We investigate the effectiveness of a simple solution to the common problem of deep learning in medical image analysis with limited quantities of labeled training data. The underlying idea is to assign artificial labels to abundantly available unlabeled medical images and, through a process known as surrogate supervision, pre-train a deep neural network model for the target medical image analysis task lacking sufficient labeled training data. In particular, we employ 3 surrogate supervision schemes, namely rotation, reconstruction, and colorization, in 4 different medical imaging applications representing classification and segmentation for both 2D and 3D medical images. 3 key findings emerge from our research: 1) pre-training with surrogate supervision is effective for small training sets; 2) deep models trained from initial weights pre-trained through surrogate supervision outperform the same models when trained from scratch, suggesting that pre-training with surrogate supervision should be considered prior to training any deep 3D models; 3) pre-training models in the medical domain with surrogate supervision is more effective than transfer learning from an unrelated domain (e.g., natural images), indicating the practical value of abundant unlabeled medical image data.
Self-supervised learning with surrogate supervision is a relatively new trend in computer vision, with promising schemes appearing only in recent years. Consequently, the literature on the effectiveness of surrogate supervision in medical imaging is meager. @cite_5 proposed longitudinal relationships between medical images as the surrogate task to pre-train model weights. To generate surrogate supervision, they assign a label of 1 if two longitudinal studies belong to the same patient and 0 otherwise. @cite_4 used noise removal in small image patches as the surrogate task, wherein the surrogate supervision was created by mapping the patches with user-injected noise to the original clean image patches. @cite_18 used image colorization as the surrogate task, wherein color colonoscopy images are converted to gray-scale and then recovered using a conditional Generative Adversarial Network (GAN).
@cite_5 @cite_18 @cite_4
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We investigate the effectiveness of a simple solution to the common problem of deep learning in medical image analysis with limited quantities of labeled training data. The underlying idea is to assign artificial labels to abundantly available unlabeled medical images and, through a process known as surrogate supervision, pre-train a deep neural network model for the target medical image analysis task lacking sufficient labeled training data. In particular, we employ 3 surrogate supervision schemes, namely rotation, reconstruction, and colorization, in 4 different medical imaging applications representing classification and segmentation for both 2D and 3D medical images. 3 key findings emerge from our research: 1) pre-training with surrogate supervision is effective for small training sets; 2) deep models trained from initial weights pre-trained through surrogate supervision outperform the same models when trained from scratch, suggesting that pre-training with surrogate supervision should be considered prior to training any deep 3D models; 3) pre-training models in the medical domain with surrogate supervision is more effective than transfer learning from an unrelated domain (e.g., natural images), indicating the practical value of abundant unlabeled medical image data. Deep convolutional networks have proven to be very successful in learning task specific features that allow for unprecedented performance on various computer vision tasks. Training of such networks follows mostly the supervised learning paradigm, where sufficiently many input-output pairs are required for training. Acquisition of large training sets is one of the key challenges, when approaching a new task. In this paper, we aim for generic feature learning and present an approach for training a convolutional network using only unlabeled data. To this end, we train the network to discriminate between a set of surrogate classes. Each surrogate class is formed by applying a variety of transformations to a randomly sampled ‘seed’ image patch. In contrast to supervised network training, the resulting feature representation is not class specific. It rather provides robustness to the transformations that have been applied during training. This generic feature representation allows for classification results that outperform the state of the art for unsupervised learning on several popular datasets (STL-10, CIFAR-10, Caltech-101, Caltech-256). While features learned with our approach cannot compete with class specific features from supervised training on a classification task, we show that they are advantageous on geometric matching problems, where they also outperform the SIFT descriptor. In recent years, binary coding techniques are becoming increasingly popular because of their high efficiency in handling large-scale computer vision applications. It has been demonstrated that supervised binary coding techniques that leverage supervised information can significantly enhance the coding quality, and