Minimally invasive surgeries and related applications demand surgical tool classification and segmentation at the instance level. Surgical tools are similar in appearance and are long, thin, and handled at an angle. The fine-tuning of state-of-the-art (SOTA) instance segmentation models trained on natural images for instrument segmentation has difficulty discriminating instrument classes. Our research demonstrates that while the bounding box and segmentation mask are often accurate, the classification head mis-classifies the class label of the surgical instrument. We present a new neural network framework that adds a classification module as a new stage to existing instance segmentation models. This module specializes in improving the classification of instrument masks generated by the existing model. The module comprises multi-scale mask attention, which attends to the instrument region and masks the distracting background features. We propose training our classifier module using metric learning with arc loss to handle low inter-class variance of surgical instruments. We conduct exhaustive experiments on the benchmark datasets EndoVis2017 and EndoVis2018. We demonstrate that our method outperforms all (more than 18) SOTA methods compared with, and improves the SOTA performance by at least 12 points (20%) on the EndoVis2017 benchmark challenge and generalizes effectively across the datasets.

Deep learning (DL) models have provided state-of-the-art performance in various medical imaging benchmarking challenges, including the Brain Tumor Segmentation (BraTS) challenges. However, the task of focal pathology multi-compartment segmentation (e.g., tumor and lesion sub-regions) is particularly challenging, and potential errors hinder translating DL models into clinical workflows. Quantifying the reliability of DL model predictions in the form of uncertainties could enable clinical review of the most uncertain regions, thereby building trust and paving the way toward clinical translation. Several uncertainty estimation methods have recently been introduced for DL medical image segmentation tasks. Developing scores to evaluate and compare the performance of uncertainty measures will assist the end-user in making more informed decisions. In this study, we explore and evaluate a score developed during the BraTS 2019 and BraTS 2020 task on uncertainty quantification (QU-BraTS) and designed to assess and rank uncertainty estimates for brain tumor multi-compartment segmentation. This score (1) rewards uncertainty estimates that produce high confidence in correct assertions and those that assign low confidence levels at incorrect assertions, and (2) penalizes uncertainty measures that lead to a higher percentage of under-confident correct assertions. We further benchmark the segmentation uncertainties generated by 14 independent participating teams of QU-BraTS 2020, all of which also participated in the main BraTS segmentation task. Overall, our findings confirm the importance and complementary value that uncertainty estimates provide to segmentation algorithms, highlighting the need for uncertainty quantification in medical image analyses.

Deep Neural Networks (DNNs) are often criticized for being susceptible to adversarial attacks. Most successful defense strategies adopt adversarial training or random input transformations that typically require retraining or fine-tuning the model to achieve reasonable performance. In this work, our investigations of intermediate representations of a pre-trained DNN lead to an interesting discovery pointing to intrinsic robustness to adversarial attacks. We find that we can learn a generative classifier by statistically characterizing the neural response of an intermediate layer to clean training samples. The predictions of multiple such intermediate-layer based classifiers, when aggregated, show unexpected robustness to adversarial attacks. Specifically, we devise an ensemble of these generative classifiers that rank-aggregates their predictions via a Borda count-based consensus. Our proposed approach uses a subset of the clean training data and a pre-trained model, and yet is agnostic to network architectures or the adversarial attack generation method. We show extensive experiments to establish that our defense strategy achieves state-of-the-art performance on the ImageNet validation set.

Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e. 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that undergone gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset.