Michael A. Jacobs

Vishwa S Parekh, Shuhao Lai, Vladimir Braverman et al.

Federated learning is increasingly being explored in the field of medical imaging to train deep learning models on large scale datasets distributed across different data centers while preserving privacy by avoiding the need to transfer sensitive patient information. In this manuscript, we explore federated learning in a multi-domain, multi-task setting wherein different participating nodes may contain datasets sourced from different domains and are trained to solve different tasks. We evaluated cross-domain federated learning for the tasks of object detection and segmentation across two different experimental settings: multi-modal and multi-organ. The result from our experiments on cross-domain federated learning framework were very encouraging with an overlap similarity of 0.79 for organ localization and 0.65 for lesion segmentation. Our results demonstrate the potential of federated learning in developing multi-domain, multi-task deep learning models without sharing data from different domains.

Alex E. Bocchieri, Vishwa S. Parekh, Kathryn R. Wagner. Shivani Ahlawat et al.

A current clinical challenge is identifying limb girdle muscular dystrophy 2I(LGMD2I)tissue changes in the thighs, in particular, separating fat, fat-infiltrated muscle, and muscle tissue. Deep learning algorithms have the ability to learn different features by using the inherent tissue contrasts from multiparametric magnetic resonance imaging (mpMRI). To that end, we developed a novel multiparametric deep learning network (MPDL) tissue signature model based on mpMRI and applied it to LGMD2I. We demonstrate a new tissue signature model of muscular dystrophy with the MPDL algorithm segments different tissue types with excellent results.

Vishwa S. Parekh, John Laterra, Chetan Bettegowda et al.

Radiomics is an exciting new area of texture research for extracting quantitative and morphological characteristics of pathological tissue. However, to date, only single images have been used for texture analysis. We have extended radiomic texture methods to use multiparametric (mp) data to get more complete information from all the images. These mpRadiomic methods could potentially provide a platform for stratification of tumor grade as well as assessment of treatment response in brain tumors. In brain, multiparametric MRI (mpMRI) are based on contrast enhanced T1-weighted imaging (T1WI), T2WI, Fluid Attenuated Inversion Recovery (FLAIR), Diffusion Weighted Imaging (DWI) and Perfusion Weighted Imaging (PWI). Therefore, we applied our multiparametric radiomic framework (mpRadiomic) on 24 patients with brain tumors (8 grade II and 16 grade IV). The mpRadiomic framework classified grade IV tumors from grade II tumors with a sensitivity and specificity of 93% and 100%, respectively, with an AUC of 0.95. For treatment response, the mpRadiomic framework classified pseudo-progression from true-progression with an AUC of 0.93. In conclusion, the mpRadiomic analysis was able to effectively capture the multiparametric brain MRI texture and could be used as potential biomarkers for distinguishing grade IV from grade II tumors as well as determining true-progression from pseudo-progression.

Michael A. Jacobs, Christopher Umbricht, Vishwa Parekh et al.

Purpose-Optimal use of established and imaging methods, such as multiparametric magnetic resonance imaging(mpMRI) can simultaneously identify key functional parameters and provide unique imaging phenotypes of breast cancer. Therefore, we have developed and implemented a new machine-learning informatic system that integrates clinical variables, derived from imaging and clinical health records, to compare with the 21-gene array assay, OncotypeDX. Materials and methods-We tested our informatics modeling in a subset of patients (n=81) who had ER+ disease and underwent OncotypeDX gene expression and breast mpMRI testing. The machine-learning informatic method is termed Integrated Radiomic Informatic System-IRIS was applied to the mpMRI, clinical and pathologic descriptors, as well as a gene array analysis. The IRIS method using an advanced graph theoretic model and quantitative metrics. Summary statistics (mean and standard deviations) for the quantitative imaging parameters were obtained. Sensitivity and specificity and Area Under the Curve were calculated for the classification of the patients. Results-The OncotypeDX classification by IRIS model had sensitivity of 95% and specificity of 89% with AUC of 0.92. The breast lesion size was larger for the high-risk groups and lower for both low risk and intermediate risk groups. There were significant differences in PK-DCE and ADC map values in each group. The ADC map values for high- and intermediate-risk groups were significantly lower than the low-risk group. Conclusion-These initial studies provide deeper understandings of imaging features and molecular gene array OncotypeDX score. This insight provides the foundation to relate these imaging features to the assessment of treatment response for improved personalized medicine.

