arXiv subjects

Maciej A. Mazurowski

Publications and source records attributed to Maciej A. Mazurowski.

At least 55 records · Page 3Linked to original sources

arXiv2023

A systematic study of the foreground-background imbalance problem in deep learning for object detection

The class imbalance problem in deep learning has been explored in several studies, but there has yet to be a systematic analysis of this phenomenon in object detection. Here, we present comprehensive analyses and experiments of the foreground-background (F-B) imbalance problem in object detection, which is very common and caused by small, infrequent objects of interest. We experimentally study the effects of different aspects of F-B imbalance (object size, number of objects, dataset size, object type) on detection performance. In addition, we also compare 9 leading methods for addressing this problem, including Faster-RCNN, SSD, OHEM, Libra-RCNN, Focal-Loss, GHM, PISA, YOLO-v3, and GFL with a range of datasets from different imaging domains. We conclude that (1) the F-B imbalance can indeed cause a significant drop in detection performance, (2) The detection performance is more affected by F-B imbalance when fewer training data are available, (3) in most cases, decreasing object size leads to larger performance drop than decreasing number of objects, given the same change in the ratio of object pixels to non-object pixels, (6) among all selected methods, Libra-RCNN and PISA demonstrate the best performance in addressing the issue of F-B imbalance. (7) When the training dataset size is large, the choice of method is not impactful (8) Soft-sampling methods, including focal-loss, GHM, and GFL, perform fairly well on average but are relatively unstable.

cs.CV↗

arXiv2023

Segment Anything Model for Medical Image Analysis: an Experimental Study

Training segmentation models for medical images continues to be challenging due to the limited availability of data annotations. Segment Anything Model (SAM) is a foundation model that is intended to segment user-defined objects of interest in an interactive manner. While the performance on natural images is impressive, medical image domains pose their own set of challenges. Here, we perform an extensive evaluation of SAM's ability to segment medical images on a collection of 19 medical imaging datasets from various modalities and anatomies. We report the following findings: (1) SAM's performance based on single prompts highly varies depending on the dataset and the task, from IoU=0.1135 for spine MRI to IoU=0.8650 for hip X-ray. (2) Segmentation performance appears to be better for well-circumscribed objects with prompts with less ambiguity and poorer in various other scenarios such as the segmentation of brain tumors. (3) SAM performs notably better with box prompts than with point prompts. (4) SAM outperforms similar methods RITM, SimpleClick, and FocalClick in almost all single-point prompt settings. (5) When multiple-point prompts are provided iteratively, SAM's performance generally improves only slightly while other methods' performance improves to the level that surpasses SAM's point-based performance. We also provide several illustrations for SAM's performance on all tested datasets, iterative segmentation, and SAM's behavior given prompt ambiguity. We conclude that SAM shows impressive zero-shot segmentation performance for certain medical imaging datasets, but moderate to poor performance for others. SAM has the potential to make a significant impact in automated medical image segmentation in medical imaging, but appropriate care needs to be applied when using it.

cs.CV↗

arXiv2023

Deep Learning for Classification of Thyroid Nodules on Ultrasound: Validation on an Independent Dataset

Objectives: The purpose is to apply a previously validated deep learning algorithm to a new thyroid nodule ultrasound image dataset and compare its performances with radiologists. Methods: Prior study presented an algorithm which is able to detect thyroid nodules and then make malignancy classifications with two ultrasound images. A multi-task deep convolutional neural network was trained from 1278 nodules and originally tested with 99 separate nodules. The results were comparable with that of radiologists. The algorithm was further tested with 378 nodules imaged with ultrasound machines from different manufacturers and product types than the training cases. Four experienced radiologists were requested to evaluate the nodules for comparison with deep learning. Results: The Area Under Curve (AUC) of the deep learning algorithm and four radiologists were calculated with parametric, binormal estimation. For the deep learning algorithm, the AUC was 0.69 (95% CI: 0.64 - 0.75). The AUC of radiologists were 0.63 (95% CI: 0.59 - 0.67), 0.66 (95% CI:0.61 - 0.71), 0.65 (95% CI: 0.60 - 0.70), and 0.63 (95%CI: 0.58 - 0.67). Conclusion: In the new testing dataset, the deep learning algorithm achieved similar performances with all four radiologists. The relative performance difference between the algorithm and the radiologists is not significantly affected by the difference of ultrasound scanner.

