Rucha Deshpande

Rucha Deshpande, Muzaffer Özbey, Hua Li et al.

Diffusion models have emerged as a popular family of deep generative models (DGMs). In the literature, it has been claimed that one class of diffusion models -- denoising diffusion probabilistic models (DDPMs) -- demonstrate superior image synthesis performance as compared to generative adversarial networks (GANs). To date, these claims have been evaluated using either ensemble-based methods designed for natural images, or conventional measures of image quality such as structural similarity. However, there remains an important need to understand the extent to which DDPMs can reliably learn medical imaging domain-relevant information, which is referred to as `spatial context' in this work. To address this, a systematic assessment of the ability of DDPMs to learn spatial context relevant to medical imaging applications is reported for the first time. A key aspect of the studies is the use of stochastic context models (SCMs) to produce training data. In this way, the ability of the DDPMs to reliably reproduce spatial context can be quantitatively assessed by use of post-hoc image analyses. Error-rates in DDPM-generated ensembles are reported, and compared to those corresponding to a modern GAN. The studies reveal new and important insights regarding the capacity of DDPMs to learn spatial context. Notably, the results demonstrate that DDPMs hold significant capacity for generating contextually correct images that are `interpolated' between training samples, which may benefit data-augmentation tasks in ways that GANs cannot.

Varun A. Kelkar, Rucha Deshpande, Arindam Banerjee et al.

Generative models have gained popularity for their potential applications in imaging science, such as image reconstruction, posterior sampling and data sharing. Flow-based generative models are particularly attractive due to their ability to tractably provide exact density estimates along with fast, inexpensive and diverse samples. Training such models, however, requires a large, high quality dataset of objects. In applications such as computed imaging, it is often difficult to acquire such data due to requirements such as long acquisition time or high radiation dose, while acquiring noisy or partially observed measurements of these objects is more feasible. In this work, we propose AmbientFlow, a framework for learning flow-based generative models directly from noisy and incomplete data. Using variational Bayesian methods, a novel framework for establishing flow-based generative models from noisy, incomplete data is proposed. Extensive numerical studies demonstrate the effectiveness of AmbientFlow in learning the object distribution. The utility of AmbientFlow in a downstream inference task of image reconstruction is demonstrated.

Rucha Deshpande, Ashish Avachat, Frank J. Brooks et al.

Quantitative phase retrieval (QPR) in propagation-based x-ray phase contrast imaging of heterogeneous and structurally complicated objects is challenging under laboratory conditions due to partial spatial coherence and polychromaticity. A learning-based method (LBM) provides a non-linear approach to this problem while not being constrained by restrictive assumptions about object properties and beam coherence. In this work, a LBM was assessed for its applicability under practical scenarios by evaluating its robustness and generalizability under typical experimental variations. Towards this end, an end-to-end LBM was employed for QPR under laboratory conditions and its robustness was investigated across various system and object conditions. The robustness of the method was tested via varying propagation distances and its generalizability with respect to object structure and experimental data was also tested. Although the LBM was stable under the studied variations, its successful deployment was found to be affected by choices pertaining to data pre-processing, network training considerations and system modeling. To our knowledge, we demonstrated for the first time, the potential applicability of an end-to-end learning-based quantitative phase retrieval method, trained on simulated data, to experimental propagation-based x-ray phase contrast measurements acquired under laboratory conditions. We considered conditions of polychromaticity, partial spatial coherence, and high noise levels, typical to laboratory conditions. This work further explored the robustness of this method to practical variations in propagation distances and object structure with the goal of assessing its potential for experimental use. Such an exploration of any LBM (irrespective of its network architecture) before practical deployment provides an understanding of its potential behavior under experimental settings.

Rucha Deshpande, Tahsin Rahman, Miguel Lago et al.

Synthetic data provides a promising approach to address data scarcity for training machine learning models; however, adoption without proper quality assessments may introduce artifacts, distortions, and unrealistic features that compromise model performance and clinical utility. This work introduces a novel knowledge-based anomaly detection method for detecting network-induced shape artifacts in synthetic images. The introduced method utilizes a two-stage framework comprising (i) a novel feature extractor that constructs a specialized feature space by analyzing the per-image distribution of angle gradients along anatomical boundaries, and (ii) an isolation forest-based anomaly detector. We demonstrate the effectiveness of the method for identifying network-induced shape artifacts in two synthetic mammography datasets from models trained on CSAW-M and VinDr-Mammo patient datasets respectively. Quantitative evaluation shows that the method successfully concentrates artifacts in the most anomalous partition (1st percentile), with AUC values of 0.97 (CSAW-syn) and 0.91 (VMLO-syn). In addition, a reader study involving three imaging scientists confirmed that images identified by the method as containing network-induced shape artifacts were also flagged by human readers with mean agreement rates of 66% (CSAW-syn) and 68% (VMLO-syn) for the most anomalous partition, approximately 1.5-2 times higher than the least anomalous partition. Kendall-Tau correlations between algorithmic and human rankings were 0.45 and 0.43 for the two datasets, indicating reasonable agreement despite the challenging nature of subtle artifact detection. This method is a step forward in the responsible use of synthetic data, as it allows developers to evaluate synthetic images for known anatomic constraints and pinpoint and address specific issues to improve the overall quality of a synthetic dataset.

Rucha Deshpande, Varun A. Kelkar, Dimitrios Gotsis et al.

