Author
Mert R. Sabuncu
Other affiliations: Massachusetts Institute of Technology, Harvard University
Bio: Mert R. Sabuncu is an academic researcher from Cornell University. The author has contributed to research in topics: Computer science & Convolutional neural network. The author has an hindex of 24, co-authored 118 publications receiving 9297 citations. Previous affiliations of Mert R. Sabuncu include Massachusetts Institute of Technology & Harvard University.
Papers
More filters
••
TL;DR: In this paper, the organization of networks in the human cerebrum was explored using resting-state functional connectivity MRI data from 1,000 subjects and a clustering approach was employed to identify and replicate networks of functionally coupled regions across the cerebral cortex.
Abstract: Information processing in the cerebral cortex involves interactions among distributed areas. Anatomical connectivity suggests that certain areas form local hierarchical relations such as within the visual system. Other connectivity patterns, particularly among association areas, suggest the presence of large-scale circuits without clear hierarchical relations. In this study the organization of networks in the human cerebrum was explored using resting-state functional connectivity MRI. Data from 1,000 subjects were registered using surface-based alignment. A clustering approach was employed to identify and replicate networks of functionally coupled regions across the cerebral cortex. The results revealed local networks confined to sensory and motor cortices as well as distributed networks of association regions. Within the sensory and motor cortices, functional connectivity followed topographic representations across adjacent areas. In association cortex, the connectivity patterns often showed abrupt transitions between network boundaries. Focused analyses were performed to better understand properties of network connectivity. A canonical sensory-motor pathway involving primary visual area, putative middle temporal area complex (MT+), lateral intraparietal area, and frontal eye field was analyzed to explore how interactions might arise within and between networks. Results showed that adjacent regions of the MT+ complex demonstrate differential connectivity consistent with a hierarchical pathway that spans networks. The functional connectivity of parietal and prefrontal association cortices was next explored. Distinct connectivity profiles of neighboring regions suggest they participate in distributed networks that, while showing evidence for interactions, are embedded within largely parallel, interdigitated circuits. We conclude by discussing the organization of these large-scale cerebral networks in relation to monkey anatomy and their potential evolutionary expansion in humans to support cognition.
6,284 citations
••
TL;DR: VoxelMorph promises to speed up medical image analysis and processing pipelines while facilitating novel directions in learning-based registration and its applications and demonstrates that the unsupervised model’s accuracy is comparable to the state-of-the-art methods while operating orders of magnitude faster.
Abstract: We present VoxelMorph, a fast learning-based framework for deformable, pairwise medical image registration. Traditional registration methods optimize an objective function for each pair of images, which can be time-consuming for large datasets or rich deformation models. In contrast to this approach, and building on recent learning-based methods, we formulate registration as a function that maps an input image pair to a deformation field that aligns these images. We parameterize the function via a convolutional neural network (CNN), and optimize the parameters of the neural network on a set of images. Given a new pair of scans, VoxelMorph rapidly computes a deformation field by directly evaluating the function. In this work, we explore two different training strategies. In the first (unsupervised) setting, we train the model to maximize standard image matching objective functions that are based on the image intensities. In the second setting, we leverage auxiliary segmentations available in the training data. We demonstrate that the unsupervised model's accuracy is comparable to state-of-the-art methods, while operating orders of magnitude faster. We also show that VoxelMorph trained with auxiliary data improves registration accuracy at test time, and evaluate the effect of training set size on registration. Our method promises to speed up medical image analysis and processing pipelines, while facilitating novel directions in learning-based registration and its applications. Our code is freely available at this http URL.
860 citations
•
03 Dec 2018TL;DR: In this paper, a theoretically grounded set of noise-robust loss functions that can be seen as a generalization of mean absolute error (MAE) and categorical cross entropy (CCE) loss is proposed.
Abstract: Deep neural networks (DNNs) have achieved tremendous success in a variety of applications across many disciplines. Yet, their superior performance comes with the expensive cost of requiring correctly annotated large-scale datasets. Moreover, due to DNNs' rich capacity, errors in training labels can hamper performance. To combat this problem, mean absolute error (MAE) has recently been proposed as a noise-robust alternative to the commonly-used categorical cross entropy (CCE) loss. However, as we show in this paper, MAE can perform poorly with DNNs and challenging datasets. Here, we present a theoretically grounded set of noise-robust loss functions that can be seen as a generalization of MAE and CCE. Proposed loss functions can be readily applied with any existing DNN architecture and algorithm, while yielding good performance in a wide range of noisy label scenarios. We report results from experiments conducted with CIFAR-10, CIFAR-100 and FASHION-MNIST datasets and synthetically generated noisy labels.
703 citations
••
07 Feb 2018TL;DR: The proposed method uses a spatial transform layer to reconstruct one image from another while imposing smoothness constraints on the registration field, and demonstrates registration accuracy comparable to state-of-the-art 3D image registration, while operating orders of magnitude faster in practice.