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arXiv2023

Reverse Engineering Breast MRIs: Predicting Acquisition Parameters Directly from Images

The image acquisition parameters (IAPs) used to create MRI scans are central to defining the appearance of the images. Deep learning models trained on data acquired using certain parameters might not generalize well to images acquired with different parameters. Being able to recover such parameters directly from an image could help determine whether a deep learning model is applicable, and could assist with data harmonization and/or domain adaptation. Here, we introduce a neural network model that can predict many complex IAPs used to generate an MR image with high accuracy solely using the image, with a single forward pass. These predicted parameters include field strength, echo and repetition times, acquisition matrix, scanner model, scan options, and others. Even challenging parameters such as contrast agent type can be predicted with good accuracy. We perform a variety of experiments and analyses of our model's ability to predict IAPs on many MRI scans of new patients, and demonstrate its usage in a realistic application. Predicting IAPs from the images is an important step toward better understanding the relationship between image appearance and IAPs. This in turn will advance the understanding of many concepts related to the generalizability of neural network models on medical images, including domain shift, domain adaptation, and data harmonization.

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arXiv2023

Deep Learning for Breast MRI Style Transfer with Limited Training Data

In this work we introduce a novel medical image style transfer method, StyleMapper, that can transfer medical scans to an unseen style with access to limited training data. This is made possible by training our model on unlimited possibilities of simulated random medical imaging styles on the training set, making our work more computationally efficient when compared with other style transfer methods. Moreover, our method enables arbitrary style transfer: transferring images to styles unseen in training. This is useful for medical imaging, where images are acquired using different protocols and different scanner models, resulting in a variety of styles that data may need to be transferred between. Methods: Our model disentangles image content from style and can modify an image's style by simply replacing the style encoding with one extracted from a single image of the target style, with no additional optimization required. This also allows the model to distinguish between different styles of images, including among those that were unseen in training. We propose a formal description of the proposed model. Results: Experimental results on breast magnetic resonance images indicate the effectiveness of our method for style transfer. Conclusion: Our style transfer method allows for the alignment of medical images taken with different scanners into a single unified style dataset, allowing for the training of other downstream tasks on such a dataset for tasks such as classification, object detection and others.

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arXiv2022

Detection of masses and architectural distortions in digital breast tomosynthesis: a publicly available dataset of 5,060 patients and a deep learning model

Breast cancer screening is one of the most common radiological tasks with over 39 million exams performed each year. While breast cancer screening has been one of the most studied medical imaging applications of artificial intelligence, the development and evaluation of the algorithms are hindered due to the lack of well-annotated large-scale publicly available datasets. This is particularly an issue for digital breast tomosynthesis (DBT) which is a relatively new breast cancer screening modality. We have curated and made publicly available a large-scale dataset of digital breast tomosynthesis images. It contains 22,032 reconstructed DBT volumes belonging to 5,610 studies from 5,060 patients. This included four groups: (1) 5,129 normal studies, (2) 280 studies where additional imaging was needed but no biopsy was performed, (3) 112 benign biopsied studies, and (4) 89 studies with cancer. Our dataset included masses and architectural distortions which were annotated by two experienced radiologists. Additionally, we developed a single-phase deep learning detection model and tested it using our dataset to serve as a baseline for future research. Our model reached a sensitivity of 65% at 2 false positives per breast. Our large, diverse, and highly-curated dataset will facilitate development and evaluation of AI algorithms for breast cancer screening through providing data for training as well as common set of cases for model validation. The performance of the model developed in our study shows that the task remains challenging and will serve as a baseline for future model development.

