Recent work has shown that convolutional networks can be substantially deeper, more accurate, and efficient to train if they contain shorter connections between layers close to the input and those close to the output. In this paper, we embrace this observation and introduce the Dense Convolutional Network (DenseNet), which connects each layer to every other layer in a feed-forward fashion. Whereas traditional convolutional networks with L layers have L connections&#x2014;one between each layer and its subsequent layer&#x2014;our network has L(L+1)/2 direct connections. For each layer, the feature-maps of all preceding layers are used as inputs, and its own feature-maps are used as inputs into all subsequent layers. DenseNets have several compelling advantages: they alleviate the vanishing-gradient problem, strengthen feature propagation, encourage feature reuse, and substantially reduce the number of parameters. We evaluate our proposed architecture on four highly competitive object recognition benchmark tasks (CIFAR-10, CIFAR-100, SVHN, and ImageNet). DenseNets obtain significant improvements over the state-of-the-art on most of them, whilst requiring less memory and computation to achieve high performance. Code and pre-trained models are available at https://github.com/liuzhuang13/DenseNet.

/pdf/densely-connected-convolutional-networks-i745msea9d.pdf

Densely Connected Convolutional Networks

The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

Integrative analysis of 111 reference human epigenomes

Big Data applications are typically associated with systems involving large numbers of users, massive complex software systems, and large-scale heterogeneous computing and storage architectures. The construction of such systems involves many distributed design choices. The end products (e.g., recommendation systems, medical analysis tools, real-time game engines, speech recognizers) thus involve many tunable configuration parameters. These parameters are often specified and hard-coded into the software by various developers or teams. If optimized jointly, these parameters can result in significant improvements. Bayesian optimization is a powerful tool for the joint optimization of design choices that is gaining great popularity in recent years. It promises greater automation so as to increase both product quality and human productivity. This review paper introduces Bayesian optimization, highlights some of its methodological aspects, and showcases a wide range of applications.

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Taking the Human Out of the Loop: A Review of Bayesian Optimization

We quantitatively investigate how machine learning models leak information about the individual data records on which they were trained. We focus on the basic membership inference attack: given a data record and black-box access to a model, determine if the record was in the model's training dataset. To perform membership inference against a target model, we make adversarial use of machine learning and train our own inference model to recognize differences in the target model's predictions on the inputs that it trained on versus the inputs that it did not train on. We empirically evaluate our inference techniques on classification models trained by commercial "machine learning as a service" providers such as Google and Amazon. Using realistic datasets and classification tasks, including a hospital discharge dataset whose membership is sensitive from the privacy perspective, we show that these models can be vulnerable to membership inference attacks. We then investigate the factors that influence this leakage and evaluate mitigation strategies.

/pdf/membership-inference-attacks-against-machine-learning-models-2tzchejf91.pdf

Membership Inference Attacks Against Machine Learning Models

We present the Word Mover's Distance (WMD), a novel distance function between text documents. Our work is based on recent results in word embeddings that learn semantically meaningful representations for words from local cooccurrences in sentences. The WMD distance measures the dissimilarity between two text documents as the minimum amount of distance that the embedded words of one document need to "travel" to reach the embedded words of another document. We show that this distance metric can be cast as an instance of the Earth Mover's Distance, a well studied transportation problem for which several highly efficient solvers have been developed. Our metric has no hyperparameters and is straight-forward to implement. Further, we demonstrate on eight real world document classification data sets, in comparison with seven state-of-the-art baselines, that the WMD metric leads to unprecedented low k-nearest neighbor document classification error rates.

/pdf/from-word-embeddings-to-document-distances-2qevvhrrb0.pdf

From Word Embeddings To Document Distances

Despite advances in scalable models, the inference tools used for Gaussian processes (GPs) have yet to fully capitalize on developments in computing hardware. We present an efficient and general approach to GP inference based on Blackbox Matrix-Matrix multiplication (BBMM). BBMM inference uses a modified batched version of the conjugate gradients algorithm to derive all terms for training and inference in a single call. BBMM reduces the asymptotic complexity of exact GP inference from $O(n^3)$ to $O(n^2)$. Adapting this algorithm to scalable approximations and complex GP models simply requires a routine for efficient matrix-matrix multiplication with the kernel and its derivative. In addition, BBMM uses a specialized preconditioner to substantially speed up convergence. In experiments we show that BBMM effectively uses GPU hardware to dramatically accelerate both exact GP inference and scalable approximations. Additionally, we provide GPyTorch, a software platform for scalable GP inference via BBMM, built on PyTorch.

