Evaluating the clinical similarities between pairwise patients is a fundamental problem in healthcare informatics. A proper patient similarity measure enables various downstream applications, such as cohort study and treatment comparative effectiveness research. One major carrier for conducting patient similarity research is Electronic Health Records(EHRs), which are usually heterogeneous, longitudinal, and sparse. Though existing studies on learning patient similarity from EHRs have shown being useful in solving real clinical problems, their applicability is limited due to the lack of medical interpretations. Moreover, most previous methods assume a vector-based representation for patients, which typically requires aggregation of medical events over a certain time period. As a consequence, temporal information will be lost. In this paper, we propose a patient similarity evaluation framework based on the temporal matching of longitudinal patient EHRs. Two efficient methods are presented, unsupervised and supervised, both of which preserve the temporal properties in EHRs. The supervised scheme takes a convolutional neural network architecture and learns an optimal representation of patient clinical records with medical concept embedding. The empirical results on real-world clinical data demonstrate substantial improvement over the baselines. We make our code and sample data available for further study.
With medical concept embedding, we look forward to calculating the similarity amongst patients according to their EHRs. Considering the representations of patient medical events do not have a common time dimension, we cannot compare the patient event matrix directly. @cite_26 provided a relevant similarity measures between temporal series of brain functional images belonging to different subjects. Similar to @cite_26 , we adopt the RV coefficient to measure patient similarities. Note, however, that this coefficient only considers linear relationships between two data sets. To do more systematic research on measuring similarity of patient, our model also measures non-linear correlation between two patients using dCov coefficient. Apart from those unsupervised approach, we adopt the supervised learning method. We modify the Convolutional Neural Network(CNN) to derive the similarity scores for pairs of patients. The Convolutional networks models which are originally invented for image processing have wide applications in other domains. @cite_22 @cite_31 and @cite_7 respectively obtains the continuous representations of the sentences or short texts by a convolutional deep network, then the similarity can be effectively established.
@cite_31 @cite_26 @cite_22 @cite_7
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The widespread availability of electronic health records (EHRs) promises to usher in the era of personalized medicine. However, the problem of extracting useful clinical representations from longitudinal EHR data remains challenging. In this paper, we explore deep neural network models with learned medical feature embedding to deal with the problems of high dimensionality and temporality. Specifically, we use a multi-layer convolutional neural network (CNN) to parameterize the model and is thus able to capture complex non-linear longitudinal evolution of EHRs. Our model can effectively capture local short temporal dependency in EHRs, which is beneficial for risk prediction. To account for high dimensionality, we use the embedding medical features in the CNN model which hold the natural medical concepts. Our initial experiments produce promising results and demonstrate the effectiveness of both the medical feature embedding and the proposed convolutional neural network in risk prediction on cohorts of congestive heart failure and diabetes patients compared with several strong baselines. Convolutional networks (ConvNets) have achieved great successes in various challenging vision tasks. However, the performance of ConvNets would degrade when encountering the domain shift. The domain adaptation is more significant while challenging in the field of biomedical image analysis, where cross-modality data have largely different distributions. Given that annotating the medical data is especially expensive, the supervised transfer learning approaches are not quite optimal. In this paper, we propose an unsupervised domain adaptation framework with adversarial learning for cross-modality biomedical image segmentations. Specifically, our model is based on a dilated fully convolutional network for pixel-wise prediction. Moreover, we build a plug-and-play domain adaptation module (DAM) to map the target input to features which are aligned with source domain feature space. A domain critic module (DCM) is set up for discriminating the feature space of both domains. We optimize the DAM and DCM via an adversarial loss without using any target domain label. Our proposed method is validated by adapting a ConvNet trained with MRI images to unpaired CT data for cardiac structures segmentations, and achieved very promising results. Recent studies suggest that deep Convolutional Neural Network (CNN) models show higher representational similarity, compared to any other existing object recognition models, with macaque inferior temporal (IT) cortical responses, human ventral stream fMRI activations and human object recognition. These studies employed natural images of objects. A long research tradition employed abstract shapes to probe the selectivity of IT neurons. If CNN models provide a realistic model of IT responses, then they should capture the IT selectivity for such shapes. Here, we compare the activations of CNN units to a stimulus set of 2D regular and irregular shapes with the response selectivity of macaque IT neurons and with human similarity judgements. The shape set consisted of regular shapes that differed in nonaccidental properties, and irregular, asymmetrical shapes with curved or straight boundaries. We found that deep CNNs (Alexnet, VGG-16 and VGG-19) that were trained to classify natural images show response modulations to these shapes that were similar to those of IT neurons. Untrained CNNs with the same architecture than trained CNNs, but with random weights, demonstrated a poorer similarity than CNNs trained in classification. The difference between the trained and untrained CNNs emerged at the deep convolutional layers, where the similarity between the shape-related response modulations of IT neurons and the trained CNNs was high. Unlike IT neurons, human similarity judgements of the same shapes correlated best with the last layers of the trained CNNs. In particular, these deepest layers showed an enhanced sensitivity for straight versus curved irregular shapes, similar to that shown in human shape judgments. In conclusion, the representations of abstract shape similarity are highly comparable between macaque IT neurons and deep convolutional layers of CNNs that were trained to classify natural images, while human shape similarity judgments correlate better with the deepest layers. Recently, neuron activations extracted from a pre-trained convolutional neural network (CNN) show promising performance in various visual tasks. However, due to the domain and task bias, using the features generated from the model pre-trained for image classification as image representations for instance retrieval is problematic. In this paper, we propose quartet-net learning to improve the discriminative power of CNN features for instance retrieval. The general idea is to map the features into a space where the image similarity can be better evaluated. Our network differs from the traditional Siamese-net in two ways. First, we adopt a double-margin contrastive loss with a dynamic margin tuning strategy to train the network which leads to more robust performance. Second, we introduce in the mimic learning regularization to improve the generalization ability of the network by preventing it from overfitting to the training data. Catering for the network learning, we collect a large-scale dataset, namely GeoPair, which consists of 68k matching image pairs and 63k non-matching pairs. Experiments on several standard instance retrieval datasets demonstrate the effectiveness of our method.