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arXiv2022

Lightweight Transformer Backbone for Medical Object Detection

Lesion detection in digital breast tomosynthesis (DBT) is an important and a challenging problem characterized by a low prevalence of images containing tumors. Due to the label scarcity problem, large deep learning models and computationally intensive algorithms are likely to fail when applied to this task. In this paper, we present a practical yet lightweight backbone to improve the accuracy of tumor detection. Specifically, we propose a novel modification of visual transformer (ViT) on image feature patches to connect the feature patches of a tumor with healthy backgrounds of breast images and form a more robust backbone for tumor detection. To the best of our knowledge, our model is the first work of Transformer backbone object detection for medical imaging. Our experiments show that this model can considerably improve the accuracy of lesion detection and reduce the amount of labeled data required in typical ViT. We further show that with additional augmented tumor data, our model significantly outperforms the Faster R-CNN model and state-of-the-art SWIN transformer model.

cs.CV↗

arXiv2022

Deep learning-based algorithm for assessment of knee osteoarthritis severity in radiographs matches performance of radiologists

A fully-automated deep learning algorithm matched performance of radiologists in assessment of knee osteoarthritis severity in radiographs using the Kellgren-Lawrence grading system. To develop an automated deep learning-based algorithm that jointly uses Posterior-Anterior (PA) and Lateral (LAT) views of knee radiographs to assess knee osteoarthritis severity according to the Kellgren-Lawrence grading system. We used a dataset of 9739 exams from 2802 patients from Multicenter Osteoarthritis Study (MOST). The dataset was divided into a training set of 2040 patients, a validation set of 259 patients and a test set of 503 patients. A novel deep learning-based method was utilized for assessment of knee OA in two steps: (1) localization of knee joints in the images, (2) classification according to the KL grading system. Our method used both PA and LAT views as the input to the model. The scores generated by the algorithm were compared to the grades provided in the MOST dataset for the entire test set as well as grades provided by 5 radiologists at our institution for a subset of the test set. The model obtained a multi-class accuracy of 71.90% on the entire test set when compared to the ratings provided in the MOST dataset. The quadratic weighted Kappa coefficient for this set was 0.9066. The average quadratic weighted Kappa between all pairs of radiologists from our institution who took a part of study was 0.748. The average quadratic-weighted Kappa between the algorithm and the radiologists at our institution was 0.769. The proposed model performed demonstrated equivalency of KL classification to MSK radiologists, but clearly superior reproducibility. Our model also agreed with radiologists at our institution to the same extent as the radiologists with each other. The algorithm could be used to provide reproducible assessment of knee osteoarthritis severity.

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arXiv2022

Knee arthritis severity measurement using deep learning: a publicly available algorithm with a multi-institutional validation showing radiologist-level performance

The assessment of knee osteoarthritis (KOA) severity on knee X-rays is a central criteria for the use of total knee arthroplasty. However, this assessment suffers from imprecise standards and a remarkably high inter-reader variability. An algorithmic, automated assessment of KOA severity could improve overall outcomes of knee replacement procedures by increasing the appropriateness of its use. We propose a novel deep learning-based five-step algorithm to automatically grade KOA from posterior-anterior (PA) views of radiographs: (1) image preprocessing (2) localization of knees joints in the image using the YOLO v3-Tiny model, (3) initial assessment of the severity of osteoarthritis using a convolutional neural network-based classifier, (4) segmentation of the joints and calculation of the joint space narrowing (JSN), and (5), a combination of the JSN and the initial assessment to determine a final Kellgren-Lawrence (KL) score. Furthermore, by displaying the segmentation masks used to make the assessment, our algorithm demonstrates a higher degree of transparency compared to typical "black box" deep learning classifiers. We perform a comprehensive evaluation using two public datasets and one dataset from our institution, and show that our algorithm reaches state-of-the art performance. Moreover, we also collected ratings from multiple radiologists at our institution and showed that our algorithm performs at the radiologist level. The software has been made publicly available at https://github.com/MaciejMazurowski/osteoarthritis-classification.

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arXiv2022

The Intrinsic Manifolds of Radiological Images and their Role in Deep Learning

The manifold hypothesis is a core mechanism behind the success of deep learning, so understanding the intrinsic manifold structure of image data is central to studying how neural networks learn from the data. Intrinsic dataset manifolds and their relationship to learning difficulty have recently begun to be studied for the common domain of natural images, but little such research has been attempted for radiological images. We address this here. First, we compare the intrinsic manifold dimensionality of radiological and natural images. We also investigate the relationship between intrinsic dimensionality and generalization ability over a wide range of datasets. Our analysis shows that natural image datasets generally have a higher number of intrinsic dimensions than radiological images. However, the relationship between generalization ability and intrinsic dimensionality is much stronger for medical images, which could be explained as radiological images having intrinsic features that are more difficult to learn. These results give a more principled underpinning for the intuition that radiological images can be more challenging to apply deep learning to than natural image datasets common to machine learning research. We believe rather than directly applying models developed for natural images to the radiological imaging domain, more care should be taken to developing architectures and algorithms that are more tailored to the specific characteristics of this domain. The research shown in our paper, demonstrating these characteristics and the differences from natural images, is an important first step in this direction.

