Exploring connections of spectral analysis and transfer learning in medical imaging

In this paper, we use spectral analysis to investigate transfer learning and study model sensitivity to frequency shortcuts in medical imaging. By analyzing the power spectrum density of both pre-trained and fine-tuned model gradients, as well as artificially generated frequency shortcuts, we observe notable differences in learning priorities between models pre-trained on natural vs medical images, which generally persist during fine-tuning. We find that when a model's learning priority aligns with the power spectrum density of an artifact, it results in overfitting to that artifact. Based on these observations, we show that source data editing can alter the model's resistance to shortcut learning.

Source Matters: Source Dataset Impact on Model Robustness in Medical Imaging

Transfer learning has become an essential part of medical imaging classification algorithms, often leveraging ImageNet weights. However, the domain shift from natural to medical images has prompted alternatives such as RadImageNet, often demonstrating comparable classification performance. However, it remains unclear whether the performance gains from transfer learning stem from improved generalization or shortcut learning. To address this, we investigate potential confounders -- whether synthetic or sampled from the data -- across two publicly available chest X-ray and CT datasets. We show that ImageNet and RadImageNet achieve comparable classification performance, yet ImageNet is much more prone to overfitting to confounders. We recommend that researchers using ImageNet-pretrained models reexamine their model robustness by conducting similar experiments. Our code and experiments are available at https://github.com/DovileDo/source-matters.

Towards actionability for open medical imaging datasets: lessons from community-contributed platforms for data management and stewardship

Medical imaging datasets are fundamental to artificial intelligence (AI) in healthcare. The accuracy, robustness and fairness of diagnostic algorithms depend on the data (and its quality) on which the models are trained and evaluated. Medical imaging datasets have become increasingly available to the public, and are often hosted on Community-Contributed Platforms (CCP), including private companies 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 investigate medical imaging datasets on CCPs and how they are documented, shared, and maintained. We first highlight some differences between medical imaging and computer vision, particularly in the potentially harmful downstream effects due to poor adoption of recommended dataset management practices. We then analyze 20 (10 medical and 10 computer vision) popular datasets on CCPs and find vague licenses, lack of persistent identifiers and storage, duplicates and missing metadata, with differences between the platforms. We present "actionability" as a conceptual metric to reveal the data quality gap between characteristics of data on CCPs and the desired characteristics of data for AI in healthcare. Finally, we propose a commons-based stewardship model for documenting, sharing and maintaining datasets on CCPs and end with a discussion of limitations and open questions.

Data usage and citation practices in medical imaging conferences

Medical imaging papers often focus on methodology, but the quality of the algorithms and the validity of the conclusions are highly dependent on the datasets used. As creating datasets requires a lot of effort, researchers often use publicly available datasets, there is however no adopted standard for citing the datasets used in scientific papers, leading to difficulty in tracking dataset usage. In this work, we present two open-source tools we created that could help with the detection of dataset usage, a pipeline \url{https://github.com/TheoSourget/Public_Medical_Datasets_References} using OpenAlex and full-text analysis, and a PDF annotation software \url{https://github.com/TheoSourget/pdf_annotator} used in our study to manually label the presence of datasets. We applied both tools on a study of the usage of 20 publicly available medical datasets in papers from MICCAI and MIDL. We compute the proportion and the evolution between 2013 and 2023 of 3 types of presence in a paper: cited, mentioned in the full text, cited and mentioned. Our findings demonstrate the concentration of the usage of a limited set of datasets. We also highlight different citing practices, making the automation of tracking difficult.

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 chest X-ray images. 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 CXR14, and 1k annotations for 4 different tube types in PadChest. 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 ground truth annotations. We make our annotations and code available.

Why is the winner the best?

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multi-center study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and postprocessing (66%). The "typical" lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work.

Revisiting Hidden Representations in Transfer Learning for Medical Imaging

While a key component to the success of deep learning is the availability of massive amounts of training data, medical image datasets are often limited in diversity and size. Transfer learning has the potential to bridge the gap between related yet different domains. For medical applications, however, it remains unclear whether it is more beneficial to pre-train on natural or medical images. We aim to shed light on this problem by comparing initialization on ImageNet and RadImageNet on seven medical classification tasks. We investigate their learned representations with Canonical Correlation Analysis (CCA) and compare the predictions of the different models. We find that overall the models pre-trained on ImageNet outperform those trained on RadImageNet. Our results show that, contrary to intuition, ImageNet and RadImageNet converge to distinct intermediate representations, and that these representations are even more dissimilar after fine-tuning. Despite these distinct representations, the predictions of the models remain similar. Our findings challenge the notion that transfer learning is effective due to the reuse of general features in the early layers of a convolutional neural network and show that weight similarity before and after fine-tuning is negatively related to performance gains.

Understanding metric-related pitfalls in image analysis validation

Validation metrics are key for the reliable tracking of scientific progress and for bridging the current chasm between artificial intelligence (AI) research and its translation into practice. However, increasing evidence shows that particularly in image analysis, metrics are often chosen inadequately in relation to the underlying research problem. This could be attributed to a lack of accessibility of metric-related knowledge: While taking into account the individual strengths, weaknesses, and limitations of validation metrics is a critical prerequisite to making educated choices, the relevant knowledge is currently scattered and poorly accessible to individual researchers. Based on a multi-stage Delphi process conducted by a multidisciplinary expert consortium as well as extensive community feedback, the present work provides the first reliable and comprehensive common point of access to information on pitfalls related to validation metrics in image analysis. Focusing on biomedical image analysis but with the potential of transfer to other fields, the addressed pitfalls generalize across application domains and are categorized according to a newly created, domain-agnostic taxonomy. To facilitate comprehension, illustrations and specific examples accompany each pitfall. As a structured body of information accessible to researchers of all levels of expertise, this work enhances global comprehension of a key topic in image analysis validation.

Biomedical image analysis competitions: The state of current participation practice

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

Detecting Shortcuts in Medical Images -- A Case Study in Chest X-rays

The availability of large public datasets and the increased amount of computing power have shifted the interest of the medical community to high-performance algorithms. However, little attention is paid to the quality of the data and their annotations. High performance on benchmark datasets may be reported without considering possible shortcuts or artifacts in the data, besides, models are not tested on subpopulation groups. With this work, we aim to raise awareness about shortcuts problems. We validate previous findings, and present a case study on chest X-rays using two publicly available datasets. We share annotations for a subset of pneumothorax images with drains. We conclude with general recommendations for medical image classification.