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Register a new userPre-training of Graph Augmented Transformers for Medication Recommendation
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Junyuan Shang
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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Medication recommendation is an important healthcare application. It is commonly formulated as a temporal prediction task. Hence, most existing works only utilize longitudinal electronic health records (EHRs) from a small number of patients with multiple visits ignoring a large number of patients with a single visit (selection bias). Moreover, important hierarchical knowledge such as diagnosis hierarchy is not leveraged in the representation learning process. To address these challenges, we propose G-BERT, a new model to combine the power of Graph Neural Networks (GNNs) and BERT (Bidirectional Encoder Representations from Transformers) for medical code representation and medication recommendation. We use GNNs to represent the internal hierarchical structures of medical codes. Then we integrate the GNN representation into a transformer-based visit encoder and pre-train it on EHR data from patients only with a single visit. The pre-trained visit encoder and representation are then fine-tuned for downstream predictive tasks on longitudinal EHRs from patients with multiple visits. G-BERT is the first to bring the language model pre-training schema into the healthcare domain and it achieved state-of-the-art performance on the medication recommendation task.
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Recent progress in deep learning is revolutionizing the healthcare domain including providing solutions to medication recommendations, especially recommending medication combination for patients with complex health conditions. Existing approaches either do not customize based on patient health history, or ignore existing knowledge on drug-drug interactions (DDI) that might lead to adverse outcomes. To fill this gap, we propose the Graph Augmented Memory Networks (GAMENet), which integrates the drug-drug interactions knowledge graph by a memory module implemented as a graph convolutional networks, and models longitudinal patient records as the query. It is trained end-to-end to provide safe and personalized recommendation of medication combination. We demonstrate the effectiveness and safety of GAMENet by comparing with several state-of-the-art methods on real EHR data. GAMENet outperformed all baselines in all effectiveness measures, and also achieved 3.60% DDI rate reduction from existing EHR data.
Recommending medications for patients using electronic health records (EHRs) is a crucial data mining task for an intelligent healthcare system. It can assist doctors in making clinical decisions more efficiently. However, the inherent complexity of the EHR data renders it as a challenging task: (1) Multilevel structures: the EHR data typically contains multilevel structures which are closely related with the decision-making pathways, e.g., laboratory results lead to disease diagnoses, and then contribute to the prescribed medications; (2) Multiple sequences interactions: multiple sequences in EHR data are usually closely correlated with each other; (3) Abundant noise: lots of task-unrelated features or noise information within EHR data generally result in suboptimal performance. To tackle the above challenges, we propose a multilevel selective and interactive network (MeSIN) for medication recommendation. Specifically, MeSIN is designed with three components. First, an attentional selective module (ASM) is applied to assign flexible attention scores to different medical codes embeddings by their relevance to the recommended medications in every admission. Second, we incorporate a novel interactive long-short term memory network (InLSTM) to reinforce the interactions of multilevel medical sequences in EHR data with the help of the calibrated memory-augmented cell and an enhanced input gate. Finally, we employ a global selective fusion module (GSFM) to infuse the multi-sourced information embeddings into final patient representations for medications recommendation. To validate our method, extensive experiments have been conducted on a real-world clinical dataset. The results demonstrate a consistent superiority of our framework over several baselines and testify the effectiveness of our proposed approach.
The Transformer architecture deeply changed the natural language processing, outperforming all previous state-of-the-art models. However, well-known Transformer models like BERT, RoBERTa, and GPT-2 require a huge compute budget to create a high quality contextualised representation. In this paper, we study several efficient pre-training objectives for Transformers-based models. By testing these objectives on different tasks, we determine which of the ELECTRA models new features is the most relevant. We confirm that Transformers pre-training is improved when the input does not contain masked tokens and that the usage of the whole output to compute the loss reduces training time. Moreover, inspired by ELECTRA, we study a model composed of two blocks; a discriminator and a simple generator based on a statistical model with no impact on the computational performances. Besides, we prove that eliminating the MASK token and considering the whole output during the loss computation are essential choices to improve performance. Furthermore, we show that it is possible to efficiently train BERT-like models using a discriminative approach as in ELECTRA but without a complex generator, which is expensive. Finally, we show that ELECTRA benefits heavily from a state-of-the-art hyper-parameters search.
Side information of items, e.g., images and text description, has shown to be effective in contributing to accurate recommendations. Inspired by the recent success of pre-training models on natural language and images, we propose a pre-training strategy to learn item representations by considering both item side information and their relationships. We relate items by common user activities, e.g., co-purchase, and construct a homogeneous item graph. This graph provides a unified view of item relations and their associated side information in multimodality. We develop a novel sampling algorithm named MCNSampling to select contextual neighbors for each item. The proposed Pre-trained Multimodal Graph Transformer (PMGT) learns item representations with two objectives: 1) graph structure reconstruction, and 2) masked node feature reconstruction. Experimental results on real datasets demonstrate that the proposed PMGT model effectively exploits the multimodality side information to achieve better accuracies in downstream tasks including item recommendation, item classification, and click-through ratio prediction. We also report a case study of testing the proposed PMGT model in an online setting with 600 thousand users.
Recommender systems aim to provide item recommendations for users, and are usually faced with data sparsity problem (e.g., cold start) in real-world scenarios. Recently pre-trained models have shown their effectiveness in knowledge transfer between domains and tasks, which can potentially alleviate the data sparsity problem in recommender systems. In this survey, we first provide a review of recommender systems with pre-training. In addition, we show the benefits of pre-training to recommender systems through experiments. Finally, we discuss several promising directions for future research for recommender systems with pre-training.
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