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arXiv2022

Multi-Label Annotation of Chest Abdomen Pelvis Computed Tomography Text Reports Using Deep Learning

Purpose: To develop high throughput multi-label annotators for body (chest, abdomen, and pelvis) Computed Tomography (CT) reports that can be applied across a variety of abnormalities, organs, and disease states. Approach: We used a dictionary approach to develop rule-based algorithms (RBA) for extraction of disease labels from radiology text reports. We targeted three organ systems (lungs/pleura, liver/gallbladder, kidneys/ureters) with four diseases per system based on their prevalence in our dataset. To expand the algorithms beyond pre-defined keywords, attention-guided recurrent neural networks (RNN) were trained using the RBA-extracted labels to classify reports as being positive for one or more diseases or normal for each organ system. Confounding effects on model performance were evaluated using random initialization or pre-trained embedding as well as different sizes of training datasets. Performance was evaluated using the receiver operating characteristic (ROC) area under the curve (AUC) against 2,158 manually obtained labels. Results: Our models extracted disease labels from 261,229 radiology reports of 112,501 unique subjects. Pre-trained models outperformed random initialization across all diseases. As the training dataset size was reduced, performance was robust except for a few diseases with relatively small number of cases. Pre-trained classification AUCs achieved > 0.95 for all five disease outcomes across all three organ systems. Conclusions: Our label-extracting pipeline was able to encompass a variety of cases and diseases by generalizing beyond strict rules with exceptional accuracy. This method can be easily adapted to enable automated labeling of hospital-scale medical data sets for training image-based disease classifiers.

cs.AI↗

arXiv2022

Virtual vs. Reality: External Validation of COVID-19 Classifiers using XCAT Phantoms for Chest Computed Tomography

Research studies of artificial intelligence models in medical imaging have been hampered by poor generalization. This problem has been especially concerning over the last year with numerous applications of deep learning for COVID-19 diagnosis. Virtual imaging trials (VITs) could provide a solution for objective evaluation of these models. In this work utilizing the VITs, we created the CVIT-COVID dataset including 180 virtually imaged computed tomography (CT) images from simulated COVID-19 and normal phantom models under different COVID-19 morphology and imaging properties. We evaluated the performance of an open-source, deep-learning model from the University of Waterloo trained with multi-institutional data and an in-house model trained with the open clinical dataset called MosMed. We further validated the model's performance against open clinical data of 305 CT images to understand virtual vs. real clinical data performance. The open-source model was published with nearly perfect performance on the original Waterloo dataset but showed a consistent performance drop in external testing on another clinical dataset (AUC=0.77) and our simulated CVIT-COVID dataset (AUC=0.55). The in-house model achieved an AUC of 0.87 while testing on the internal test set (MosMed test set). However, performance dropped to an AUC of 0.65 and 0.69 when evaluated on clinical and our simulated CVIT-COVID dataset. The VIT framework offered control over imaging conditions, allowing us to show there was no change in performance as CT exposure was changed from 28.5 to 57 mAs. The VIT framework also provided voxel-level ground truth, revealing that performance of in-house model was much higher at AUC=0.87 for diffuse COVID-19 infection size >2.65% lung volume versus AUC=0.52 for focal disease with <2.65% volume. The virtual imaging framework enabled these uniquely rigorous analyses of model performance.