The findings of the 2023 AAPM Grand Challenge on Deep Generative Modeling for Learning Medical Image Statistics are reported in this Special Report. The goal of this challenge was to promote the development of deep generative models (DGMs) for medical imaging and to emphasize the need for their domain-relevant assessment via the analysis of relevant image statistics. As part of this Grand Challenge, a training dataset was developed based on 3D anthropomorphic breast phantoms from the VICTRE virtual imaging toolbox. A two-stage evaluation procedure consisting of a preliminary check for memorization and image quality (based on the Frechet Inception distance (FID)), and a second stage evaluating the reproducibility of image statistics corresponding to domain-relevant radiomic features was developed. A summary measure was employed to rank the submissions. Additional analyses of submissions was performed to assess DGM performance specific to individual feature families, and to identify various artifacts. 58 submissions from 12 unique users were received for this Challenge. The top-ranked submission employed a conditional latent diffusion model, whereas the joint runners-up employed a generative adversarial network, followed by another network for image superresolution. We observed that the overall ranking of the top 9 submissions according to our evaluation method (i) did not match the FID-based ranking, and (ii) differed with respect to individual feature families. Another important finding from our additional analyses was that different DGMs demonstrated similar kinds of artifacts. This Grand Challenge highlighted the need for domain-specific evaluation to further DGM design as well as deployment. It also demonstrated that the specification of a DGM may differ depending on its intended use.

Jason Granstedt, Prabhat Kc, Rucha Deshpande et al.

Computer methods in medical devices are frequently imperfect and are known to produce errors in clinical or diagnostic tasks. However, when deep learning and data-based approaches yield output that exhibit errors, the devices are frequently said to hallucinate. Drawing from theoretical developments and empirical studies in multiple medical device areas, we introduce a practical and universal definition that denotes hallucinations as a type of error that is plausible and can be either impactful or benign to the task at hand. The definition aims at facilitating the evaluation of medical devices that suffer from hallucinations across product areas. Using examples from imaging and non-imaging applications, we explore how the proposed definition relates to evaluation methodologies and discuss existing approaches for minimizing the prevalence of hallucinations.

Seyed Kahaki, Alexander R. Webber, Ghada Zamzmi et al.

In modern cancer diagnostics, Whole Slide Imaging (WSI) is widely used to digitize tissue specimens for detailed, high-resolution examination; however, other diagnostic approaches, such as liquid biopsy and molecular testing, are also utilized based on the cancer type and clinical context. While WSI has revolutionized digital histopathology by enabling automated, precise analysis, it remains vulnerable to artifacts introduced during slide preparation and scanning. These artifacts can compromise downstream image analysis. To address this challenge, we propose and compare three robust artifact detection approaches for WSIs: (1) a foundation model-based approach (FMA) using a fine-tuned Unified Neural Image (UNI) architecture, (2) a deep learning approach (DLA) built on a ResNet50 backbone, and (3) a knowledge-based approach (KBA) leveraging handcrafted features from texture, color, and frequency-based metrics. The methods target six common artifact types: tissue folds, out-of-focus regions, air bubbles, tissue damage, marker traces, and blood contamination. Evaluations were conducted on 50,000+ image patches from diverse scanners (Hamamatsu, Philips, Leica Aperio AT2) across multiple sites. The FMA achieved the highest patch-wise AUROC of 0.995 (95% CI [0.994, 0.995]), outperforming the ResNet50-based method (AUROC: 0.977, 95% CI [0.977, 0.978]) and the KBA (AUROC: 0.940, 95% CI [0.933, 0.946]). To translate detection into actionable insights, we developed a quality report scorecard that quantifies high-quality patches and visualizes artifact distributions.

Frank J. Brooks, Rucha Deshpande

Super-resolution, in-painting, whole-image generation, unpaired style-transfer, and network-constrained image reconstruction each include an aspect of machine-learned image synthesis where the actual ground truth is not known at time of use. It is generally difficult to quantitatively and authoritatively evaluate the quality of synthetic images; however, in mission-critical biomedical scenarios robust evaluation is paramount. In this work, all practical image-to-image comparisons really are relative qualifications, not absolute difference quantifications; and, therefore, meaningful evaluation of generated image quality can be accomplished using the Tversky Index, which is a well-established measure for assessing perceptual similarity. This evaluation procedure is developed and then demonstrated using multiple image data sets, both real and simulated. The main result is that when the subjectivity and intrinsic deficiencies of any feature-encoding choice are put upfront, Tversky's method leads to intuitive results, whereas traditional methods based on summarizing distances in deep feature spaces do not.

Rucha Deshpande, Mark A. Anastasio, Frank J. Brooks

Deep generative models (DGMs) have the potential to revolutionize diagnostic imaging. Generative adversarial networks (GANs) are one kind of DGM which are widely employed. The overarching problem with deploying GANs, and other DGMs, in any application that requires domain expertise in order to actually use the generated images is that there generally is not adequate or automatic means of assessing the domain-relevant quality of generated images. In this work, we demonstrate several objective tests of images output by two popular GAN architectures. We designed several stochastic context models (SCMs) of distinct image features that can be recovered after generation by a trained GAN. Several of these features are high-order, algorithmic pixel-arrangement rules which are not readily expressed in covariance matrices. We designed and validated statistical classifiers to detect specific effects of the known arrangement rules. We then tested the rates at which two different GANs correctly reproduced the feature context under a variety of training scenarios, and degrees of feature-class similarity. We found that ensembles of generated images can appear largely accurate visually, and show high accuracy in ensemble measures, while not exhibiting the known spatial arrangements. Furthermore, GANs trained on a spectrum of distinct spatial orders did not respect the given prevalence of those orders in the training data. The main conclusion is that SCMs can be engineered to quantify numerous errors, per image, that may not be captured in ensemble statistics but plausibly can affect subsequent use of the GAN-generated images.