hence greatly benefit visual search tasks. Typically, a modern binary coding method seeks to learn a group of coding functions which compress data samples into binary codes. However, few methods pursued the coding functions such that the precision at the top of a ranking list according to Hamming distances of the generated binary codes is optimized. In this paper, we propose a novel supervised binary coding approach, namely Top Rank Supervised Binary Coding (Top-RSBC), which explicitly focuses on optimizing the precision of top positions in a Hamming-distance ranking list towards preserving the supervision information. The core idea is to train the disciplined coding functions, by which the mistakes at the top of a Hamming-distance ranking list are penalized more than those at the bottom. To solve such coding functions, we relax the original discrete optimization objective with a continuous surrogate, and derive a stochastic gradient descent to optimize the surrogate objective. To further reduce the training time cost, we also design an online learning algorithm to optimize the surrogate objective more efficiently. Empirical studies based upon three benchmark image datasets demonstrate that the proposed binary coding approach achieves superior image search accuracy over the state-of-the-arts. Current methods for training convolutional neural networks depend on large amounts of labeled samples for supervised training. In this paper we present an approach for training a convolutional neural network using only unlabeled data. We train the network to discriminate between a set of surrogate classes. Each surrogate class is formed by applying a variety of transformations to a randomly sampled 'seed' image patch. We find that this simple feature learning algorithm is surprisingly successful when applied to visual object recognition. The feature representation learned by our algorithm achieves classification results matching or outperforming the current state-of-the-art for unsupervised learning on several popular datasets (STL-10, CIFAR-10, Caltech-101). Comparing two images from different views has been a long-standing challenging problem in computer vision, as visual features are not stable under large view point changes. In this paper, given a single input image of an object, we synthesize its features for other views, leveraging an existing modestly-sized 3D model collection of related but not identical objects. To accomplish this, we study the relationship of image patches between different views of the same object, seeking what we call surrogate patches -- patches in one view whose feature content predicts well the features of a patch in another view. Based upon these surrogate relationships, we can create feature sets for all views of the latent object on a per patch basis, providing us an augmented multi-view representation of the object. We provide theoretical and empirical analysis of the feature synthesis process, and evaluate the augmented features in fine-grained image retrieval recognition and instance retrieval tasks. Experimental results show that our synthesized features do enable view-independent comparison between images and perform significantly better than other traditional approaches in this respect. When deep learning is applied to visual object recognition, data augmentation is often used to generate additional training data without extra labeling cost. It helps to reduce overfitting and increase the performance of the algorithm. In this paper we investigate if it is possible to use data augmentation as the main component of an unsupervised feature learning architecture. To that end we sample a set of random image patches and declare each of them to be a separate single-image surrogate class. We then extend these trivial one-element classes by applying a variety of transformations to the initial 'seed' patches. Finally we train a convolutional neural network to discriminate between these surrogate classes. The feature representation learned by the network can then be used in various vision tasks. We find that this simple feature learning algorithm is surprisingly successful, achieving competitive classification results on several popular vision datasets (STL-10, CIFAR-10, Caltech-101). Weakly supervised object detection has attracted extensive research efforts in recent years. Without the need of annotating bounding boxes, the existing methods usually follow a two multi-stage pipeline with an online compulsive stage to extract object proposals, which is an order of magnitude slower than fast fully supervised object detectors such as SSD [31] and YOLO [34]. In this paper, we speedup online weakly supervised object detectors by orders of magnitude by proposing a novel generative adversarial learning paradigm. In the proposed paradigm, the generator is a one-stage object detector to generate bounding boxes from images. To guide the learning of object-level generator, a surrogator is introduced to mine high-quality bounding boxes for training. We further adapt a structural similarity loss in combination with an adversarial loss into the training objective, which solves the challenge that the bounding boxes produced by the surrogator may not well capture their ground