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arXiv2022

Quality or Quantity: Toward a Unified Approach for Multi-organ Segmentation in Body CT

Organ segmentation of medical images is a key step in virtual imaging trials. However, organ segmentation datasets are limited in terms of quality (because labels cover only a few organs) and quantity (since case numbers are limited). In this study, we explored the tradeoffs between quality and quantity. Our goal is to create a unified approach for multi-organ segmentation of body CT, which will facilitate the creation of large numbers of accurate virtual phantoms. Initially, we compared two segmentation architectures, 3D-Unet and DenseVNet, which were trained using XCAT data that is fully labeled with 22 organs, and chose the 3D-Unet as the better performing model. We used the XCAT-trained model to generate pseudo-labels for the CT-ORG dataset that has only 7 organs segmented. We performed two experiments: First, we trained 3D-UNet model on the XCAT dataset, representing quality data, and tested it on both XCAT and CT-ORG datasets. Second, we trained 3D-UNet after including the CT-ORG dataset into the training set to have more quantity. Performance improved for segmentation in the organs where we have true labels in both datasets and degraded when relying on pseudo-labels. When organs were labeled in both datasets, Exp-2 improved Average DSC in XCAT and CT-ORG by 1. This demonstrates that quality data is the key to improving the model's performance.

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arXiv2021

Classification of Multiple Diseases on Body CT Scans using Weakly Supervised Deep Learning

Purpose: To design multi-disease classifiers for body CT scans for three different organ systems using automatically extracted labels from radiology text reports.Materials & Methods: This retrospective study included a total of 12,092 patients (mean age 57 +- 18; 6,172 women) for model development and testing (from 2012-2017). Rule-based algorithms were used to extract 19,225 disease labels from 13,667 body CT scans from 12,092 patients. Using a three-dimensional DenseVNet, three organ systems were segmented: lungs and pleura; liver and gallbladder; and kidneys and ureters. For each organ, a three-dimensional convolutional neural network classified no apparent disease versus four common diseases for a total of 15 different labels across all three models. Testing was performed on a subset of 2,158 CT volumes relative to 2,875 manually derived reference labels from 2133 patients (mean age 58 +- 18;1079 women). Performance was reported as receiver operating characteristic area under the curve (AUC) with 95% confidence intervals by the DeLong method. Results: Manual validation of the extracted labels confirmed 91% to 99% accuracy across the 15 different labels. AUCs for lungs and pleura labels were: atelectasis 0.77 (95% CI: 0.74, 0.81), nodule 0.65 (0.61, 0.69), emphysema 0.89 (0.86, 0.92), effusion 0.97 (0.96, 0.98), and no apparent disease 0.89 (0.87, 0.91). AUCs for liver and gallbladder were: hepatobiliary calcification 0.62 (95% CI: 0.56, 0.67), lesion 0.73 (0.69, 0.77), dilation 0.87 (0.84, 0.90), fatty 0.89 (0.86, 0.92), and no apparent disease 0.82 (0.78, 0.85). AUCs for kidneys and ureters were: stone 0.83 (95% CI: 0.79, 0.87), atrophy 0.92 (0.89, 0.94), lesion 0.68 (0.64, 0.72), cyst 0.70 (0.66, 0.73), and no apparent disease 0.79 (0.75, 0.83). Conclusion: Weakly-supervised deep learning models were able to classify diverse diseases in multiple organ systems.

cs.CV↗

arXiv2021

Normalization of breast MRIs using Cycle-Consistent Generative Adversarial Networks

Dynamic Contrast Enhanced-Magnetic Resonance Imaging (DCE-MRI) is widely used to complement ultrasound examinations and x-ray mammography during the early detection and diagnosis of breast cancer. However, images generated by various MRI scanners (e.g. GE Healthcare vs Siemens) differ both in intensity and noise distribution, preventing algorithms trained on MRIs from one scanner to generalize to data from other scanners successfully. We propose a method for image normalization to solve this problem. MRI normalization is challenging because it requires both normalizing intensity values and mapping between the noise distributions of different scanners. We utilize a cycle-consistent generative adversarial network to learn a bidirectional mapping between MRIs produced by GE Healthcare and Siemens scanners. This allows us learning the mapping between two different scanner types without matched data, which is not commonly available. To ensure the preservation of breast shape and structures within the breast, we propose two technical innovations. First, we incorporate a mutual information loss with the CycleGAN architecture to ensure that the structure of the breast is maintained. Second, we propose a modified discriminator architecture which utilizes a smaller field-of-view to ensure the preservation of finer details in the breast tissue. Quantitative and qualitative evaluations show that the second proposed method was able to consistently preserve a high level of detail in the breast structure while also performing the proper intensity normalization and noise mapping. Our results demonstrate that the proposed model can successfully learn a bidirectional mapping between MRIs produced by different vendors, potentially enabling improved accuracy of downstream computational algorithms for diagnosis and detection of breast cancer. All the data used in this study are publicly available.

