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Estimating three-dimensional conformations of a molecular graph allows insight into the molecule's biological and chemical functions. Fast generation of valid conformations is thus central to molecular modeling. Recent advances in graph-based deep networks have accelerated conformation generation from hours to seconds. However, current network architectures do not scale well to large molecules. Here we present ConfFlow, a flow-based model for conformation generation based on transformer networks. In contrast with existing approaches, ConfFlow directly samples in the coordinate space without enforcing any explicit physical constraints. The generative procedure is highly interpretable and is akin to force field updates in molecular dynamics simulation. When applied to the generation of large molecule conformations, ConfFlow improve accuracy by up to $40\%$ relative to state-of-the-art learning-based methods. The source code is made available at https://github.com/IntelLabs/ConfFlow., Comment: Technical Report. Code available at https://github.com/IntelLabs/ConfFlow

We study a planner's provision of information to manage workplace occupancy when strategic workers (agents) face risk of infectious disease transmission. The planner implements an information mechanism to signal information about the underlying risk of infection at the workplace. Agents update their belief over the risk parameter using this information and choose to work in-person or remotely. We address the design of the optimal signaling mechanism that best aligns the workplace occupancy with the planner's preference (i.e., maintaining safe capacity limits and operational efficiency at workplace). For various forms of planner preferences, we show numerical and analytical proof that interval-based information mechanisms are optimal. These mechanisms partition the continuous domain of the risk parameter into disjoint intervals and provision information based on interval-specific probability distributions over a finite set of signals. When the planner seeks to achieve an occupancy that lies in one of finitely many pre-specified ranges independent of the underlying risk, we provide an optimal mechanism that uses at most two intervals. On the other hand, when the preference on the occupancy is risk-dependent, we show that an approximately optimal interval-based mechanism can be computed efficiently. We bound the approximation loss for preferences that are expressed through a Lipschitz continuous function of both occupancy and risk parameter. We provide examples that demonstrate the improvement of proposed signaling mechanisms relative to the common benchmarks in information provision. Our findings suggest that information provision over the risk of disease transmission is an effective intervention for maintaining desirable occupancy levels at the workplace.

We study the problem of information provision by a strategic central planner who can publicly signal about an uncertain infectious risk parameter. Signalling leads to an updated public belief over the parameter, and agents then make equilibrium choices on whether to work remotely or in-person. The planner maintains a set of desirable outcomes for each realization of the uncertain parameter and seeks to maximize the probability that agents choose an acceptable outcome for the true parameter. We distinguish between stateless and stateful objectives. In the former, the set of desirable outcomes does not change as a function of the risk parameter, whereas in the latter it does. For stateless objectives, we reduce the problem to maximizing the probability of inducing mean beliefs that lie in intervals computable from the set of desirable outcomes. We derive the optimal signalling mechanism and show that it partitions the parameter domain into at most two intervals with the signals generated according to an interval-specific distribution. For the stateful case, we consider a practically relevant situation in which the planner can enforce in-person work capacity limits that progressively get more stringent as the risk parameter increases. We show that the optimal signalling mechanism for this case can be obtained by solving a linear program. We numerically verify the improvement in achieving desirable outcomes using our information design relative to no information and full information benchmarks.

We present an approach to synthesizing new graph structures from empirically specified distributions. The generative model is an auto-decoder that learns to synthesize graphs from latent codes. The graph synthesis model is learned jointly with an empirical distribution over the latent codes. Graphs are synthesized using self-attention modules that are trained to identify likely connectivity patterns. Graph-based normalizing flows are used to sample latent codes from the distribution learned by the auto-decoder. The resulting model combines accuracy and scalability. On benchmark datasets of large graphs, the presented model outperforms the state of the art by a factor of 1.5 in mean accuracy and average rank across at least three different graph statistics, with a 2x speedup during inference.

Probability density estimation is a classical and well studied problem, but standard density estimation methods have historically lacked the power to model complex and high-dimensional image distributions. More recent generative models leverage the power of neural networks to implicitly learn and represent probability models over complex images. We describe methods to extract explicit probability density estimates from GANs, and explore the properties of these image density functions. We perform sanity check experiments to provide evidence that these probabilities are reasonable. However, we also show that density functions of natural images are difficult to interpret and thus limited in use. We study reasons for this lack of interpretability, and show that we can get interpretability back by doing density estimation on latent representations of images.

