arXiv subjects

Daniel Rubin

Publications and source records attributed to Daniel Rubin.

34 records · Page 2Linked to original sources

arXiv2020

Deep Active Lesion Segmentation

Lesion segmentation is an important problem in computer-assisted diagnosis that remains challenging due to the prevalence of low contrast, irregular boundaries that are unamenable to shape priors. We introduce Deep Active Lesion Segmentation (DALS), a fully automated segmentation framework for that leverages the powerful nonlinear feature extraction abilities of fully Convolutional Neural Networks (CNNs) and the precise boundary delineation abilities of Active Contour Models (ACMs). Our DALS framework benefits from an improved level-set ACM formulation with a per-pixel-parameterized energy functional and a novel multiscale encoder-decoder CNN that learns an initialization probability map along with parameter maps for the ACM. We evaluate our lesion segmentation model on a new Multiorgan Lesion Segmentation (MLS) dataset that contains images of various organs, including brain, liver, and lung, across different imaging modalities---MR and CT. Our results demonstrate favorable performance compared to competing methods, especially for small training datasets. Source code : $\text{https://github.com/ahatamiz/dals}$

eess.IV↗

arXiv2020

Bounding Zolotarev numbers using Faber rational functions

By closely following a construction by Ganelius, we construct Faber rational functions that allow us to derive tight and explicit bounds on Zolotarev numbers. We use our results to bound the singular values of matrices, including complex-valued Cauchy matrices and Vandermonde matrices with nodes inside the unit disk. We construct Faber rational functions using doubly-connected conformal maps and use their zeros and poles to supply shift parameters in the alternating direction implicit method.

math.CV↗

arXiv2020

Random Bundle: Brain Metastases Segmentation Ensembling through Annotation Randomization

We introduce a novel ensembling method, Random Bundle (RB), that improves performance for brain metastases segmentation. We create our ensemble by training each network on our dataset with 50% of our annotated lesions censored out. We also apply a lopsided bootstrap loss to recover performance after inducing an in silico 50% false negative rate and make our networks more sensitive. We improve our network detection of lesions's mAP value by 39% and more than triple the sensitivity at 80% precision. We also show slight improvements in segmentation quality through DICE score. Further, RB ensembling improves performance over baseline by a larger margin than a variety of popular ensembling strategies. Finally, we show that RB ensembling is computationally efficient by comparing its performance to a single network when both systems are constrained to have the same compute.

cs.CV↗

arXiv2020

Brain Metastasis Segmentation Network Trained with Robustness to Annotations with Multiple False Negatives

Deep learning has proven to be an essential tool for medical image analysis. However, the need for accurately labeled input data, often requiring time- and labor-intensive annotation by experts, is a major limitation to the use of deep learning. One solution to this challenge is to allow for use of coarse or noisy labels, which could permit more efficient and scalable labeling of images. In this work, we develop a lopsided loss function based on entropy regularization that assumes the existence of a nontrivial false negative rate in the target annotations. Starting with a carefully annotated brain metastasis lesion dataset, we simulate data with false negatives by (1) randomly censoring the annotated lesions and (2) systematically censoring the smallest lesions. The latter better models true physician error because smaller lesions are harder to notice than the larger ones. Even with a simulated false negative rate as high as 50%, applying our loss function to randomly censored data preserves maximum sensitivity at 97% of the baseline with uncensored training data, compared to just 10% for a standard loss function. For the size-based censorship, performance is restored from 17% with the current standard to 88% with our lopsided bootstrap loss. Our work will enable more efficient scaling of the image labeling process, in parallel with other approaches on creating more efficient user interfaces and tools for annotation.

cs.CV↗

arXiv2019

Handling Missing MRI Input Data in Deep Learning Segmentation of Brain Metastases: A Multi-Center Study

The purpose was to assess the clinical value of a novel DropOut model for detecting and segmenting brain metastases, in which a neural network is trained on four distinct MRI sequences using an input dropout layer, thus simulating the scenario of missing MRI data by training on the full set and all possible subsets of the input data. This retrospective, multi-center study, evaluated 165 patients with brain metastases. A deep learning based segmentation model for automatic segmentation of brain metastases, named DropOut, was trained on multi-sequence MRI from 100 patients, and validated/tested on 10/55 patients. The segmentation results were compared with the performance of a state-of-the-art DeepLabV3 model. The MR sequences in the training set included pre- and post-gadolinium (Gd) T1-weighted 3D fast spin echo, post-Gd T1-weighted inversion recovery (IR) prepped fast spoiled gradient echo, and 3D fluid attenuated inversion recovery (FLAIR), whereas the test set did not include the IR prepped image-series. The ground truth were established by experienced neuroradiologists. The results were evaluated using precision, recall, Dice score, and receiver operating characteristics (ROC) curve statistics, while the Wilcoxon rank sum test was used to compare the performance of the two neural networks. The area under the ROC curve (AUC), averaged across all test cases, was 0.989+-0.029 for the DropOut model and 0.989+-0.023 for the DeepLabV3 model (p=0.62). The DropOut model showed a significantly higher Dice score compared to the DeepLabV3 model (0.795+-0.105 vs. 0.774+-0.104, p=0.017), and a significantly lower average false positive rate of 3.6/patient vs. 7.0/patient (p<0.001) using a 10mm3 lesion-size limit. The DropOut model may facilitate accurate detection and segmentation of brain metastases on a multi-center basis, even when the test cohort is missing MRI input data.