Vishwa S. Parekh, Michael A. Jacobs

Radiomics is a rapidly growing field that deals with modeling the textural information present in the different tissues of interest for clinical decision support. However, the process of generating radiomic images is computationally very expensive and could take substantial time per radiological image for certain higher order features, such as, gray-level co-occurrence matrix(GLCM), even with high-end GPUs. To that end, we developed RadSynth, a deep convolutional neural network(CNN) model, to efficiently generate radiomic images. RadSynth was tested on a breast cancer patient cohort of twenty-four patients(ten benign, ten malignant and four normal) for computation of GLCM entropy images from post-contrast DCE-MRI. RadSynth produced excellent synthetic entropy images compared to traditional GLCM entropy images. The average percentage difference and correlation between the two techniques were 0.07 $\pm$ 0.06 and 0.97, respectively. In conclusion, RadSynth presents a new powerful tool for fast computation and visualization of the textural information present in the radiological images.

Vishwa S. Parekh, Michael A. Jacobs

Multiparametric radiological imaging is vital for detection, characterization and diagnosis of many different diseases. The use of radiomics for quantitative extraction of textural features from radiological imaging is increasing moving towards clinical decision support. However, current methods in radiomics are limited to using single images for the extraction of these textural features and may limit the applicable scope of radiomics in different clinical settings. Thus, in the current form, they are not capable of capturing the true underlying tissue characteristics in high dimensional multiparametric imaging space. To overcome this challenge, we have developed a multiparametric imaging radiomic framework termed MPRAD for extraction of radiomic features from high dimensional datasets. MPRAD was tested on two different organs and diseases; breast cancer and cerebrovascular accidents in brain, commonly referred to as stroke. The MPRAD framework classified malignant from benign breast lesions with excellent sensitivity and specificity of 87% and 80.5% respectively with an AUC of 0.88 providing a 9%-28% increase in AUC over single radiomic parameters. More importantly, in breast, the glandular tissue MPRAD were similar between each group with no significance differences. Similarly, the MPRAD features in brain stroke demonstrated increased performance in distinguishing the perfusion-diffusion mismatch compared to single parameter radiomics and there were no differences within the white and gray matter tissue. In conclusion, we have introduced the use of multiparametric radiomics into a clinical setting

Sanghyun Choi, Nikita Ivkin, Vladimir Braverman et al.

Extracting information from electronic health records (EHR) is a challenging task since it requires prior knowledge of the reports and some natural language processing algorithm (NLP). With the growing number of EHR implementations, such knowledge is increasingly challenging to obtain in an efficient manner. We address this challenge by proposing a novel methodology to analyze large sets of EHRs using a modified Count Sketch data streaming algorithm termed DreamNLP. By using DreamNLP, we generate a dictionary of frequently occurring terms or heavy hitters in the EHRs using low computational memory compared to conventional counting approach other NLP programs use. We demonstrate the extraction of the most important breast diagnosis features from the EHRs in a set of patients that underwent breast imaging. Based on the analysis, extraction of these terms would be useful for defining important features for downstream tasks such as machine learning for precision medicine.

Vishwa S. Parekh, Katarzyna J. Macura, Susan Harvey et al.

A new paradigm is beginning to emerge in Radiology with the advent of increased computational capabilities and algorithms. This has led to the ability of real time learning by computer systems of different lesion types to help the radiologist in defining disease. For example, using a deep learning network, we developed and tested a multiparametric deep learning (MPDL) network for segmentation and classification using multiparametric magnetic resonance imaging (mpMRI) radiological images. The MPDL network was constructed from stacked sparse autoencoders with inputs from mpMRI. Evaluation of MPDL consisted of cross-validation, sensitivity, and specificity. Dice similarity between MPDL and post-DCE lesions were evaluated. We demonstrate high sensitivity and specificity for differentiation of malignant from benign lesions of 90% and 85% respectively with an AUC of 0.93. The Integrated MPDL method accurately segmented and classified different breast tissue from multiparametric breast MRI using deep leaning tissue signatures.