arXiv subjects

Veronika Cheplygina

Publications and source records attributed to Veronika Cheplygina.

At least 37 records · Page 2Linked to original sources

arXiv2024

[Citation needed] 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.

cs.CV↗

arXiv2024

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. The domain shift from natural to medical images has prompted alternatives such as RadImageNet, often showing 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 conceptualize confounders by introducing the Medical Imaging Contextualized Confounder Taxonomy (MICCAT) and investigate a range of confounders across it -- whether synthetic or sampled from the data -- using two public 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.

cs.CV↗

arXiv2024

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.

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arXiv2024

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.

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arXiv2024

Metrics reloaded: Recommendations for image analysis validation

Increasing evidence shows that flaws in machine learning (ML) algorithm validation are an underestimated global problem. Particularly in automatic biomedical image analysis, chosen performance metrics often do not reflect the domain interest, thus failing to adequately measure scientific progress and hindering translation of ML techniques into practice. To overcome this, our large international expert consortium created Metrics Reloaded, a comprehensive framework guiding researchers in the problem-aware selection of metrics. Following the convergence of ML methodology across application domains, Metrics Reloaded fosters the convergence of validation methodology. The framework was developed in a multi-stage Delphi process and is based on the novel concept of a problem fingerprint - a structured representation of the given problem that captures all aspects that are relevant for metric selection, from the domain interest to the properties of the target structure(s), data set and algorithm output. Based on the problem fingerprint, users are guided through the process of choosing and applying appropriate validation metrics while being made aware of potential pitfalls. Metrics Reloaded targets image analysis problems that can be interpreted as a classification task at image, object or pixel level, namely image-level classification, object detection, semantic segmentation, and instance segmentation tasks. To improve the user experience, we implemented the framework in the Metrics Reloaded online tool, which also provides a point of access to explore weaknesses, strengths and specific recommendations for the most common validation metrics. The broad applicability of our framework across domains is demonstrated by an instantiation for various biological and medical image analysis use cases.

cs.CV↗

arXiv2023

Common Limitations of Image Processing Metrics: A Picture Story

While the importance of automatic image analysis is continuously increasing, recent meta-research revealed major flaws with respect to algorithm validation. Performance metrics are particularly key for meaningful, objective, and transparent performance assessment and validation of the used automatic algorithms, but relatively little attention has been given to the practical pitfalls when using specific metrics for a given image analysis task. These are typically related to (1) the disregard of inherent metric properties, such as the behaviour in the presence of class imbalance or small target structures, (2) the disregard of inherent data set properties, such as the non-independence of the test cases, and (3) the disregard of the actual biomedical domain interest that the metrics should reflect. This living dynamically document has the purpose to illustrate important limitations of performance metrics commonly applied in the field of image analysis. In this context, it focuses on biomedical image analysis problems that can be phrased as image-level classification, semantic segmentation, instance segmentation, or object detection task. The current version is based on a Delphi process on metrics conducted by an international consortium of image analysis experts from more than 60 institutions worldwide.

eess.IV↗

arXiv2023

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. Our work includes a replication study, which yields results contrary to previously published findings. In our experiments, ResNet50 models pre-trained on ImageNet tend to outperform those trained on RadImageNet. To gain further insights, we investigate the learned representations using Canonical Correlation Analysis (CCA) and compare the predictions of the different models. Our results indicate that, contrary to intuition, ImageNet and RadImageNet may converge to distinct intermediate representations, which appear to diverge further during fine-tuning. Despite these distinct representations, the predictions of the models remain similar. Our findings show that the similarity between networks before and after fine-tuning does not correlate with performance gains, suggesting that the advantages of transfer learning might not solely originate from the reuse of features in the early layers of a convolutional neural network.

cs.CV↗

arXiv2023

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.

cs.CV↗

arXiv2023

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.

cs.CV↗

arXiv2022

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.

cs.CV↗

arXiv2022

Detection of Furigana Text in Images

Furigana are pronunciation notes used in Japanese writing. Being able to detect these can help improve optical character recognition (OCR) performance or make more accurate digital copies of Japanese written media by correctly displaying furigana. This project focuses on detecting furigana in Japanese books and comics. While there has been research into the detection of Japanese text in general, there are currently no proposed methods for detecting furigana. We construct a new dataset containing Japanese written media and annotations of furigana. We propose an evaluation metric for such data which is similar to the evaluation protocols used in object detection except that it allows groups of objects to be labeled by one annotation. We propose a method for detection of furigana that is based on mathematical morphology and connected component analysis. We evaluate the detections of the dataset and compare different methods for text extraction. We also evaluate different types of images such as books and comics individually and discuss the challenges of each type of image. The proposed method reaches an F1-score of 76\% on the dataset. The method performs well on regular books, but less so on comics, and books of irregular format. Finally, we show that the proposed method can improve the performance of OCR by 5\% on the manga109 dataset. Source code is available via \texttt{\url{https://github.com/nikolajkb/FuriganaDetection}}

cs.CV↗

arXiv2022

How I failed machine learning in medical imaging -- shortcomings and recommendations

Medical imaging is an important research field with many opportunities for improving patients' health. However, there are a number of challenges that are slowing down the progress of the field as a whole, such optimizing for publication. In this paper we reviewed several problems related to choosing datasets, methods, evaluation metrics, and publication strategies. With a review of literature and our own analysis, we show that at every step, potential biases can creep in. On a positive note, we also see that initiatives to counteract these problems are already being started. Finally we provide a broad range of recommendations on how to further these address problems in the future. For reproducibility, data and code for our analyses are available on \url{https://github.com/GaelVaroquaux/ml_med_imaging_failures}

eess.IV↗

arXiv2022

Predicting Bearings' Degradation Stages for Predictive Maintenance in the Pharmaceutical Industry

