreover, we compare our annotations to those provided by experts and show "moderate" to "almost perfect" agreement. Finally, we present a pathology agreement study to raise awareness about the quality of ground truth annotations. We make our dataset available on Zenodo at https://zenodo.org/records/14944064 and our code available at https://github.com/purrlab/chestxr-label-reliability.

cs.CV↗

arXiv2025

SeagrassFinder: Deep Learning for Eelgrass Detection and Coverage Estimation in the Wild

Seagrass meadows play a crucial role in marine ecosystems, providing benefits such as carbon sequestration, water quality improvement, and habitat provision. Monitoring the distribution and abundance of seagrass is essential for environmental impact assessments and conservation efforts. However, the current manual methods of analyzing underwater video data to assess seagrass coverage are time-consuming and subjective. This work explores the use of deep learning models to automate the process of seagrass detection and coverage estimation from underwater video data. We create a new dataset of over 8,300 annotated underwater images, and subsequently evaluate several deep learning architectures, including ResNet, InceptionNetV3, DenseNet, and Vision Transformer for the task of binary classification on the presence and absence of seagrass by transfer learning. The results demonstrate that deep learning models, particularly Vision Transformers, can achieve high performance in predicting eelgrass presence, with AUROC scores exceeding 0.95 on the final test dataset. The application of underwater image enhancement further improved the models' prediction capabilities. Furthermore, we introduce a novel approach for estimating seagrass coverage from video data, showing promising preliminary results that align with expert manual labels, and indicating potential for consistent and scalable monitoring. The proposed methodology allows for the efficient processing of large volumes of video data, enabling the acquisition of much more detailed information on seagrass distributions in comparison to current manual methods. This information is crucial for environmental impact assessments and monitoring programs, as seagrasses are important indicators of coastal ecosystem health. This project demonstrates the value that deep learning can bring to the field of marine ecology and environmental monitoring.

cs.CV↗

arXiv2024

On dataset transferability in medical image classification

Current transferability estimation methods designed for natural image datasets are often suboptimal in medical image classification. These methods primarily focus on estimating the suitability of pre-trained source model features for a target dataset, which can lead to unrealistic predictions, such as suggesting that the target dataset is the best source for itself. To address this, we propose a novel transferability metric that combines feature quality with gradients to evaluate both the suitability and adaptability of source model features for target tasks. We evaluate our approach in two new scenarios: source dataset transferability for medical image classification and cross-domain transferability. Our results show that our method outperforms existing transferability metrics in both settings. We also provide insight into the factors influencing transfer performance in medical image classification, as well as the dynamics of cross-domain transfer from natural to medical images. Additionally, we provide ground-truth transfer performance benchmarking results to encourage further research into transferability estimation for medical image classification. Our code and experiments are available at https://github.com/DovileDo/transferability-in-medical-imaging.

cs.CV↗

arXiv2024

Dataset Distribution Impacts Model Fairness: Single vs. Multi-Task Learning

The influence of bias in datasets on the fairness of model predictions is a topic of ongoing research in various fields. We evaluate the performance of skin lesion classification using ResNet-based CNNs, focusing on patient sex variations in training data and three different learning strategies. We present a linear programming method for generating datasets with varying patient sex and class labels, taking into account the correlations between these variables. We evaluated the model performance using three different learning strategies: a single-task model, a reinforcing multi-task model, and an adversarial learning scheme. Our observations include: 1) sex-specific training data yields better results, 2) single-task models exhibit sex bias, 3) the reinforcement approach does not remove sex bias, 4) the adversarial model eliminates sex bias in cases involving only female patients, and 5) datasets that include male patients enhance model performance for the male subgroup, even when female patients are the majority. To generalise these findings, in future research, we will examine more demographic attributes, like age, and other possibly confounding factors, such as skin colour and artefacts in the skin lesions. We make all data and models available on GitHub.

cs.LG↗

arXiv2024

Copycats: the many lives of a publicly available medical imaging dataset

Medical Imaging (MI) datasets are fundamental to artificial intelligence in healthcare. The accuracy, robustness, and fairness of diagnostic algorithms depend on the data (and its quality) used to train and evaluate the models. MI datasets used to be proprietary, but have become increasingly available to the public, including on community-contributed platforms (CCPs) like Kaggle or HuggingFace. While open data is important to enhance the redistribution of data's public value, we find that the current CCP governance model fails to uphold the quality needed and recommended practices for sharing, documenting, and evaluating datasets. In this paper, we conduct an analysis of publicly available machine learning datasets on CCPs, discussing datasets' context, and identifying limitations and gaps in the current CCP landscape. We highlight differences between MI and computer vision datasets, particularly in the potentially harmful downstream effects from poor adoption of recommended dataset management practices. We compare the analyzed datasets across several dimensions, including data sharing, data documentation, and maintenance. We find vague licenses, lack of persistent identifiers and storage, duplicates, and missing metadata, with differences between the platforms. Our research contributes to efforts in responsible data curation and AI algorithms for healthcare.

cs.CV↗

arXiv2024

Confidence intervals uncovered: Are we ready for real-world medical imaging AI?

Medical imaging is spearheading the AI transformation of healthcare. Performance reporting is key to determine which methods should be translated into clinical practice. Frequently, broad conclusions are simply derived from mean performance values. In this paper, we argue that this common practice is often a misleading simplification as it ignores performance variability. Our contribution is threefold. (1) Analyzing all MICCAI segmentation papers (n = 221) published in 2023, we first observe that more than 50% of papers do not assess performance variability at all. Moreover, only one (0.5%) paper reported confidence intervals (CIs) for model performance. (2) To address the reporting bottleneck, we show that the unreported standard deviation (SD) in segmentation papers can be approximated by a second-order polynomial function of the mean Dice similarity coefficient (DSC). Based on external validation data from 56 previous MICCAI challenges, we demonstrate that this approximation can accurately reconstruct the CI of a method using information provided in publications. (3) Finally, we reconstructed 95% CIs around the mean DSC of MICCAI 2023 segmentation papers. The median CI width was 0.03 which is three times larger than the median performance gap between the first and second ranked method. For more than 60% of papers, the mean performance of the second-ranked method was within the CI of the first-ranked method. We conclude that current publications typically do not provide sufficient evidence to support which models could potentially be translated into clinical practice.

cs.CV↗