Semixup: In- and Out-of-Manifold Regularization for Deep Semi-Supervised Knee Osteoarthritis Severity Grading from Plain Radiographs

Knee osteoarthritis (OA) is one of the highest disability factors in the world in humans. This musculoskeletal disorder is assessed from clinical symptoms, and typically confirmed via radiographic assessment. This visual assessment done by a radiologist requires experience, and suffers from high inter-observer variability. The recent development in the literature has shown that deep learning (DL) methods can reliably perform the OA severity assessment according to the gold standard Kellgren-Lawrence (KL) grading system. However, these methods require large amounts of labeled data, which are costly to obtain. In this study, we propose the Semixup algorithm, a semi-supervised learning (SSL) approach to leverage unlabeled data. Semixup relies on consistency regularization using in- and out-of-manifold samples, together with interpolated consistency. On an independent test set, our method significantly outperformed other state-of-the-art SSL methods in most cases, and even achieved a comparable performance to a well-tuned fully supervised learning (SL) model that required over 12 times more labeled data.

Optimizing the Dice Score and Jaccard Index for Medical Image Segmentation: Theory & Practice

The Dice score and Jaccard index are commonly used metrics for the evaluation of segmentation tasks in medical imaging. Convolutional neural networks trained for image segmentation tasks are usually optimized for (weighted) cross-entropy. This introduces an adverse discrepancy between the learning optimization objective (the loss) and the end target metric. Recent works in computer vision have proposed soft surrogates to alleviate this discrepancy and directly optimize the desired metric, either through relaxations (soft-Dice, soft-Jaccard) or submodular optimization (Lov\'asz-softmax). The aim of this study is two-fold. First, we investigate the theoretical differences in a risk minimization framework and question the existence of a weighted cross-entropy loss with weights theoretically optimized to surrogate Dice or Jaccard. Second, we empirically investigate the behavior of the aforementioned loss functions w.r.t. evaluation with Dice score and Jaccard index on five medical segmentation tasks. Through the application of relative approximation bounds, we show that all surrogates are equivalent up to a multiplicative factor, and that no optimal weighting of cross-entropy exists to approximate Dice or Jaccard measures. We validate these findings empirically and show that, while it is important to opt for one of the target metric surrogates rather than a cross-entropy-based loss, the choice of the surrogate does not make a statistical difference on a wide range of medical segmentation tasks.

Generating superpixels using deep image representations

Superpixel algorithms are a common pre-processing step for computer vision algorithms such as segmentation, object tracking and localization. Many superpixel methods only rely on colors features for segmentation, limiting performance in low-contrast regions and applicability to infrared or medical images where object boundaries have wide appearance variability. We study the inclusion of deep image features in the SLIC superpixel algorithm to exploit higher-level image representations. In addition, we devise a trainable superpixel algorithm, yielding an intermediate domain-specific image representation that can be applied to different tasks. A clustering-based superpixel algorithm is transformed into a pixel-wise classification task and superpixel training data is derived from semantic segmentation datasets. Our results demonstrate that this approach is able to improve superpixel quality consistently.

Scattering Networks for Hybrid Representation Learning

Scattering networks are a class of designed Convolutional Neural Networks (CNNs) with fixed weights. We argue they can serve as generic representations for modelling images. In particular, by working in scattering space, we achieve competitive results both for supervised and unsupervised learning tasks, while making progress towards constructing more interpretable CNNs. For supervised learning, we demonstrate that the early layers of CNNs do not necessarily need to be learned, and can be replaced with a scattering network instead. Indeed, using hybrid architectures, we achieve the best results with predefined representations to-date, while being competitive with end-to-end learned CNNs. Specifically, even applying a shallow cascade of small-windowed scattering coefficients followed by 1$\times$1-convolutions results in AlexNet accuracy on the ILSVRC2012 classification task. Moreover, by combining scattering networks with deep residual networks, we achieve a single-crop top-5 error of 11.4% on ILSVRC2012. Also, we show they can yield excellent performance in the small sample regime on CIFAR-10 and STL-10 datasets, exceeding their end-to-end counterparts, through their ability to incorporate geometrical priors. For unsupervised learning, scattering coefficients can be a competitive representation that permits image recovery. We use this fact to train hybrid GANs to generate images. Finally, we empirically analyze several properties related to stability and reconstruction of images from scattering coefficients.

Learning to Discover Sparse Graphical Models

We consider structure discovery of undirected graphical models from observational data. Inferring likely structures from few examples is a complex task often requiring the formulation of priors and sophisticated inference procedures. Popular methods rely on estimating a penalized maximum likelihood of the precision matrix. However, in these approaches structure recovery is an indirect consequence of the data-fit term, the penalty can be difficult to adapt for domain-specific knowledge, and the inference is computationally demanding. By contrast, it may be easier to generate training samples of data that arise from graphs with the desired structure properties. We propose here to leverage this latter source of information as training data to learn a function, parametrized by a neural network that maps empirical covariance matrices to estimated graph structures. Learning this function brings two benefits: it implicitly models the desired structure or sparsity properties to form suitable priors, and it can be tailored to the specific problem of edge structure discovery, rather than maximizing data likelihood. Applying this framework, we find our learnable graph-discovery method trained on synthetic data generalizes well: identifying relevant edges in both synthetic and real data, completely unknown at training time. We find that on genetics, brain imaging, and simulation data we obtain performance generally superior to analytical methods.