truth. Our one-stage detector outperforms all existing schemes in terms of detection accuracy, running at 118 frames per second, which is up to 438A— faster than the state-of-the-art weakly supervised detectors [8, 30, 15, 27, 45]. The code will be available publicly soon. We present a theoretical analysis of supervised ranking, providing necessary and sufficient conditions for the asymptotic consistency of algorithms based on minimizing a surrogate loss function. We show that many commonly used surrogate losses are inconsistent; surprisingly, we show inconsistency even in low-noise settings. We present a new value-regularized linear loss, establish its consistency under reasonable assumptions on noise, and show that it outperforms conventional ranking losses in a collaborative filtering experiment. Learning with non-modular losses is an important problem when sets of predictions are made simultaneously. The main tools for constructing convex surrogate loss functions for set prediction are margin rescaling and slack rescaling. In this work, we show that these strategies lead to tight convex surrogates iff the underlying loss function is increasing in the number of incorrect predictions. However, gradient or cutting-plane computation for these functions is NP-hard for nonsupermodular loss functions. We propose instead a novel convex surrogate loss function for submodular losses, the Lovasz hinge, which leads to O(p log p) complexity with O(p) oracle accesses to the loss function to compute a gradient or cutting-plane. As a result, we have developed the first tractable convex surrogates in the literature for submodular losses. We demonstrate the utility of this novel convex surrogate through a real world image labeling task. Display Omitted De-identification shared task for longitudinal clinical records.Protected Health Information in records replaced with realistic surrogates.First corpus of its kind available for distribution.Used for Track 1 of the 2014 i2b2 UTHealth NLP shared task. The 2014 i2b2 UTHealth natural language processing shared task featured a track focused on the de-identification of longitudinal medical records. For this track, we de-identified a set of 1304 longitudinal medical records describing 296 patients. This corpus was de-identified under a broad interpretation of the HIPAA guidelines using double-annotation followed by arbitration, rounds of sanity checking, and proof reading. The average token-based F1 measure for the annotators compared to the gold standard was 0.927. The resulting annotations were used both to de-identify the data and to set the gold standard for the de-identification track of the 2014 i2b2 UTHealth shared task. All annotated private health information were replaced with realistic surrogates automatically and then read over and corrected manually. The resulting corpus is the first of its kind made available for de-identification research. This corpus was first used for the 2014 i2b2 UTHealth shared task, during which the systems achieved a mean F-measure of 0.872 and a maximum F-measure of 0.964 using entity-based micro-averaged evaluations. Algorithm selection as well as hyperparameter optimization are tedious task that have to be dealt with when applying machine learning to real-world problems. Sequential model-based optimization (SMBO), based on so-called “surrogate models”, has been employed to allow for faster and more direct hyperparameter optimization. A surrogate model is a machine learning regression model which is trained on the meta-level instances in order to predict the performance of an algorithm on a specific data set given the hyperparameter settings and data set descriptors. Gaussian processes, for example, make good surrogate models as they provide probability distributions over labels. Recent work on SMBO also includes meta-data, i.e. observed hyperparameter performances on other data sets, into the process of hyperparameter optimization. This can, for example, be accomplished by learning transfer surrogate models on all available instances of meta-knowledge; however, the increasing amount of meta-information can make Gaussian processes infeasible, as they require the inversion of a large covariance matrix which grows with the number of instances. Consequently, instead of learning a joint surrogate model on all of the meta-data, we propose to learn individual surrogate models on the observations of each data set and then combine all surrogates to a joint one using ensembling techniques. The final surrogate is a weighted sum of all data set specific surrogates plus an additional surrogate that is solely learned on the target observations. Within our framework, any surrogate model can be used and explore Gaussian processes in this scenario. We present two different strategies for finding the weights used in the ensemble: the first is based on a probabilistic product of experts approach, and the second is based on kernel regression. Additionally, we extend the framework to directly estimate the acquisition function in the same setting, using a novel technique which we name the “transfer acquisition function”. In an empirical evaluation including comparisons to the current state-of-the-art on two publicly available meta-data sets, we