eess.IV↗

arXiv2019

MRI Pulse Sequence Integration for Deep-Learning Based Brain Metastasis Segmentation

Magnetic resonance (MR) imaging is an essential diagnostic tool in clinical medicine. Recently, a variety of deep learning methods have been applied to segmentation tasks in medical images, with promising results for computer-aided diagnosis. For MR images, effectively integrating different pulse sequences is important to optimize performance. However, the best way to integrate different pulse sequences remains unclear. In this study, we evaluate multiple architectural features and characterize their effects in the task of metastasis segmentation. Specifically, we consider (1) different pulse sequence integration schemas, (2) different modes of weight sharing for parallel network branches, and (3) a new approach for enabling robustness to missing pulse sequences. We find that levels of integration and modes of weight sharing that favor low variance work best in our regime of small data (n = 100). By adding an input-level dropout layer, we could preserve the overall performance of these networks while allowing for inference on inputs with missing pulse sequence. We illustrate not only the generalizability of the network but also the utility of this robustness when applying the trained model to data from a different center, which does not use the same pulse sequences. Finally, we apply network visualization methods to better understand which input features are most important for network performance. Together, these results provide a framework for building networks with enhanced robustness to missing data while maintaining comparable performance in medical imaging applications.

eess.IV↗

arXiv2019

Deep Learning for Prostate Pathology

The current study detects different morphologies related to prostate pathology using deep learning models; these models were evaluated on 2,121 hematoxylin and eosin (H&E) stain histology images captured using bright field microscopy, which spanned a variety of image qualities, origins (whole slide, tissue micro array, whole mount, Internet), scanning machines, timestamps, H&E staining protocols, and institutions. For case usage, these models were applied for the annotation tasks in clinician-oriented pathology reports for prostatectomy specimens. The true positive rate (TPR) for slides with prostate cancer was 99.7% by a false positive rate of 0.785%. The F1-scores of Gleason patterns reported in pathology reports ranged from 0.795 to 1.0 at the case level. TPR was 93.6% for the cribriform morphology and 72.6% for the ductal morphology. The correlation between the ground truth and the prediction for the relative tumor volume was 0.987 n. Our models cover the major components of prostate pathology and successfully accomplish the annotation tasks.

q-bio.TO↗

arXiv2019

Cross-Modal Data Programming Enables Rapid Medical Machine Learning

Labeling training datasets has become a key barrier to building medical machine learning models. One strategy is to generate training labels programmatically, for example by applying natural language processing pipelines to text reports associated with imaging studies. We propose cross-modal data programming, which generalizes this intuitive strategy in a theoretically-grounded way that enables simpler, clinician-driven input, reduces required labeling time, and improves with additional unlabeled data. In this approach, clinicians generate training labels for models defined over a target modality (e.g. images or time series) by writing rules over an auxiliary modality (e.g. text reports). The resulting technical challenge consists of estimating the accuracies and correlations of these rules; we extend a recent unsupervised generative modeling technique to handle this cross-modal setting in a provably consistent way. Across four applications in radiography, computed tomography, and electroencephalography, and using only several hours of clinician time, our approach matches or exceeds the efficacy of physician-months of hand-labeling with statistical significance, demonstrating a fundamentally faster and more flexible way of building machine learning models in medicine.

cs.LG↗

arXiv2019

A Deep-learning Approach for Prognosis of Age-Related Macular Degeneration Disease using SD-OCT Imaging Biomarkers

We propose a hybrid sequential deep learning model to predict the risk of AMD progression in non-exudative AMD eyes at multiple timepoints, starting from short-term progression (3-months) up to long-term progression (21-months). Proposed model combines radiomics and deep learning to handle challenges related to imperfect ratio of OCT scan dimension and training cohort size. We considered a retrospective clinical trial dataset that includes 671 fellow eyes with 13,954 dry AMD observations for training and validating the machine learning models on a 10-fold cross validation setting. The proposed RNN model achieved high accuracy (0.96 AUCROC) for the prediction of both short term and long-term AMD progression, and outperformed the traditional random forest model trained. High accuracy achieved by the RNN establishes the ability to identify AMD patients at risk of progressing to advanced AMD at an early stage which could have a high clinical impact as it allows for optimal clinical follow-up, with more frequent screening and potential earlier treatment for those patients at high risk.