Abstract: We present a fast learning-based algorithm for deformable, pairwise 3D medical image registration. Current registration methods optimize an objective function independently for each pair of images, which can be time-consuming for large data. We define registration as a parametric function, and optimize its parameters given a set of images from a collection of interest. Given a new pair of scans, we can quickly compute a registration field by directly evaluating the function using the learned parameters. We model this function using a CNN, and use a spatial transform layer to reconstruct one image from another while imposing smoothness constraints on the registration field. The proposed method does not require supervised information such as ground truth registration fields or anatomical landmarks. We demonstrate registration accuracy comparable to state-of-the-art 3D image registration, while operating orders of magnitude faster in practice. Our method promises to significantly speed up medical image analysis and processing pipelines, while facilitating novel directions in learning-based registration and its applications. Our code is available at https://github.com/balakg/voxelmorph.
549 citations
••
TL;DR: Zhou et al. as mentioned in this paper proposed VoxelMorph, a fast learning-based framework for deformable, pairwise medical image registration, which parameterizes the function via a convolutional neural network and optimizes the parameters of the neural network on a set of images.
Abstract: We present VoxelMorph, a fast learning-based framework for deformable, pairwise medical image registration. Traditional registration methods optimize an objective function for each pair of images, which can be time-consuming for large datasets or rich deformation models. In contrast to this approach and building on recent learning-based methods, we formulate registration as a function that maps an input image pair to a deformation field that aligns these images. We parameterize the function via a convolutional neural network and optimize the parameters of the neural network on a set of images. Given a new pair of scans, VoxelMorph rapidly computes a deformation field by directly evaluating the function. In this paper, we explore two different training strategies. In the first (unsupervised) setting, we train the model to maximize standard image matching objective functions that are based on the image intensities. In the second setting, we leverage auxiliary segmentations available in the training data. We demonstrate that the unsupervised model’s accuracy is comparable to the state-of-the-art methods while operating orders of magnitude faster. We also show that VoxelMorph trained with auxiliary data improves registration accuracy at test time and evaluate the effect of training set size on registration. Our method promises to speed up medical image analysis and processing pipelines while facilitating novel directions in learning-based registration and its applications. Our code is freely available at https://github.com/voxelmorph/voxelmorph .
486 citations
Cited by
More filters
••
[...]
TL;DR: Machine learning addresses many of the same research questions as the fields of statistics, data mining, and psychology, but with differences of emphasis.
Abstract: Machine Learning is the study of methods for programming computers to learn. Computers are applied to a wide range of tasks, and for most of these it is relatively easy for programmers to design and implement the necessary software. However, there are many tasks for which this is difficult or impossible. These can be divided into four general categories. First, there are problems for which there exist no human experts. For example, in modern automated manufacturing facilities, there is a need to predict machine failures before they occur by analyzing sensor readings. Because the machines are new, there are no human experts who can be interviewed by a programmer to provide the knowledge necessary to build a computer system. A machine learning system can study recorded data and subsequent machine failures and learn prediction rules. Second, there are problems where human experts exist, but where they are unable to explain their expertise. This is the case in many perceptual tasks, such as speech recognition, hand-writing recognition, and natural language understanding. Virtually all humans exhibit expert-level abilities on these tasks, but none of them can describe the detailed steps that they follow as they perform them. Fortunately, humans can provide machines with examples of the inputs and correct outputs for these tasks, so machine learning algorithms can learn to map the inputs to the outputs. Third, there are problems where phenomena are changing rapidly. In finance, for example, people would like to predict the future behavior of the stock market, of consumer purchases, or of exchange rates. These behaviors change frequently, so that even if a programmer could construct a good predictive computer program, it would need to be rewritten frequently. A learning program can relieve the programmer of this burden by constantly modifying and tuning a set of learned prediction rules. Fourth, there are applications that need to be customized for each computer user separately. Consider, for example, a program to filter unwanted electronic mail messages. Different users will need different filters. It is unreasonable to expect each user to program his or her own rules, and it is infeasible to provide every user with a software engineer to keep the rules up-to-date. A machine learning system can learn which mail messages the user rejects and maintain the filtering rules automatically. Machine learning addresses many of the same research questions as the fields of statistics, data mining, and psychology, but with differences of emphasis. Statistics focuses on understanding the phenomena that have generated the data, often with the goal of testing different hypotheses about those phenomena. Data mining seeks to find patterns in the data that are understandable by people. Psychological studies of human learning aspire to understand the mechanisms underlying the various learning behaviors exhibited by people (concept learning, skill acquisition, strategy change, etc.).
13,246 citations
01 Jan 2006
TL;DR: Probability distributions of linear models for regression and classification are given in this article, along with a discussion of combining models and combining models in the context of machine learning and classification.
Abstract: Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.
10,141 citations
••
TL;DR: Progress made during the first half of the Human Connectome Project project in refining the methods for data acquisition and analysis provides grounds for optimism that the HCP datasets and associated methods and software will become increasingly valuable resources for characterizing human brain connectivity and function, their relationship to behavior, and their heritability and genetic underpinnings.
4,388 citations
•
3,940 citations