The Lovász Hinge: A Novel Convex Surrogate for Submodular Losses

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 non-supermodular loss functions. We propose instead a novel surrogate loss function for submodular losses, the Lov\'asz 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. We prove that the Lov\'asz hinge is convex and yields an extension. 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 several set prediction tasks, including on the PASCAL VOC and Microsoft COCO datasets.

A Convex Surrogate Operator for General Non-Modular Loss Functions

Empirical risk minimization frequently employs convex surrogates to underlying discrete loss functions in order to achieve computational tractability during optimization. However, classical convex surrogates can only tightly bound modular loss functions, sub-modular functions or supermodular functions separately while maintaining polynomial time computation. In this work, a novel generic convex surrogate for general non-modular loss functions is introduced, which provides for the first time a tractable solution for loss functions that are neither super-modular nor submodular. This convex surro-gate is based on a submodular-supermodular decomposition for which the existence and uniqueness is proven in this paper. It takes the sum of two convex surrogates that separately bound the supermodular component and the submodular component using slack-rescaling and the Lov{\'a}sz hinge, respectively. It is further proven that this surrogate is convex , piecewise linear, an extension of the loss function, and for which subgradient computation is polynomial time. Empirical results are reported on a non-submodular loss based on the S{{\o}}rensen-Dice difference function, and a real-world face track dataset with tens of thousands of frames, demonstrating the improved performance, efficiency, and scalabil-ity of the novel convex surrogate.

A U-statistic Approach to Hypothesis Testing for Structure Discovery in Undirected Graphical Models

Structure discovery in graphical models is the determination of the topology of a graph that encodes conditional independence properties of the joint distribution of all variables in the model. For some class of probability distributions, an edge between two variables is present if and only if the corresponding entry in the precision matrix is non-zero. For a finite sample estimate of the precision matrix, entries close to zero may be due to low sample effects, or due to an actual association between variables; these two cases are not readily distinguishable. %Fisher provided a hypothesis test based on a parametric approximation to the distribution of an entry in the precision matrix of a Gaussian distribution, but this may not provide valid upper bounds on $p$-values for non-Gaussian distributions. Many related works on this topic consider potentially restrictive distributional or sparsity assumptions that may not apply to a data sample of interest, and direct estimation of the uncertainty of an estimate of the precision matrix for general distributions remains challenging. Consequently, we make use of results for $U$-statistics and apply them to the covariance matrix. By probabilistically bounding the distortion of the covariance matrix, we can apply Weyl's theorem to bound the distortion of the precision matrix, yielding a conservative, but sound test threshold for a much wider class of distributions than considered in previous works. The resulting test enables one to answer with statistical significance whether an edge is present in the graph, and convergence results are known for a wide range of distributions. The computational complexities is linear in the sample size enabling the application of the test to large data samples for which computation time becomes a limiting factor. We experimentally validate the correctness and scalability of the test on multivariate distributions for which the distributional assumptions of competing tests result in underestimates of the false positive ratio. By contrast, the proposed test remains sound, promising to be a useful tool for hypothesis testing for diverse real-world problems.

A low variance consistent test of relative dependency

We describe a novel non-parametric statistical hypothesis test of relative dependence between a source variable and two candidate target variables. Such a test enables us to determine whether one source variable is significantly more dependent on a first target variable or a second. Dependence is measured via the Hilbert-Schmidt Independence Criterion (HSIC), resulting in a pair of empirical dependence measures (source-target 1, source-target 2). We test whether the first dependence measure is significantly larger than the second. Modeling the covariance between these HSIC statistics leads to a provably more powerful test than the construction of independent HSIC statistics by sub-sampling. The resulting test is consistent and unbiased, and (being based on U-statistics) has favorable convergence properties. The test can be computed in quadratic time, matching the computational complexity of standard empirical HSIC estimators. The effectiveness of the test is demonstrated on several real-world problems: we identify language groups from a multilingual corpus, and we prove that tumor location is more dependent on gene expression than chromosomal imbalances. Source code is available for download at https://github.com/wbounliphone/reldep.

B-tests: Low Variance Kernel Two-Sample Tests

A family of maximum mean discrepancy (MMD) kernel two-sample tests is introduced. Members of the test family are called Block-tests or B-tests, since the test statistic is an average over MMDs computed on subsets of the samples. The choice of block size allows control over the tradeoff between test power and computation time. In this respect, the $B$-test family combines favorable properties of previously proposed MMD two-sample tests: B-tests are more powerful than a linear time test where blocks are just pairs of samples, yet they are more computationally efficient than a quadratic time test where a single large block incorporating all the samples is used to compute a U-statistic. A further important advantage of the B-tests is their asymptotically Normal null distribution: this is by contrast with the U-statistic, which is degenerate under the null hypothesis, and for which estimates of the null distribution are computationally demanding. Recent results on kernel selection for hypothesis testing transfer seamlessly to the B-tests, yielding a means to optimize test power via kernel choice.