q-bio.QM↗

arXiv2017

Asymptotic slopes of the Aubin-Yau functional and calculation of the Donaldson-Futaki invariant

We derive an explicit formula for the asymptotic slope of the Aubin-Yau functional along a Bergman geodesic on a surface of complex dimension 2, extending the work of Phong-Sturm on Riemann surfaces. This is equivalent to an explicit calculation of the Donaldson-Futaki invariant of a test configuration. The slope is given as a rational linear combination of period integrals of rational functions that sum to a rational number. The result gives a way to check directly whether a two dimensional projective variety is K-stable.

math.DG↗

arXiv2017

Optimizing and Visualizing Deep Learning for Benign/Malignant Classification in Breast Tumors

Breast cancer has the highest incidence and second highest mortality rate for women in the US. Our study aims to utilize deep learning for benign/malignant classification of mammogram tumors using a subset of cases from the Digital Database of Screening Mammography (DDSM). Though it was a small dataset from the view of Deep Learning (about 1000 patients), we show that currently state of the art architectures of deep learning can find a robust signal, even when trained from scratch. Using convolutional neural networks (CNNs), we are able to achieve an accuracy of 85% and an ROC AUC of 0.91, while leading hand-crafted feature based methods are only able to achieve an accuracy of 71%. We investigate an amalgamation of architectures to show that our best result is reached with an ensemble of the lightweight GoogLe Nets tasked with interpreting both the coronal caudal view and the mediolateral oblique view, simply averaging the probability scores of both views to make the final prediction. In addition, we have created a novel method to visualize what features the neural network detects for the benign/malignant classification, and have correlated those features with well known radiological features, such as spiculation. Our algorithm significantly improves existing classification methods for mammography lesions and identifies features that correlate with established clinical markers.

cs.CV↗

arXiv2014

The Monge-Ampère Equation with Guillemin Boundary Conditions

Existence and boundary regularity away from the corners are established for two-dimensional Monge-Ampère equations on convex polytopes with Guillemin boundary conditions. An important step is to derive an expansion in terms of functions $y^n$ and $y^n\log y$ for solutions to equations of the form $\det D^2u(x,y) = y^{-1}$ in a half-ball.

math.AP↗

arXiv2013

Likelihood reweighting methods to reduce potential bias in noninferiority trials which rely on historical data to make inference

It is generally believed that bias is minimized in well-controlled randomized clinical trials. However, bias can arise in active controlled noninferiority trials because the inference relies on a previously estimated effect size obtained from a historical trial that may have been conducted for a different population. By implementing a likelihood reweighting method through propensity scoring, a study designed to estimate a treatment effect in one trial population can be used to estimate the treatment effect size in a different target population. We illustrate this method in active controlled noninferiority trials, although it can also be used in other types of studies, such as historically controlled trials, meta-analyses, and comparative effectiveness analyses.

stat.AP↗

arXiv2012

Classification of Hepatic Lesions using the Matching Metric

In this paper we present a methodology of classifying hepatic (liver) lesions using multidimensional persistent homology, the matching metric (also called the bottleneck distance), and a support vector machine. We present our classification results on a dataset of 132 lesions that have been outlined and annotated by radiologists. We find that topological features are useful in the classification of hepatic lesions. We also find that two-dimensional persistent homology outperforms one-dimensional persistent homology in this application.

cs.CV↗

arXiv2012

A Hybrid Method for Distance Metric Learning

We consider the problem of learning a measure of distance among vectors in a feature space and propose a hybrid method that simultaneously learns from similarity ratings assigned to pairs of vectors and class labels assigned to individual vectors. Our method is based on a generative model in which class labels can provide information that is not encoded in feature vectors but yet relates to perceived similarity between objects. Experiments with synthetic data as well as a real medical image retrieval problem demonstrate that leveraging class labels through use of our method improves retrieval performance significantly.

cs.LG↗

arXiv2008

Computing points of small height for cubic polynomials

Let f in Q[z] be a polynomial of degree d at least two. The associated canonical height \hat{h}_f is a certain real-valued function on Q that returns zero precisely at preperiodic rational points of f. Morton and Silverman conjectured in 1994 that the number of such points is bounded above by a constant depending only on d. A related conjecture claims that at non-preperiodic rational points, \hat{h}_f is bounded below by a positive constant (depending only on d) times some kind of height of f itself. In this paper, we provide support for these conjectures in the case d=3 by computing the set of small height points for several billion cubic polynomials.

math.NT↗