Single-particle electron cryomicroscopy (cryo-EM) is a powerful method for determining the structures of biological macromolecules. With automated microscopes, cryo-EM data can often be obtained in a few days. However, processing cryo-EM image data to reveal heterogeneity in the protein structure and to refine 3D maps to high resolution frequently becomes a severe bottleneck, requiring expert intervention, prior structural knowledge, and weeks of calculations on expensive computer clusters. Here we show that stochastic gradient descent (SGD) and branch-and-bound maximum likelihood optimization algorithms permit the major steps in cryo-EM structure determination to be performed in hours or minutes on an inexpensive desktop computer. Furthermore, SGD with Bayesian marginalization allows ab initio 3D classification, enabling automated analysis and discovery of unexpected structures without bias from a reference map. These algorithms are combined in a user-friendly computer program named cryoSPARC (http://www.cryosparc.com).

Stan is a probabilistic programming language for specifying statistical models. A Stan program imperatively defines a log probability function over parameters conditioned on specified data and constants. As of version 2.14.0, Stan provides full Bayesian inference for continuous-variable models through Markov chain Monte Carlo methods such as the No-U-Turn sampler, an adaptive form of Hamiltonian Monte Carlo sampling. Penalized maximum likelihood estimates are calculated using optimization methods such as the limited memory Broyden-Fletcher-Goldfarb-Shanno algorithm.Stan is also a platform for computing log densities and their gradients and Hessians, which can be used in alternative algorithms such as variational Bayes, expectation propagation, and marginal inference using approximate integration. To this end, Stan is set up so that the densities, gradients, and Hessians, along with intermediate quantities of the algorithm such as acceptance probabilities, are easily accessible.Stan can be called from the command line using the cmdstan package, through R using the rstan package, and through Python using the pystan package. All three interfaces support sampling and optimization-based inference with diagnostics and posterior analysis. rstan and pystan also provide access to log probabilities, gradients, Hessians, parameter transforms, and specialized plotting.

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Direct detector device (DDD) cameras have revolutionized single particle electron cryomicroscopy (cryo-EM). In addition to an improved camera detective quantum efficiency, acquisition of DDD movies allows for correction of movement of the specimen, due to both instabilities in the microscope specimen stage and electron beam-induced movement. Unlike specimen stage drift, beam-induced movement is not always homogeneous within an image. Local correlation in the trajectories of nearby particles suggests that beam-induced motion is due to deformation of the ice layer. Algorithms have already been described that can correct movement for large regions of frames and for >1 MDa protein particles. Another algorithm allows individual <1 MDa protein particle trajectories to be estimated, but requires rolling averages to be calculated from frames and fits linear trajectories for particles. Here we describe an algorithm that allows for individual <1 MDa particle images to be aligned without frame averaging or linear trajectories. The algorithm maximizes the overall correlation of the shifted frames with the sum of the shifted frames. The optimum in this single objective function is found efficiently by making use of analytically calculated derivatives of the function. To smooth estimates of particle trajectories, rapid changes in particle positions between frames are penalized in the objective function and weighted averaging of nearby trajectories ensures local correlation in trajectories. This individual particle motion correction, in combination with weighting of Fourier components to account for increasing radiation damage in later frames, can be used to improve 3-D maps from single particle cryo-EM.

Knowledge graphs (KGs) typically contain temporal facts indicating relationships among entities at different times. Due to their incompleteness, several approaches have been proposed to infer new facts for a KG based on the existing ones–a problem known as KG completion. KG embedding approaches have proved effective for KG completion, however, they have been developed mostly for static KGs. Developing temporal KG embedding models is an increasingly important problem. In this paper, we build novel models for temporal KG completion through equipping static models with a diachronic entity embedding function which provides the characteristics of entities at any point in time. This is in contrast to the existing temporal KG embedding approaches where only static entity features are provided. The proposed embedding function is model-agnostic and can be potentially combined with any static model. We prove that combining it with SimplE, a recent model for static KG embedding, results in a fully expressive model for temporal KG completion. Our experiments indicate the superiority of our proposal compared to existing baselines.

Modeling and synthesizing image noise is an important aspect in many computer vision applications. The long-standing additive white Gaussian and heteroscedastic (signal-dependent) noise models widely used in the literature provide only a coarse approximation of real sensor noise. This paper introduces Noise Flow, a powerful and accurate noise model based on recent normalizing flow architectures. Noise Flow combines well-established basic parametric noise models (e.g., signal-dependent noise) with the flexibility and expressiveness of normalizing flow networks. The result is a single, comprehensive, compact noise model containing fewer than 2500 parameters yet able to represent multiple cameras and gain factors. Noise Flow dramatically outperforms existing noise models, with 0.42 nats/pixel improvement over the camera-calibrated noise level functions, which translates to 52% improvement in the likelihood of sampled noise. Noise Flow represents the first serious attempt to go beyond simple parametric models to one that leverages the power of deep learning and datadriven noise distributions.

In this paper we propose an affordable solution to selflocalization, which utilizes visual odometry and road maps as the only inputs. To this end, we present a probabilistic model as well as an efficient approximate inference algorithm, which is able to utilize distributed computation to meet the real-time requirements of autonomous systems. Because of the probabilistic nature of the model we are able to cope with uncertainty due to noisy visual odometry and inherent ambiguities in the map (e.g., in a Manhattan world). By exploiting freely available, community developed maps and visual odometry measurements, we are able to localize a vehicle up to 3m after only a few seconds of driving on maps which contain more than 2,150km of drivable roads.

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