GPyTorch: Blackbox Matrix-Matrix Gaussian Process Inference with GPU Acceleration.

Bayesian optimization is a powerful framework for minimizing expensive objective functions while using very few function evaluations. It has been successfully applied to a variety of problems, including hyperparameter tuning and experimental design. However, this framework has not been extended to the inequality-constrained optimization setting, particularly the setting in which evaluating feasibility is just as expensive as evaluating the objective. Here we present constrained Bayesian optimization, which places a prior distribution on both the objective and the constraint functions. We evaluate our method on simulated and real data, demonstrating that constrained Bayesian optimization can quickly find optimal and feasible points, even when small feasible regions cause standard methods to fail.

/pdf/bayesian-optimization-with-inequality-constraints-27n32milf3.pdf

Bayesian Optimization with Inequality Constraints

Despite advances in scalable models, the inference tools used for Gaussian processes (GPs) have yet to fully capitalize on developments in computing hardware. We present an efficient and general approach to GP inference based on Blackbox Matrix-Matrix multiplication (BBMM). BBMM inference uses a modified batched version of the conjugate gradients algorithm to derive all terms for training and inference in a single call. BBMM reduces the asymptotic complexity of exact GP inference from O(n^3) to O(n^2). Adapting this algorithm to scalable approximations and complex GP models simply requires a routine for efficient matrix-matrix multiplication with the kernel and its derivative. In addition, BBMM uses a specialized preconditioner to substantially speed up convergence. In experiments we show that BBMM effectively uses GPU hardware to dramatically accelerate both exact GP inference and scalable approximations. Additionally, we provide GPyTorch, a software platform for scalable GP inference via BBMM, built on PyTorch.

/pdf/gpytorch-blackbox-matrix-matrix-gaussian-process-inference-47txe0w8z7.pdf

GPyTorch: Blackbox Matrix-Matrix Gaussian Process Inference with GPU Acceleration

We propose Deep Feature Interpolation (DFI), a new data-driven baseline for automatic high-resolution image transformation. As the name suggests, DFI relies only on simple linear interpolation of deep convolutional features from pre-trained convnets. We show that despite its simplicity, DFI can perform high-level semantic transformations like make older/younger, make bespectacled, add smile, among others, surprisingly well&#x2013;sometimes even matching or outperforming the state-of-the-art. This is particularly unexpected as DFI requires no specialized network architecture or even any deep network to be trained for these tasks. DFI therefore can be used as a new baseline to evaluate more complex algorithms and provides a practical answer to the question of which image transformation tasks are still challenging after the advent of deep learning.

/pdf/deep-feature-interpolation-for-image-content-changes-4nmwqrlon1.pdf

Deep Feature Interpolation for Image Content Changes

We propose an intriguingly simple method for the construction of adversarial images in the black-box setting. In constrast to the white-box scenario, constructing black-box adversarial images has the additional constraint on query budget, and efficient attacks remain an open problem to date. With only the mild assumption of continuous-valued confidence scores, our highly query-efficient algorithm utilizes the following simple iterative principle: we randomly sample a vector from a predefined orthonormal basis and either add or subtract it to the target image. Despite its simplicity, the proposed method can be used for both untargeted and targeted attacks -- resulting in previously unprecedented query efficiency in both settings. We demonstrate the efficacy and efficiency of our algorithm on several real world settings including the Google Cloud Vision API. We argue that our proposed algorithm should serve as a strong baseline for future black-box attacks, in particular because it is extremely fast and its implementation requires less than 20 lines of PyTorch code.

/pdf/simple-black-box-adversarial-attacks-4yyi0bmt59.pdf

Jacob R. Gardner

Papers

GPyTorch: Blackbox Matrix-Matrix Gaussian Process Inference with GPU Acceleration.

Bayesian Optimization with Inequality Constraints

GPyTorch: Blackbox Matrix-Matrix Gaussian Process Inference with GPU Acceleration

Deep Feature Interpolation for Image Content Changes

Simple Black-box Adversarial Attacks