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  1. Automatic assessment of impairment and disease severity is a key challenge in data-driven medicine. We propose a framework to address this challenge, which leverages AI models trained exclusively on healthy individuals. The COnfidence-Based chaRacterization of Anomalies (COBRA) score exploits the decrease in confidence of these models when presented with impaired or diseased patients to quantify their deviation from the healthy population. We applied the COBRA score to address a key limitation of current clinical evaluation of upper-body impairment in stroke patients. The gold-standard Fugl-Meyer Assessment (FMA) requires in-person administration by a trained assessor for 30-45 minutes, which restricts monitoring frequency and precludes physicians from adapting rehabilitation protocols to the progress of each patient. The COBRA score, computed automatically in under one minute, is shown to be strongly correlated with the FMA on an independent test cohort for two different data modalities: wearable sensors (ρ = 0.814, 95% CI [0.700,0.888]) and video (ρ = 0.736, 95% C.I [0.584, 0.838]). To demonstrate the generalizability of the approach to other conditions, the COBRA score was also applied to quantify severity of knee osteoarthritis from magnetic-resonance imaging scans, again achieving significant correlation with an independent clinical assessment (ρ = 0.644, 95% C.I [0.585,0.696]). 
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    Free, publicly-accessible full text available July 6, 2025
  2. Machine learning (ML) is revolutionizing protein structural analysis, including an important subproblem of predicting protein residue contact maps, i.e., which ami-no-acid residues are in close spatial proximity given the amino-acid sequence of a protein. Despite recent progresses in ML-based protein contact prediction, predict-ing contacts with a wide range of distances (commonly classified into short-, me-dium- and long-range contacts) remains a challenge. Here, we propose a multiscale graph neural network (GNN) based approach taking a cue from multiscale physics simulations, in which a standard pipeline involving a recurrent neural network (RNN) is augmented with three GNNs to refine predictive capability for short-, medium- and long-range residue contacts, respectively. Test results on the Pro-teinNet dataset show improved accuracy for contacts of all ranges using the pro-posed multiscale RNN+GNN approach over the conventional approach, including the most challenging case of long-range contact prediction. 
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  5. This paper details the first application of a software tagging algorithm to reduce radon-induced backgrounds in liquid noble element time projection chambers, such as XENON1T and XENONnT. The convection velocity field in XENON1T was mapped out usingRn222andPo218events, and the rms convection speed was measured to be0.30±0.01cm/s. Given this velocity field,Pb214background events can be tagged when they are followed byBi214andPo214decays, or preceded byPo218decays. This was achieved by evolving a point cloud in the direction of a measured convection velocity field, and searching forBi214andPo214decays orPo218decays within a volume defined by the point cloud. In XENON1T, this tagging system achieved aPb214background reduction of6.20.9+0.4%with an exposure loss of1.8±0.2%, despite the timescales of convection being smaller than the relevant decay times. We show that the performance can be improved in XENONnT, and that the performance of such a software-tagging approach can be expected to be further improved in a diffusion-limited scenario. Finally, a similar method might be useful to tag the cosmogenicXe137background, which is relevant to the search for neutrinoless double-beta decay.

    Published by the American Physical Society2024 
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    Free, publicly-accessible full text available July 1, 2025