Many imaging tasks require global information about all pixels in an image. Conventional bottom-up classification networks globalize information by decreasing resolution; features are pooled and downsampled into a single output. But for semantic segmentation and object detection tasks, a network must provide higher-resolution pixel-level outputs. To globalize information while preserving resolution, many researchers propose the inclusion of sophisticated auxiliary blocks, but these come at the cost of a considerable increase in network size and computational cost. This paper proposes stacked u-nets (SUNets), which iteratively combine features from different resolution scales while maintaining resolution. SUNets leverage the information globalization power of u-nets in a deeper network architectures that is capable of handling the complexity of natural images. SUNets perform extremely well on semantic segmentation tasks using a small number of parameters., Comment: The code is available at https://github.com/shahsohil/sunets

Clustering high-dimensional datasets is hard because interpoint distances become less informative in high-dimensional spaces. We present a clustering algorithm that performs nonlinear dimensionality reduction and clustering jointly. The data is embedded into a lower-dimensional space by a deep autoencoder. The autoencoder is optimized as part of the clustering process. The resulting network produces clustered data. The presented approach does not rely on prior knowledge of the number of ground-truth clusters. Joint nonlinear dimensionality reduction and clustering are formulated as optimization of a global continuous objective. We thus avoid discrete reconfigurations of the objective that characterize prior clustering algorithms. Experiments on datasets from multiple domains demonstrate that the presented algorithm outperforms state-of-the-art clustering schemes, including recent methods that use deep networks., Comment: The code is available at http://github.com/shahsohil/DCC

Adversarial neural networks solve many important problems in data science, but are notoriously difficult to train. These difficulties come from the fact that optimal weights for adversarial nets correspond to saddle points, and not minimizers, of the loss function. The alternating stochastic gradient methods typically used for such problems do not reliably converge to saddle points, and when convergence does happen it is often highly sensitive to learning rates. We propose a simple modification of stochastic gradient descent that stabilizes adversarial networks. We show, both in theory and practice, that the proposed method reliably converges to saddle points, and is stable with a wider range of training parameters than a non-prediction method. This makes adversarial networks less likely to "collapse," and enables faster training with larger learning rates., Comment: Accepted at ICLR 2018

Typical textual descriptions that accompany online videos are 'weak': i.e., they mention the main concepts in the video but not their corresponding spatio-temporal locations. The concepts in the description are typically heterogeneous (e.g., objects, persons, actions). Certain location constraints on these concepts can also be inferred from the description. The goal of this paper is to present a generalization of the Indian Buffet Process (IBP) that can (a) systematically incorporate heterogeneous concepts in an integrated framework, and (b) enforce location constraints, for efficient classification and localization of the concepts in the videos. Finally, we develop posterior inference for the proposed formulation using mean-field variational approximation. Comparative evaluations on the Casablanca and the A2D datasets show that the proposed approach significantly outperforms other state-of-the-art techniques: 24% relative improvement for pairwise concept classification in the Casablanca dataset and 9% relative improvement for localization in the A2D dataset as compared to the most competitive baseline., Comment: To appear at ECCV 2016

Semidefinite programming is an indispensable tool in computer vision, but general-purpose solvers for semidefinite programs are often too slow and memory intensive for large-scale problems. We propose a general framework to approximately solve large-scale semidefinite problems (SDPs) at low complexity. Our approach, referred to as biconvex relaxation (BCR), transforms a general SDP into a specific biconvex optimization problem, which can then be solved in the original, low-dimensional variable space at low complexity. The resulting biconvex problem is solved using an efficient alternating minimization (AM) procedure. Since AM has the potential to get stuck in local minima, we propose a general initialization scheme that enables BCR to start close to a global optimum - this is key for our algorithm to quickly converge to optimal or near-optimal solutions. We showcase the efficacy of our approach on three applications in computer vision, namely segmentation, co-segmentation, and manifold metric learning. BCR achieves solution quality comparable to state-of-the-art SDP methods with speedups between 4X and 35X. At the same time, BCR handles a more general set of SDPs than previous approaches, which are more specialized.

Conventional algorithms for sparse signal recovery and sparse representation rely on $l_1$-norm regularized variational methods. However, when applied to the reconstruction of $\textit{sparse images}$, i.e., images where only a few pixels are non-zero, simple $l_1$-norm-based methods ignore potential correlations in the support between adjacent pixels. In a number of applications, one is interested in images that are not only sparse, but also have a support with smooth (or contiguous) boundaries. Existing algorithms that take into account such a support structure mostly rely on non-convex methods and---as a consequence---do not scale well to high-dimensional problems and/or do not converge to global optima. In this paper, we explore the use of new block $l_1$-norm regularizers, which enforce image sparsity while simultaneously promoting smooth support structure. By exploiting the convexity of our regularizers, we develop new computationally-efficient recovery algorithms that guarantee global optimality. We demonstrate the efficacy of our regularizers on a variety of imaging tasks including compressive image recovery, image restoration, and robust PCA., Comment: To appear at CVPR 2016