Proteins are responsible for most of the functions in life, and thus are the central focus of many areas of biomedicine. Protein structure is strongly related to protein function, but is difficult to elucidate experimentally, therefore computational structure prediction is a crucial task on the way to solve many biological questions. A contact map is a compact representation of the three-dimensional structure of a protein via the pairwise contacts between the amino acids constituting the protein. We use a convolutional network to calculate protein contact maps from detailed evolutionary coupling statistics between positions in the protein sequence. The input to the network has an image-like structure amenable to convolutions, but every "pixel" instead of color channels contains a bipartite undirected edge-weighted graph. We propose several methods for treating such "graph-valued images" in a convolutional network. The proposed method outperforms state-of-the-art methods by a considerable margin.

Neural Information Processing Systems http://nips.cc/

We study a surprising phenomenon related to the representation of a cloud of data points using polynomials. We start with the previously unnoticed empirical observation that, given a collection (a cloud) of data points, the sublevel sets of a certain distinguished polynomial capture the shape of the cloud very accurately. This distinguished polynomial is a sum-of-squares (SOS) derived in a simple manner from the inverse of the empirical moment matrix. In fact, this SOS polynomial is directly related to orthogonal polynomials and the Christoffel function. This allows to generalize and interpret extremality properties of orthogonal polynomials and to provide a mathematical rationale for the observed phenomenon. Among diverse potential applications, we illustrate the relevance of our results on a network intrusion detection task for which we obtain performances similar to existing dedicated methods reported in the literature.

The use of Bayesian methods in large-scale data settings is attractive because of the rich hierarchical models, uncertainty quantification, and prior specification they provide. Standard Bayesian inference algorithms are computationally expensive, however, making their direct application to large datasets difficult or infeasible. Recent work on scaling Bayesian inference has focused on modifying the underlying algorithms to, for example, use only a random data subsample at each iteration. We leverage the insight that data is often redundant to instead obtain a weighted subset of the data (called a coreset) that is much smaller than the original dataset. We can then use this small coreset in any number of existing posterior inference algorithms without modification.

Optimal transport (OT) defines a powerful framework to compare probability distributions in a geometrically faithful way. However, the practical impact of OT is still limited because of its computational burden. We propose a new class of stochastic optimization algorithms to cope with large-scale OT problems. These methods can handle arbitrary distributions (either discrete or continuous) as long as one is able to draw samples from them, which is the typical setup in highdimensional learning problems.

We present a theoretical analysis of active learning with more realistic interactions with human oracles. Previous empirical studies have shown oracles abstaining on difficult queries until accumulating enough information to make label decisions. We formalize this phenomenon with an "oracle epiphany model" and analyze active learning query complexity under such oracles for both the realizable and the agnostic cases. Our analysis shows that active learning is possible with oracle epiphany, but incurs an additional cost depending on when the epiphany happens. Our results suggest new, principled active learning approaches with realistic oracles.

We analyze stochastic algorithms for optimizing nonconvex, nonsmooth finite-sum problems, where the nonsmooth part is convex. Surprisingly, unlike the smooth case, our knowledge of this fundamental problem is very limited. For example, it is not known whether the proximal stochastic gradient method with constant minibatch converges to a stationary point. To tackle this issue, we develop fast stochastic algorithms that provably converge to a stationary point for constant minibatches. Furthermore, using a variant of these algorithms, we obtain provably faster convergence than batch proximal gradient descent. Our results are based on the recent variance reduction techniques for convex optimization but with a novel analysis for handling nonconvex and nonsmooth functions. We also prove global linear convergence rate for an interesting subclass of nonsmooth nonconvex functions, which subsumes several recent works.

We present CYCLADES, a general framework for parallelizing stochastic optimization algorithms in a shared memory setting. CYCLADES is asynchronous during model updates, and requires no memory locking mechanisms, similar to HOGWILD!-type algorithms. Unlike HOGWILD!, CYCLADES introduces no conflicts during parallel execution, and offers a black-box analysis for provable speedups across a large family of algorithms. Due to its inherent cache locality and conflictfree nature, our multi-core implementation of CYCLADES consistently outperforms HOGWILD!-type algorithms on sufficiently sparse datasets, leading to up to 40% speedup gains compared to HOGWILD!, and up to 5 gains over asynchronous implementations of variance reduction algorithms.

Neural Information Processing Systems http://nips.cc/

We present an effective method for supervised feature construction. The main goal of the approach is to construct a feature representation for which a set of linear hypotheses is of sufficient capacity - large enough to contain a satisfactory solution to the considered problem and small enough to allow good generalization from a small number of training examples. We achieve this goal with a greedy procedure that constructs features by empirically fitting squared error residuals. The proposed constructive procedure is consistent and can output a rich set of features. The effectiveness of the approach is evaluated empirically by fitting a linear ridge regression model in the constructed feature space and our empirical results indicate a superior performance of our approach over competing methods.