Objective:Develop and validate an algorithm for analyzing the layout of PDF clinical documents to improve the performance of downstream natural language processing tasks. Materials and Methods: We designed an algorithm to process clinical PDF documents and extract only clinically relevant text. The algorithm consists of several steps: initial text extraction using a PDF parser, followed by classification into categories such as body text, left notes, and footers using a Transformer deep neural network architecture, and finally an aggregation step to compile the lines of a given label in the text. We evaluated the technical performance of the body text extraction algorithm by applying it to a random sample of documents that were annotated. Medical performance was evaluated by examining the extraction of medical concepts of interest from the text in their respective sections. Finally, we tested an end-to-end system on a medical use case of automatic detection of acute infection described in the hospital report. Results:Our algorithm achieved per-line precision, recall, and F1 score of 98.4, 97.0, and 97.7, respectively, for body line extraction. The precision, recall, and F1 score per document for the acute infection detection algorithm were 82.54 (95CI 72.86-91.60), 85.24 (95CI 76.61-93.70), 83.87 (95CI 76, 92-90.08) with exploitation of the results of the advanced body extraction algorithm, respectively. Conclusion:We have developed and validated a system for extracting body text from clinical documents in PDF format by identifying their layout. We were able to demonstrate that this preprocessing allowed us to obtain better performances for a common downstream task, i.e., the extraction of medical concepts in their respective sections, thus proving the interest of this method on a clinical use case.

Deep kernel learning provides an elegant and principled framework for combining the structural properties of deep learning algorithms with the flexibility of kernel methods. By means of a deep neural network, it consists of learning a kernel operator which is combined with a differentiable kernel algorithm for inference. While previous work within this framework has mostly explored learning a single kernel for large datasets, we focus herein on learning a kernel family for a variety of tasks in few-shot regression settings. Compared to single deep kernel learning, our novel algorithm permits finding the appropriate kernel for each task during inference, rather than using the same for all tasks. As such, our algorithm performs more effectively with complex task distributions in few-shot learning, which we demonstrate by benchmarking against existing state-of-the-art algorithms using real-world, few-shot regression tasks related to drug discovery.

Increasing urban concentration raises operational challenges that can benefit from integrated monitoring and decision support. Such complex systems need to leverage the full stack of analytical methods, from state estimation using multi-sensor fusion for situational awareness, to prediction and computation of optimal responses. The FASTER platform that we describe in this work, deployed at nation scale and handling 1.5 billion public transport trips a year, offers such a full stack of techniques for this large-scale, real-time problem. FASTER provides fine-grained situational awareness and real-time decision support with the objective of improving the public transport commuter experience. The methods employed range from statistical machine learning to agent-based simulation and mixed-integer optimization. In this work we present an overview of the challenges and methods involved, with details of the commuter movement prediction module, as well as a discussion of open problems.