Trend estimation and short-term forecasting of COVID-19 cases and deaths worldwide.

Since the beginning of the COVID-19 pandemic, many dashboards have emerged as useful tools to monitor its evolution, inform the public, and assist governments in decision-making. Here, we present a globally applicable method, integrated in a daily updated dashboard that provides an estimate of the trend in the evolution of the number of cases and deaths from reported data of more than 200 countries and territories, as well as 7-d forecasts. One of the significant difficulties in managing a quickly propagating epidemic is that the details of the dynamic needed to forecast its evolution are obscured by the delays in the identification of cases and deaths and by irregular reporting. Our forecasting methodology substantially relies on estimating the underlying trend in the observed time series using robust seasonal trend decomposition techniques. This allows us to obtain forecasts with simple yet effective extrapolation methods in linear or log scale. We present the results of an assessment of our forecasting methodology and discuss its application to the production of global and regional risk maps.

Semantic-aware Video Representation for Few-shot Action Recognition.

Recent work on action recognition leverages 3D features and textual information to achieve state-of-the-art performance. However, most of the current few-shot action recognition methods still rely on 2D frame-level representations, often require additional components to model temporal relations, and employ complex distance functions to achieve accurate alignment of these representations. In addition, existing methods struggle to effectively integrate textual semantics, some resorting to concatenation or addition of textual and visual features, and some using text merely as an additional supervision without truly achieving feature fusion and information transfer from different modalities. In this work, we propose a simple yet effective Semantic-Aware Few-Shot Action Recognition (SAFSAR) model to address these issues. We show that directly leveraging a 3D feature extractor combined with an effective feature-fusion scheme, and a simple cosine similarity for classification can yield better performance without the need of extra components for temporal modeling or complex distance functions. We introduce an innovative scheme to encode the textual semantics into the video representation which adaptively fuses features from text and video, and encourages the visual encoder to extract more semantically consistent features. In this scheme, SAFSAR achieves alignment and fusion in a compact way. Experiments on five challenging few-shot action recognition benchmarks under various settings demonstrate that the proposed SAFSAR model significantly improves the state-of-the-art performance.

TORO Indexer: a PyTorch-based indexing algorithm for kilohertz serial crystallography.

Serial crystallography (SX) involves combining observations from a very large number of diffraction patterns coming from crystals in random orientations. To compile a complete data set, these patterns must be indexed (i.e. their orientation determined), integrated and merged. Introduced here is TORO (Torch-powered robust optimization) Indexer, a robust and adaptable indexing algorithm developed using the PyTorch framework. TORO is capable of operating on graphics processing units (GPUs), central processing units (CPUs) and other hardware accelerators supported by PyTorch, ensuring compatibility with a wide variety of computational setups. In tests, TORO outpaces existing solutions, indexing thousands of frames per second when running on GPUs, which positions it as an attractive candidate to produce real-time indexing and user feedback. The algorithm streamlines some of the ideas introduced by previous indexers like DIALS real-space grid search [Gildea, Waterman, Parkhurst, Axford, Sutton, Stuart, Sauter, Evans & Winter (2014). Acta Cryst. D70, 2652-2666] and XGandalf [Gevorkov, Yefanov, Barty, White, Mariani, Brehm, Tolstikova, Grigat & Chapman (2019). Acta Cryst. A75, 694-704] and refines them using faster and principled robust optimization techniques which result in a concise code base consisting of less than 500 lines. On the basis of evaluations across four proteins, TORO consistently matches, and in certain instances outperforms, established algorithms such as XGandalf and MOSFLM [Powell (1999). Acta Cryst. D55, 1690-1695], occasionally amplifying the quality of the consolidated data while achieving superior indexing speed. The inherent modularity of TORO and the versatility of PyTorch code bases facilitate its deployment into a wide array of architectures, software platforms and bespoke applications, highlighting its prospective significance in SX.

The Fastest l1,∞ Prox in the West.

Proximal operators are of particular interest in optimization problems dealing with non-smooth objectives because in many practical cases they lead to optimization algorithms whose updates can be computed in closed form or very efficiently. A well-known example is the proximal operator of the vector l1 norm, which is given by the soft-thresholding operator. In this paper we study the proximal operator of the mixed l1,∞ matrix norm and show that it can be computed in closed form by applying the well-known soft-thresholding operator to each column of the matrix. However, unlike the vector l1 norm case where the threshold is constant, in the mixed l1,∞ norm case each column of the matrix might require a different threshold and all thresholds depend on the given matrix. We propose a general iterative algorithm for computing these thresholds, as well as two efficient implementations that further exploit easy to compute lower bounds for the mixed norm of the optimal solution. Experiments on large-scale synthetic and real data indicate that the proposed methods can be orders of magnitude faster than state-of-the-art methods.

Surgical gesture classification from video and kinematic data.

Much of the existing work on automatic classification of gestures and skill in robotic surgery is based on dynamic cues (e.g., time to completion, speed, forces, torque) or kinematic data (e.g., robot trajectories and velocities). While videos could be equally or more discriminative (e.g., videos contain semantic information not present in kinematic data), they are typically not used because of the difficulties associated with automatic video interpretation. In this paper, we propose several methods for automatic surgical gesture classification from video data. We assume that the video of a surgical task (e.g., suturing) has been segmented into video clips corresponding to a single gesture (e.g., grabbing the needle, passing the needle) and propose three methods to classify the gesture of each video clip. In the first one, we model each video clip as the output of a linear dynamical system (LDS) and use metrics in the space of LDSs to classify new video clips. In the second one, we use spatio-temporal features extracted from each video clip to learn a dictionary of spatio-temporal words, and use a bag-of-features (BoF) approach to classify new video clips. In the third one, we use multiple kernel learning (MKL) to combine the LDS and BoF approaches. Since the LDS approach is also applicable to kinematic data, we also use MKL to combine both types of data in order to exploit their complementarity. Our experiments on a typical surgical training setup show that methods based on video data perform equally well, if not better, than state-of-the-art approaches based on kinematic data. In turn, the combination of both kinematic and video data outperforms any other algorithm based on one type of data alone.

String motif-based description of tool motion for detecting skill and gestures in robotic surgery.

The growing availability of data from robotic and laparoscopic surgery has created new opportunities to investigate the modeling and assessment of surgical technical performance and skill. However, previously published methods for modeling and assessment have not proven to scale well to large and diverse data sets. In this paper, we describe a new approach for simultaneous detection of gestures and skill that can be generalized to different surgical tasks. It consists of two parts: (1) descriptive curve coding (DCC), which transforms the surgical tool motion trajectory into a coded string using accumulated Frenet frames, and (2) common string model (CSM), a classification model using a similarity metric computed from longest common string motifs. We apply DCC-CSM method to detect surgical gestures and skill levels in two kinematic datasets (collected from the da Vinci surgical robot). DCC-CSM method classifies gestures and skill with 87.81% and 91.12% accuracy, respectively.