With the widespread adoption of electronic health records (EHR) data, deep learning techniques have been broadly utilized for various health prediction tasks. Nevertheless, the labeled data scarcity issue restricts the prediction power of these deep models. To enhance the generalization capability of deep learning models when faced with such situations, a common trend is to train generative adversarial networks (GANs) or diffusion models for data augmentation. However, due to limitations in sample size and potential label imbalance issues, these methods are prone to mode collapse problems. This results in the generation of new samples that fail to preserve the subtype structure within EHR data, thereby limiting their practicality in health prediction tasks that generally require detailed patient phenotyping. Aiming at the above problems, we propose a Prototype-based Mixup method, dubbed ProtoMix, which combines prior knowledge of intrinsic data features from subtype centroids (i.e., prototypes) to guide the synthesis of new samples. Specifically, ProtoMix employs a prototype-guided mixup training task to shift the decision boundary away from the subtypes. Then, ProtoMix optimizes the sampling weights in different areas of the data manifold via a prototype-guided mixup sampling strategy. Throughout the training process, ProtoMix dynamically expands the training distribution using an adaptive mixing coefficient computation method. Experimental evaluations on three real-world datasets demonstrate the efficacy of ProtoMix.

Deep learning techniques are capable of capturing complex input-output relationships, and have been widely applied to the diagnosis prediction task based on web-based patient electronic health records (EHR) data. To improve the prediction and interpretability of pure data-driven deep learning with only a limited amount of labeled data, a pervasive trend is to assist the model training with knowledge priors from online medical knowledge graphs. However, they marginally investigated the label imbalance and the task-irrelevant noise in the external knowledge graph. The imbalanced label distribution would bias the learning and knowledge extraction towards the majority categories. The task-irrelevant noise introduces extra uncertainty to the model performance. To this end, aiming at by-passing the bias-variance trade-off dilemma, we introduce a new sequential learning framework, dubbed SeqCare, for diagnosis prediction with online medical knowledge graphs. Concretely, in the first step, SeqCare learns a bias-reduced space through a self-supervised graph contrastive learning task. Secondly, SeqCare reduces the learning uncertainty by refining the supervision signal and the graph structure of the knowledge graph simultaneously. Lastly, SeqCare trains the model in the bias-variance reduced space with a self-distillation to further filter out irrelevant information in the data. Experimental evaluations on two real-world datasets show that SeqCare outperforms state-of-the-art approaches. Case studies exemplify the interpretability of SeqCare. Moreover, the medical findings discovered by SeqCare are consistent with experts and medical literature.

Exploiting the correlations between medical features is essential to the success of healthcare data analysis. However, most existing methods are either suffering large estimation variance for data insufficiency or inflexible in terms of demanding task-specific medical knowledge. In this paper, we propose a novel patient health representation learning framework dubbedSAFARI.SAFARIlearns a compact representation by imposing a clinical-fact-inspired task-agnostic correlational sparsity prior to the correlations of medical feature pairs. Specifically, we learn the compact representation by solving the bi-level optimization problem, which involves solving the high-level inter-group correlations and the nested lower-level intra-group correlations. We leverage the Laplacian kernel as a robust metric for feature grouping and graph neural networks for solving the bi-level optimization problem following the optimal value reformulation paradigm. Experiments on five datasets of various inputs and tasks demonstrate the efficacy ofSAFARI. The discovered findings are also consistent with our insights and medical literature, which can provide valuable clinical explanations.