are able to demonstrate that our proposed approach does not only scale to large meta-data, but also finds the stronger prediction models. Many of the classification algorithms developed in the machine learning literature, including the support vector machine and boosting, can be viewed as minimum contrast methods that minimize a convex surrogate of the 0–1 loss function. The convexity makes these algorithms computationally efficient. The use of a surrogate, however, has statistical consequences that must be balanced against the computational virtues of convexity. To study these issues, we provide a general quantitative relationship between the risk as assessed using the 0–1 loss and the risk as assessed using any nonnegative surrogate loss function. We show that this relationship gives nontrivial upper bounds on excess risk under the weakest possible condition on the loss function—that it satisfies a pointwise form of Fisher consistency for classification. The relationship is based on a simple variational transformation of the loss function that is easy to compute in many applications. We also present a refined version of this result in the... Colorization of grayscale images is a hot topic in computer vision. Previous research mainly focuses on producing a color image to recover the original one in a supervised learning fashion. However, since many colors share the same gray value, an input grayscale image could be diversely colorized while maintaining its reality. In this paper, we design a novel solution for unsupervised diverse colorization. Specifically, we leverage conditional generative adversarial networks to model the distribution of real-world item colors, in which we develop a fully convolutional generator with multi-layer noise to enhance diversity, with multi-layer condition concatenation to maintain reality, and with stride 1 to keep spatial information. With such a novel network architecture, the model yields highly competitive performance on the open LSUN bedroom dataset. The Turing test on 80 humans further indicates our generated color schemes are highly convincible. A major goal of unsupervised learning is to discover data representations that are useful for subsequent tasks, without access to supervised labels during training. Typically, this goal is approached by minimizing a surrogate objective, such as the negative log likelihood of a generative model, with the hope that representations useful for subsequent tasks will arise as a side effect. In this work, we propose instead to directly target a later desired task by meta-learning an unsupervised learning rule, which leads to representations useful for that task. Here, our desired task (meta-objective) is the performance of the representation on semi-supervised classification, and we meta-learn an algorithm -- an unsupervised weight update rule -- that produces representations that perform well under this meta-objective. Additionally, we constrain our unsupervised update rule to a be a biologically-motivated, neuron-local function, which enables it to generalize to novel neural network architectures. We show that the meta-learned update rule produces useful features and sometimes outperforms existing unsupervised learning techniques. We show that the meta-learned unsupervised update rule generalizes to train networks with different widths, depths, and nonlinearities. It also generalizes to train on data with randomly permuted input dimensions and even generalizes from image datasets to a text task. We study consistency properties of surrogate loss functions for general multiclass learning problems, defined by a general multiclass loss matrix. We extend the notion of classification calibration, which has been studied for binary and multiclass 0-1 classification problems (and for certain other specific learning problems), to the general multiclass setting, and derive necessary and sufficient conditions for a surrogate loss to be calibrated with respect to a loss matrix in this setting. We then introduce the notion of convex calibration dimension of a multiclass loss matrix, which measures the smallest 'size' of a prediction space in which it is possible to design a convex surrogate that is calibrated with respect to the loss matrix. We derive both upper and lower bounds on this quantity, and use these results to analyze various loss matrices. In particular, we apply our framework to study various subset ranking losses, and use the convex calibration dimension as a tool to show both the existence and non-existence of various types of convex calibrated surrogates for these losses. Our results strengthen recent results of (2010) and (2012) on the non-existence of certain types of convex calibrated surrogates in subset ranking. We anticipate the convex calibration dimension may prove to be a useful tool in the study and design of surrogate losses for general multiclass learning problems. In this paper, we study the problem of learning image classification models with label noise. Existing approaches depending on human supervision are generally not scalable as manually identifying correct or incorrect labels is time-consuming, whereas approaches not relying on human supervision are scalable but less effective. To reduce