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  1. The availability of large-scale electronic health record datasets has led to the development of artificial intel- ligence (AI) methods for clinical risk prediction that help improve patient care. However, existing studies have shown that AI models suffer from severe performance decay after several years of deployment, which might be caused by various temporal dataset shifts. When the shift occurs, we have access to large-scale pre-shift data and small-scale post-shift data that are not enough to train new models in the post-shift environment. In this study, we propose a new method to address the issue. We reweight patients from the pre-shift environ- ment to mitigate the distribution shift between pre- and post-shift environments. Moreover, we adopt a Kullback-Leibler divergence loss to force the models to learn similar patient representations in pre- and post-shift environments. Our experimental results show that our model efficiently mitigates temporal shifts, improving prediction performance. 
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    Free, publicly-accessible full text available September 1, 2024
  2. Free, publicly-accessible full text available April 1, 2024
  3. Abstract We conducted a mesocosm experiment to examine how ocean acidification (OA) affects communities of prokaryotes and eukaryotes growing on single‐use drinking bottles in subtropical eutrophic waters of the East China Sea. Based on 16S rDNA gene sequencing, simulated high CO 2 significantly altered the prokaryotic community, with the relative abundance of the phylum Planctomycetota increasing by 49%. Under high CO 2 , prokaryotes in the plastisphere had enhanced nitrogen dissimilation and ureolysis, raising the possibility that OA may modify nutrient cycling in subtropical eutrophic waters. The relative abundance of pathogenic and animal parasite bacteria also increased under simulated high CO 2 . Our results show that elevated CO 2 levels significantly affected several animal taxa based on 18S rDNA gene sequencing. For example, Mayorella amoebae were highly resistant, whereas Labyrinthula were sensitive to OA. Thus, OA may alter plastisphere food chains in subtropical eutrophic waters. 
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    Free, publicly-accessible full text available August 1, 2024
  4. Abstract—Sleep staging is a key challenge in diagnosing and treating sleep-related diseases due to its labor-intensive, time- consuming, costly, and error-prone. With the availability of large- scale sleep signal data, many deep learning methods are proposed for automatic sleep staging. However, these existing methods face several challenges including the heterogeneity of patients’ underlying health conditions and the difficulty modeling complex interactions between sleep stages. In this paper, we propose a neural network architecture named DREAM to tackle these is- sues for automatic sleep staging. DREAM consists of (i) a feature representation network that generates robust representations for sleep signals via the variational auto-encoder framework and contrastive learning and (ii) a sleep stage classification network that explicitly models the interactions between sleep stages in the sequential context at both feature representation and label classification levels via Transformer and conditional random field architectures. Our experimental results indicate that DREAM significantly outperforms existing methods for automatic sleep staging on three sleep signal datasets. 
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  5. Free, publicly-accessible full text available March 28, 2024
  6. Age-related macular degeneration (AMD) is the leading cause of irreversible blindness in developed countries. Identifying patients at high risk of progression to late AMD, the sight-threatening stage, is critical for clinical actions, including medical interventions and timely monitoring. Recently, deep-learning-based models have been developed and achieved superior performance for late AMD pre- diction. However, most existing methods are limited to the color fundus photography (CFP) from the last ophthalmic visit and do not include the longitudinal CFP history and AMD progression during the previous years’ visits. Patients in different AMD subphenotypes might have various speeds of progression in different stages of AMD disease. Capturing the progression information during the previous years’ visits might be useful for the prediction of AMD pro- gression. In this work, we propose a Contrastive-Attention-based Time-aware Long Short-Term Memory network (CAT-LSTM) to predict AMD progression. First, we adopt a convolutional neural network (CNN) model with a contrastive attention module (CA) to extract abnormal features from CFPs. Then we utilize a time-aware LSTM (T-LSTM) to model the patients’ history and consider the AMD progression information. The combination of disease pro- gression, genotype information, demographics, and CFP features are sent to T-LSTM. Moreover, we leverage an auto-encoder to represent temporal CFP sequences as fixed-size vectors and adopt k-means to cluster them into subphenotypes. We evaluate the pro- posed model based on real-world datasets, and the results show that the proposed model could achieve 0.925 on area under the receiver operating characteristic (AUROC) for 5-year late-AMD prediction and outperforms the state-of-the-art methods by more than 3%, which demonstrates the effectiveness of the proposed CAT-LSTM. After analyzing patient representation learned by an auto-encoder, we identify 3 novel subphenotypes of AMD patients with different characteristics and progression rates to late AMD, paving the way for improved personalization of AMD management. The code of CAT-LSTM can be found at GitHub . 
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  7. Despite intense efforts in basic and clinical research, an individualized ventilation strategy for critically ill patients remains a major challenge. Recently, dynamic treatment regime (DTR) with reinforcement learning (RL) on electronic health records (EHR) has attracted interest from both the healthcare industry and machine learning research community. However, most learned DTR policies might be biased due to the existence of confounders. Although some treatment actions non-survivors received may be helpful, if confounders cause the mortality, the training of RL models guided by long-term outcomes (e.g., 90-day mortality) would punish those treatment actions causing the learned DTR policies to be suboptimal. In this study, we develop a new deconfounding actor-critic network (DAC) to learn optimal DTR policies for patients. To alleviate confounding issues, we incorporate a patient resampling module and a confounding balance module into our actor-critic framework. To avoid punishing the effective treatment actions non-survivors received, we design a short-term reward to capture patients' immediate health state changes. Combining short-term with long-term rewards could further improve the model performance. Moreover, we introduce a policy adaptation method to successfully transfer the learned model to new-source small-scale datasets. The experimental results on one semi-synthetic and two different real-world datasets show the proposed model outperforms the state-of-the-art models. The proposed model provides individualized treatment decisions for mechanical ventilation that could improve patient outcomes. 
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