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arXiv2021

Do We Expect More from Radiology AI than from Radiologists?

What we expect from radiology AI algorithms will shape the selection and implementation of AI in the radiologic practice. In this paper I consider prevailing expectations of AI and compare them to expectations that we have of human readers. I observe that the expectations from AI and radiologists are fundamentally different. The expectations of AI are based on a strong and justified mistrust about the way that AI makes decisions. Because AI decisions are not well understood, it is difficult to know how the algorithms will behave in new, unexpected situations. However, this mistrust is not mirrored in our expectations of human readers. Despite well-proven idiosyncrasies and biases in human decision making, we take comfort from the assumption that others make decisions in a way as we do, and we trust our own decision making. Despite poor ability to explain decision making processes in humans, we accept explanations of decisions given by other humans. Because the goal of radiology is the most accurate radiologic interpretation, our expectations of radiologists and AI should be similar, and both should reflect a healthy mistrust of complicated and partially opaque decision processes undergoing in computer algorithms and human brains. This is generally not the case now.

cs.CY↗

arXiv2020

Weakly Supervised 3D Classification of Chest CT using Aggregated Multi-Resolution Deep Segmentation Features

Weakly supervised disease classification of CT imaging suffers from poor localization owing to case-level annotations, where even a positive scan can hold hundreds to thousands of negative slices along multiple planes. Furthermore, although deep learning segmentation and classification models extract distinctly unique combinations of anatomical features from the same target class(es), they are typically seen as two independent processes in a computer-aided diagnosis (CAD) pipeline, with little to no feature reuse. In this research, we propose a medical classifier that leverages the semantic structural concepts learned via multi-resolution segmentation feature maps, to guide weakly supervised 3D classification of chest CT volumes. Additionally, a comparative analysis is drawn across two different types of feature aggregation to explore the vast possibilities surrounding feature fusion. Using a dataset of 1593 scans labeled on a case-level basis via rule-based model, we train a dual-stage convolutional neural network (CNN) to perform organ segmentation and binary classification of four representative diseases (emphysema, pneumonia/atelectasis, mass and nodules) in lungs. The baseline model, with separate stages for segmentation and classification, results in AUC of 0.791. Using identical hyperparameters, the connected architecture using static and dynamic feature aggregation improves performance to AUC of 0.832 and 0.851, respectively. This study advances the field in two key ways. First, case-level report data is used to weakly supervise a 3D CT classifier of multiple, simultaneous diseases for an organ. Second, segmentation and classification models are connected with two different feature aggregation strategies to enhance the classification performance.

cs.CV↗

arXiv2020

Machine-Learning-Based Multiple Abnormality Prediction with Large-Scale Chest Computed Tomography Volumes

Machine learning models for radiology benefit from large-scale data sets with high quality labels for abnormalities. We curated and analyzed a chest computed tomography (CT) data set of 36,316 volumes from 19,993 unique patients. This is the largest multiply-annotated volumetric medical imaging data set reported. To annotate this data set, we developed a rule-based method for automatically extracting abnormality labels from free-text radiology reports with an average F-score of 0.976 (min 0.941, max 1.0). We also developed a model for multi-organ, multi-disease classification of chest CT volumes that uses a deep convolutional neural network (CNN). This model reached a classification performance of AUROC greater than 0.90 for 18 abnormalities, with an average AUROC of 0.773 for all 83 abnormalities, demonstrating the feasibility of learning from unfiltered whole volume CT data. We show that training on more labels improves performance significantly: for a subset of 9 labels - nodule, opacity, atelectasis, pleural effusion, consolidation, mass, pericardial effusion, cardiomegaly, and pneumothorax - the model's average AUROC increased by 10% when the number of training labels was increased from 9 to all 83. All code for volume preprocessing, automated label extraction, and the volume abnormality prediction model will be made publicly available. The 36,316 CT volumes and labels will also be made publicly available pending institutional approval.

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