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Alireza Mehrtash

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3 papers

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JBHI Journal 2023 Journal Article

Deep Learning for Detection and Localization of B-Lines in Lung Ultrasound

Ruben T. Lucassen
Mohammad H. Jafari
Nicole M. Duggan
Nick Jowkar
Alireza Mehrtash
Chanel Fischetti
Denie Bernier
Kira Prentice

Lung ultrasound (LUS) is an important imaging modality used by emergency physicians to assess pulmonary congestion at the patient bedside. B-line artifacts in LUS videos are key findings associated with pulmonary congestion. Not only can the interpretation of LUS be challenging for novice operators, but visual quantification of B-lines remains subject to observer variability. In this work, we investigate the strengths and weaknesses of multiple deep learning approaches for automated B-line detection and localization in LUS videos. We curate and publish, BEDLUS, a new ultrasound dataset comprising 1, 419 videos from 113 patients with a total of 15, 755 expert-annotated B-lines. Based on this dataset, we present a benchmark of established deep learning methods applied to the task of B-line detection. To pave the way for interpretable quantification of B-lines, we propose a novel “single-point” approach to B-line localization using only the point of origin. Our results show that (a) the area under the receiver operating characteristic curve ranges from 0. 864 to 0. 955 for the benchmarked detection methods, (b) within this range, the best performance is achieved by models that leverage multiple successive frames as input, and (c) the proposed single-point approach for B-line localization reaches an F $_{1}$ -score of 0. 65, performing on par with the inter-observer agreement. The dataset and developed methods can facilitate further biomedical research on automated interpretation of lung ultrasound with the potential to expand the clinical utility.

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NeurIPS Conference 2020 Conference Paper

PEP: Parameter Ensembling by Perturbation

Alireza Mehrtash
Purang Abolmaesumi
Polina Golland
Tina Kapur
Demian Wassermann
William Wells

Ensembling is now recognized as an effective approach for increasing the predictive performance and calibration of deep networks. We introduce a new approach, Parameter Ensembling by Perturbation (PEP), that constructs an ensemble of parameter values as random perturbations of the optimal parameter set from training by a Gaussian with a single variance parameter. The variance is chosen to maximize the log-likelihood of the ensemble average (𝕃) on the validation data set. Empirically, and perhaps surprisingly, 𝕃 has a well-defined maximum as the variance grows from zero (which corresponds to the baseline model). Conveniently, calibration level of predictions also tends to grow favorably until the peak of 𝕃 is reached. In most experiments, PEP provides a small improvement in performance, and, in some cases, a substantial improvement in empirical calibration. We show that this "PEP effect'' (the gain in log-likelihood) is related to the mean curvature of the likelihood function and the empirical Fisher information. Experiments on ImageNet pre-trained networks including ResNet, DenseNet, and Inception showed improved calibration and likelihood. We further observed a mild improvement in classification accuracy on these networks. Experiments on classification benchmarks such as MNIST and CIFAR-10 showed improved calibration and likelihood, as well as the relationship between the PEP effect and overfitting; this demonstrates that PEP can be used to probe the level of overfitting that occurred during training. In general, no special training procedure or network architecture is needed, and in the case of pre-trained networks, no additional training is needed.

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YNICL Journal 2015 Journal Article

Reconstruction of the arcuate fasciculus for surgical planning in the setting of peritumoral edema using two-tensor unscented Kalman filter tractography

Zhenrui Chen
Yanmei Tie
Olutayo Olubiyi
Laura Rigolo
Alireza Mehrtash
Isaiah Norton
Ofer Pasternak
Yogesh Rathi

BACKGROUND: Diffusion imaging tractography is increasingly used to trace critical fiber tracts in brain tumor patients to reduce the risk of post-operative neurological deficit. However, the effects of peritumoral edema pose a challenge to conventional tractography using the standard diffusion tensor model. The aim of this study was to present a novel technique using a two-tensor unscented Kalman filter (UKF) algorithm to track the arcuate fasciculus (AF) in brain tumor patients with peritumoral edema. METHODS: Ten right-handed patients with left-sided brain tumors in the vicinity of language-related cortex and evidence of significant peritumoral edema were retrospectively selected for the study. All patients underwent 3-Tesla magnetic resonance imaging (MRI) including a diffusion-weighted dataset with 31 directions. Fiber tractography was performed using both single-tensor streamline and two-tensor UKF tractography. A two-regions-of-interest approach was applied to perform the delineation of the AF. Results from the two different tractography algorithms were compared visually and quantitatively. RESULTS: Using single-tensor streamline tractography, the AF appeared disrupted in four patients and contained few fibers in the remaining six patients. Two-tensor UKF tractography delineated an AF that traversed edematous brain areas in all patients. The volume of the AF was significantly larger on two-tensor UKF than on single-tensor streamline tractography (p < 0.01). CONCLUSIONS: Two-tensor UKF tractography provides the ability to trace a larger volume AF than single-tensor streamline tractography in the setting of peritumoral edema in brain tumor patients.

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