Foreground object segmentation is a critical step for many image analysis tasks. While automated methods can produce high-quality results, their failures disappoint users in need of practical solutions. We propose a resource allocation framework for predicting how best to allocate a fixed budget of human annotation effort in order to collect higher quality segmentations for a given batch of images and automated methods. The framework is based on a prediction module that estimates the quality of given algorithm-drawn segmentations. We demonstrate the value of the framework for two novel tasks related to predicting how to distribute annotation efforts between algorithms and humans. Specifically, we develop two systems that automatically decide, for a batch of images, when to recruit humans versus computers to create (1) coarse segmentations required to initialize segmentation tools and (2) final, fine-grained segmentations. Experiments demonstrate the advantage of relying on a mix of human and computer efforts over relying on either resource alone for segmenting objects in images coming from three diverse modalities (visible, phase contrast microscopy, and fluorescence microscopy).
Our prediction framework most closely aligns with methods that predict the error quality of a given algorithm-drawn segmentation in absolute terms @cite_13 @cite_12 . In particular, we also perform supervised learning to train a regression model. However, prior work trained prediction models using segmentations created by a single popular algorithm (coming from the medical @cite_12 and computer vision @cite_13 communities respectively). In contrast, our model is trained using a diversity of popular algorithms from different communities applied to images coming from three imaging modalities (visible, phase contrast microscopy, fluorescence microscopy). Specifically, we populate our training data with 14 algorithm-generated segmentation algorithms per image as well as ground truth data to capture a rich diversity of the possible quality of segmentations. Our approach consistently predicts well, outperforming a widely-used method @cite_13 on four diverse datasets. Our experiments demonstrate the value of our prediction model for intelligently deciding which among multiple segmentation algorithms is preferable for each image.
@cite_13 @cite_12
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We present an adversarial domain adaptation based deep learning approach for automatic tumor segmentation from T2-weighted MRI. Our approach is composed of two steps: (i) a tumor-aware unsupervised cross-domain adaptation (CT to MRI), followed by (ii) semi-supervised tumor segmentation using Unet trained with synthesized and limited number of original MRIs. We introduced a novel target specific loss, called tumor-aware loss, for unsupervised cross-domain adaptation that helps to preserve tumors on synthesized MRIs produced from CT images. In comparison, state-of-the art adversarial networks trained without our tumor-aware loss produced MRIs with ill-preserved or missing tumors. All networks were trained using labeled CT images from 377 patients with non-small cell lung cancer obtained from the Cancer Imaging Archive and unlabeled T2w MRIs from a completely unrelated cohort of 6 patients with pre-treatment and 36 on-treatment scans. Next, we combined 6 labeled pre-treatment MRI scans with the synthesized MRIs to boost tumor segmentation accuracy through semi-supervised learning. Semi-supervised training of cycle-GAN produced a segmentation accuracy of 0.66 computed using Dice Score Coefficient (DSC). Our method trained with only synthesized MRIs produced an accuracy of 0.74 while the same method trained in semi-supervised setting produced the best accuracy of 0.80 on test. Our results show that tumor-aware adversarial domain adaptation helps to achieve reasonably accurate cancer segmentation from limited MRI data by leveraging large CT datasets. Many structured prediction tasks in machine vision have a collection of acceptable answers, instead of one definitive ground truth answer. Segmentation of images, for example, is subject to human labeling bias. Similarly, there are multiple possible pixel values that could plausibly complete occluded image regions. State-of-the art supervised learning methods are typically optimized to make a single test-time prediction for each query, failing to find other modes in the output space. Existing methods that allow for sampling often sacrifice speed or accuracy. We introduce a simple method for training a neural network, which enables diverse structured predictions to be made for each test-time query. For a single input, we learn to predict a range of possible answers. We compare favorably to methods that seek diversity through an ensemble of networks. Such stochastic multiple choice learning faces mode collapse, where one or more ensemble members fail to receive any training signal. Our best performing solution can be deployed for various tasks, and just involves small modifications to the existing single-mode architecture, loss function, and training regime. We demonstrate that our method results in quantitative improvements across three challenging tasks: 2D image completion, 3D volume estimation, and flow prediction. Our objective is to evaluate the efficacy of methods that use deep learning (DL) for the automatic fine-grained segmentation of optical coherence tomography (OCT) images of the retina. OCT images from 10 patients with mild non-proliferative diabetic retinopathy were used from a public (U. of Miami) dataset. For each patient, five images were available: one image of the fovea center, two images of the perifovea, and two images of the parafovea. For each image, two expert graders each manually annotated five retinal surfaces (i.e. boundaries between pairs of retinal layers). The first grader's annotations were used as ground truth and the second grader's annotations to compute inter-operator agreement. The proposed automated approach segments images using fully convolutional networks (FCNs) together with Gaussian process (GP)-based regression as a post-processing step to improve the quality of the estimates. Using 10-fold cross validation, the performance of the algorithms is determined by computing the per-pixel unsigned error (distance) between the automated estimates and the ground truth annotations generated by the first manual grader. We compare the proposed method against five state of the art automatic segmentation techniques. The results show that the proposed methods compare favorably with state of the art techniques, resulting in the smallest mean unsigned error values and associated standard deviations, and performance is comparable with human annotation of retinal layers from OCT when there is only mild retinopathy. The results suggest that semantic segmentation using FCNs, coupled with regression-based post-processing, can effectively solve the OCT segmentation problem on par with human capabilities with mild retinopathy. We address the task of learning a semantic segmentation from weakly supervised data. Our aim is to devise a system that predicts an object label for each pixel by making use of only image level labels during training – the information whether a certain object is present or not in the image. Such coarse tagging of images is faster and easier to obtain as opposed to the tedious task of pixelwise labeling required in state of the art systems. We cast this task naturally as a multiple instance learning (MIL) problem. We use Semantic Texton Forest (STF) as the basic framework and extend it for the MIL setting. We make use of multitask learning (MTL) to regularize our solution. Here, an external task of geometric context estimation is used to improve on the task of semantic segmentation. We report experimental results on the MSRC21 and the very challenging VOC2007 datasets. On MSRC21 dataset we are able, by using 276 weakly labeled images, to achieve the performance of a supervised STF trained on pixelwise labeled training set of 56 images, which is a significant reduction in supervision needed.