In the pharmaceutical industry, the maintenance of production machines must be audited by the regulator. In this context, the problem of predictive maintenance is not when to maintain a machine, but what parts to maintain at a given point in time. The focus shifts from the entire machine to its component parts and prediction becomes a classification problem. In this paper, we focus on rolling-elements bearings and we propose a framework for predicting their degradation stages automatically. Our main contribution is a k-means bearing lifetime segmentation method based on high-frequency bearing vibration signal embedded in a latent low-dimensional subspace using an AutoEncoder. Given high-frequency vibration data, our framework generates a labeled dataset that is used to train a supervised model for bearing degradation stage detection. Our experimental results, based on the FEMTO Bearing dataset, show that our framework is scalable and that it provides reliable and actionable predictions for a range of different bearings.

stat.ML↗

arXiv2022

Effect of Prior-based Losses on Segmentation Performance: A Benchmark

Today, deep convolutional neural networks (CNNs) have demonstrated state-of-the-art performance for medical image segmentation, on various imaging modalities and tasks. Despite early success, segmentation networks may still generate anatomically aberrant segmentations, with holes or inaccuracies near the object boundaries. To enforce anatomical plausibility, recent research studies have focused on incorporating prior knowledge such as object shape or boundary, as constraints in the loss function. Prior integrated could be low-level referring to reformulated representations extracted from the ground-truth segmentations, or high-level representing external medical information such as the organ's shape or size. Over the past few years, prior-based losses exhibited a rising interest in the research field since they allow integration of expert knowledge while still being architecture-agnostic. However, given the diversity of prior-based losses on different medical imaging challenges and tasks, it has become hard to identify what loss works best for which dataset. In this paper, we establish a benchmark of recent prior-based losses for medical image segmentation. The main objective is to provide intuition onto which losses to choose given a particular task or dataset. To this end, four low-level and high-level prior-based losses are selected. The considered losses are validated on 8 different datasets from a variety of medical image segmentation challenges including the Decathlon, the ISLES and the WMH challenge. Results show that whereas low-level prior-based losses can guarantee an increase in performance over the Dice loss baseline regardless of the dataset characteristics, high-level prior-based losses can increase anatomical plausibility as per data characteristics.

eess.IV↗

arXiv2021

ENHANCE (ENriching Health data by ANnotations of Crowd and Experts): A case study for skin lesion classification

We present ENHANCE, an open dataset with multiple annotations to complement the existing ISIC and PH2 skin lesion classification datasets. This dataset contains annotations of visual ABC (asymmetry, border, colour) features from non-expert annotation sources: undergraduate students, crowd workers from Amazon MTurk and classic image processing algorithms. In this paper we first analyse the correlations between the annotations and the diagnostic label of the lesion, as well as study the agreement between different annotation sources. Overall we find weak correlations of non-expert annotations with the diagnostic label, and low agreement between different annotation sources. We then study multi-task learning (MTL) with the annotations as additional labels, and show that non-expert annotations can improve (ensembles of) state-of-the-art convolutional neural networks via MTL. We hope that our dataset can be used in further research into multiple annotations and/or MTL. All data and models are available on Github: https://github.com/raumannsr/ENHANCE.

cs.CV↗

arXiv2021

Cats, not CAT scans: a study of dataset similarity in transfer learning for 2D medical image classification

Transfer learning is a commonly used strategy for medical image classification, especially via pretraining on source data and fine-tuning on target data. There is currently no consensus on how to choose appropriate source data, and in the literature we can find both evidence of favoring large natural image datasets such as ImageNet, and evidence of favoring more specialized medical datasets. In this paper we perform a systematic study with nine source datasets with natural or medical images, and three target medical datasets, all with 2D images. We find that ImageNet is the source leading to the highest performances, but also that larger datasets are not necessarily better. We also study different definitions of data similarity. We show that common intuitions about similarity may be inaccurate, and therefore not sufficient to predict an appropriate source a priori. Finally, we discuss several steps needed for further research in this field, especially with regard to other types (for example 3D) medical images. Our experiments and pretrained models are available via \url{https://www.github.com/vcheplygina/cats-scans}

cs.CV↗

arXiv2021

Using uncertainty estimation to reduce false positives in liver lesion detection

Despite the successes of deep learning techniques at detecting objects in medical images, false positive detections occur which may hinder an accurate diagnosis. We propose a technique to reduce false positive detections made by a neural network using an SVM classifier trained with features derived from the uncertainty map of the neural network prediction. We demonstrate the effectiveness of this method for the detection of liver lesions on a dataset of abdominal MR images. We find that the use of a dropout rate of 0.5 produces the least number of false positives in the neural network predictions and the trained classifier filters out approximately 90% of these false positives detections in the test-set.

eess.IV↗

arXiv2020

High-level Prior-based Loss Functions for Medical Image Segmentation: A Survey

Today, deep convolutional neural networks (CNNs) have demonstrated state of the art performance for supervised medical image segmentation, across various imaging modalities and tasks. Despite early success, segmentation networks may still generate anatomically aberrant segmentations, with holes or inaccuracies near the object boundaries. To mitigate this effect, recent research works have focused on incorporating spatial information or prior knowledge to enforce anatomically plausible segmentation. If the integration of prior knowledge in image segmentation is not a new topic in classical optimization approaches, it is today an increasing trend in CNN based image segmentation, as shown by the growing literature on the topic. In this survey, we focus on high level prior, embedded at the loss function level. We categorize the articles according to the nature of the prior: the object shape, size, topology, and the inter-regions constraints. We highlight strengths and limitations of current approaches, discuss the challenge related to the design and the integration of prior-based losses, and the optimization strategies, and draw future research directions.

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