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  1. In the aftermath of COVID-19, screening for pathogens has never been a more relevant problem. However, computational screening for pathogens is challenging due to a variety of factors, including (i) the complexity and role of the host, (ii) virulence factor divergence and dynamics, and (iii) population and community-level dynamics. Considering a potential pathogen's molecular interactions, specifically individual proteins and protein interactions can help pinpoint a potential protein of a given microbe to cause disease. However, existing tools for pathogen screening rely on existing annotations (KEGG, GO, etc), making the assessment of novel and unannotated proteins more challenging. Here, we present an LLM-inspired approach that considers protein sequence and structure to predict protein virulence. We present a two-stage model incorporating evolutionary features captured from the DistilProtBert language model and protein structure in a graph convolutional network. Our model performs better than sequence alone for virulence function when high-quality structures are present, thus representing a path forward for virulence prediction of novel and unannotated proteins. 
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    Free, publicly-accessible full text available September 3, 2024
  2. An ongoing nurse labor shortage has the potential to impact patient care well-being in the entire healthcare system. Moreover, more complex and sophisticated nursing care is required today for patients in hospitals forcing hospital-based nurses to carry out frequent training and assessment procedures, both to onboard new nurses and to validate skills of existing staff that guarantees best practices and safety. In this paper, we recognize an opportunity for the development and integration of intelligent robot tutoring technology into nursing education to tackle the growing challenges of nurse deficit. To this end, we identify specific research problems in the area of human-robot interaction that will need to be addressed to enable robot tutors for nurse training. 
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    Free, publicly-accessible full text available August 28, 2024
  3. Robotic task planning is computationally challenging. To reduce planning cost and support life-long operation, we must leverage prior planning experience. To this end, we address the problem of extracting reusable and generalizable abstract skills from successful plan executions. In previous work, we introduced a supporting framework, allowing us, theoretically, to extract an abstract skill from a single execution and later automatically adapt it and reuse it in new domains. We also proved that, given a library of such skills, we can significantly reduce the planning effort for new problems. Nevertheless, until now, abstract-skill extraction could only be performed manually. In this paper, we finally close the automation loop and explain how abstract skills can be practically and automatically extracted. We start by analyzing the desired qualities of an abstract skill and formulate skill extraction as an optimization problem. We then develop two extraction algorithms, based on the novel concept of abstraction-critical state detection. As we show experimentally, the approach is independent of any planning domain. 
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  4. Robot manipulation in cluttered environments of-ten requires complex and sequential rearrangement of multiple objects in order to achieve the desired reconfiguration of the target objects. Due to the sophisticated physical interactions involved in such scenarios, rearrangement-based manipulation is still limited to a small range of tasks and is especially vulnerable to physical uncertainties and perception noise. This paper presents a planning framework that leverages the efficiency of sampling-based planning approaches, and closes the manipulation loop by dynamically controlling the planning horizon. Our approach interleaves planning and execution to progressively approach the manipulation goal while correcting any errors or path deviations along the process. Meanwhile, our framework allows the definition of manipulation goals without requiring explicit goal configurations, enabling the robot to flexibly interact with all objects to facilitate the manipulation of the target ones. With extensive experiments both in simulation and on a real robot, we evaluate our framework on three manipulation tasks in cluttered environments: grasping, relocating, and sorting. In comparison with two baseline approaches, we show that our framework can significantly improve planning efficiency, robustness against physical uncertainties, and task success rate under limited time budgets. 
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