Despite the success of deep neural networks on text classification, their large capacity also leads to capturing task-irrelevant patterns such as label noise. Label noise is usually introduced into the data during label collection and causes nontrivial declines in performance due to the memorization effect. Though effort has been devoted to combating the label noise in other systems such as image classification, high-quality input features are necessary for discovering task-relevant patterns before memorizing the label noise. However, such a high-quality input feature requirement is hard to be satisfied for text classification due to the nature of natural language. To combat the label noise with low-quality input features in the text classification, we propose a novel framework that exploits external category descriptions to construct prototypes that can be used to denoise the input representation and alleviate the over-fitting. However, there still remains a challenge that the external category descriptions from other corpora could be semantically discrepant with the underlying task-specific classes in the training corpus. To align their semantics, we propose two regularizers that penalize sample-wise semantic-based deviations at the local level and class-wise structure-based deviations at the global level, respectively. Our extensive experiments across two open datasets and one real-world case study demonstrate that our method is superior to state-of-the-art baselines under various settings of label noise.

Multimodal electronic health record (EHR) data are widely used in clinical applications. Conventional methods usually assume that each sample (patient) is associated with the unified observed modalities, and all modalities are available for each sample. However, missing modality caused by various clinical and social reasons is a common issue in real-world clinical scenarios. Existing methods mostly rely on solving a generative model that learns a mapping from the latent space to the original input space, which is an unstable ill-posed inverse problem. To relieve the underdetermined system, we propose a model solving a direct problem, dubbed learning with Missing Modalities in Multimodal healthcare data (M3Care). M3Care is an end-to-end model compensating the missing information of the patients with missing modalities to perform clinical analysis. Instead of generating raw missing data, M3Care imputes the task-related information of the missing modalities in the latent space by the auxiliary information from each patient's similar neighbors, measured by a task-guided modality-adaptive similarity metric, and thence conducts the clinical tasks. The task-guided modality-adaptive similarity metric utilizes the uncensored modalities of the patient and the other patients who also have the same uncensored modalities to find similar patients. Experiments on real-world datasets show that M3Care outperforms the state-of-the-art baselines. Moreover, the findings discovered by M3Care are consistent with experts and medical knowledge, demonstrating the capability and the potential of providing useful insights and explanations.

While recent developments of neural network (NN) models have led to a series of record-breaking achievements in many applications, the lack of sufficiently good datasets remains a problem for some applications. For such a problem, we can however exploit a large number of unstructured text corpora as an external knowledge to complement the training data, and most prevailing neural network solutions employ word embedding methods for such purposes. In this paper, we propose LDA-Reg, a novel knowledge driven regularization framework based on Latent Dirichlet Allocation (LDA) as an alternative to the word embedding methods to adaptively utilize abundant external knowledge and to interpret the NN model. For the joint learning of the parameters, we propose EM-SGD, an effective update method which incorporates Expectation Maximization (EM) and Stochastic Gradient Descent (SGD) to update parameters iteratively. Moreover, we also devise a lazy update and sparse update method for the high-dimensional inputs and sparse inputs respectively. We validate the effectiveness of our regularization framework through an extensive experimental study over real world and standard benchmark datasets. The results show that our proposed framework not only achieves significant improvement over state-of-the-art word embedding methods but also learns interpretable and significant topics for various tasks.

Anomaly detection in healthcare data like patient records is no trivial task. The anomalies in these datasets are often caused by mismatches between different types of feature, e.g., medications that do not match with the diagnoses. Existing anomaly detection methods do not perform well when detecting "mismatches" between multiple types of feature, especially when the feature space is high-dimensional and sparse. This paper introduces a novel anomaly detection paradigm: Probabilistic-Mismatch Anomaly Detection (PMAD), which detects mismatches between features by modeling a normal instance with a common latent probability distribution that governs the generation of all types of feature. Under this paradigm, the target of anomaly detection is to find instances with dissimilar latent distributions. We further propose Topical PMAD based on an extended Latent Dirichlet Allocation (LDA) model, which is able to capture the latent relationship between features in a high-dimensional space. Experiments on both synthetic data and real-world patient records show that Topical PMAD can effectively detect anomalies with mismatched features, and is highly robust against high-dimensional data as well as inaccurate model selection. The real-world anomalies detected on a patient record dataset show a promising application prospect.