the amount of human supervision for label noise cleaning, we introduce CleanNet, a joint neural embedding network, which only requires a fraction of the classes being manually verified to provide the knowledge of label noise that can be transferred to other classes. We further integrate CleanNet and conventional convolutional neural network classifier into one framework for image classification learning. We demonstrate the effectiveness of the proposed algorithm on both of the label noise detection task and the image classification on noisy data task on several large-scale datasets. Experimental results show that CleanNet can reduce label noise detection error rate on held-out classes where no human supervision available by 41.5 compared to current weakly supervised methods. It also achieves 47 of the performance gain of verifying all images with only 3.2 images verified on an image classification task. Source code and dataset will be available at kuanghuei.github.io CleanNetProject. AUC (Area Under ROC Curve) has been an important criterion widely used in diverse learning tasks. To optimize AUC, many learning approaches have been developed, most working with pairwise surrogate losses. Thus, it is important to study the AUC consistency based on minimizing pairwise surrogate losses. In this paper, we introduce the generalized calibration for AUC optimization, and prove that it is a necessary condition for AUC consistency. We then provide a sufficient condition for AUC consistency, and show its usefulness in studying the consistency of various surrogate losses, as well as the invention of new consistent losses. We further derive regret bounds for exponential and logistic losses, and present regret bounds for more general surrogate losses in the realizable setting. Finally, we prove regret bounds that disclose the equivalence between the pairwise exponential loss of AUC and univariate exponential loss of accuracy. Convolutional neural networks (CNNs) are able to model local stationary structures in natural images in a multi-scale fashion, when learning all model parameters with supervision. While excellent performance was achieved for image classification when large amounts of labeled visual data are available, their success for unsupervised tasks such as image retrieval has been moderate so far.Our paper focuses on this latter setting and explores several methods for learning patch descriptors without supervision with application to matching and instance-level retrieval. To that effect, we propose a new family of patch representations, based on the recently introduced convolutional kernel networks. We show that our descriptor, named Patch-CKN, performs better than SIFT as well as other convolutional networks learned by artificially introducing supervision and is significantly faster to train. To demonstrate its effectiveness, we perform an extensive evaluation on standard benchmarks for patch and image retrieval where we obtain state-of-the-art results. We also introduce a new dataset called RomePatches, which allows to simultaneously study descriptor performance for patch and image retrieval. This work provides a unified framework for addressing the problem of visual supervised domain adaptation and generalization with deep models. The main idea is to exploit the Siamese architecture to learn an embedding subspace that is discriminative, and where mapped visual domains are semantically aligned and yet maximally separated. The supervised setting becomes attractive especially when only few target data samples need to be labeled. In this scenario, alignment and separation of semantic probability distributions is difficult because of the lack of data. We found that by reverting to point-wise surrogates of distribution distances and similarities provides an effective solution. In addition, the approach has a high “speed” of adaptation, which requires an extremely low number of labeled target training samples, even one per category can be effective. The approach is extended to domain generalization. For both applications the experiments show very promising results. Performance models have profound impact on hardware-software codesign, architectural explorations, and performance tuning of scientific applications. Developing algebraic performance models is becoming an increasingly challenging task. In such situations, a statistical surrogate-based performance model, fitted to a small number of input-output points obtained from empirical evaluation on the target machine, provides a range of benefits. Accurate surrogates can emulate the output of the expensive empirical evaluation at new inputs and therefore can be used to test and or aid search, compiler, and autotuning algorithms. We present an iterative parallel algorithm that builds surrogate performance models for scientific kernels and workloads on single-core and multicore and multinode architectures. We tailor to our unique parallel environment an active learning heuristic popular in the literature on the sequential design of computer experiments in order to identify the code variants whose evaluations have the best potential to improve the surrogate. We use the proposed approach in a number of case studies to illustrate its effectiveness.