Cross-Domain Missingness-Aware Time-Series Adaptation With Similarity Distillation in Medical Applications

DNA-T: Deformable Neighborhood Attention Transformer for Irregular Medical Time Series

The real-world Electronic Health Records (EHRs) present irregularities due to changes in the patient's health status, resulting in various time intervals between observations and different physiological variables examined at each observation point. There have been recent applications of Transformer-based models in the field of irregular time series. However, the full attention mechanism in Transformer overly focuses on distant information, ignoring the short-term correlations of the condition. Thereby, the model is not able to capture localized changes or short-term fluctuations in patients' conditions. Therefore, we propose a novel end-to-end Deformable Neighborhood Attention Transformer (DNA-T) for irregular medical time series. The DNA-T captures local features by dynamically adjusting the receptive field of attention and aggregating relevant deformable neighborhoods in irregular time series. Specifically, we design a Deformable Neighborhood Attention (DNA) module that enables the network to attend to relevant neighborhoods by drifting the receiving field of neighborhood attention. The DNA enhances the model's sensitivity to local information and representation of local features, thereby capturing the correlation of localized changes in patients' conditions. We conduct extensive experiments to validate the effectiveness of DNA-T, outperforming existing state-of-the-art methods in predicting the mortality risk of patients. Moreover, we visualize an example to validate the effectiveness of the proposed DNA.

BIR: Biomedical Information Retrieval System for Cancer Treatment in Electronic Health Record Using Transformers

The rapid growth of electronic health records (EHRs) has led to unprecedented biomedical data. Clinician access to the latest patient information can improve the quality of healthcare. However, clinicians have difficulty finding information quickly and easily due to the sheer data mining volume. Biomedical information retrieval (BIR) systems can help clinicians find the information required by automatically searching EHRs and returning relevant results. However, traditional BIR systems cannot understand the complex relationships between EHR entities. Transformers are a new type of neural network that is very effective for natural language processing (NLP) tasks. As a result, transformers are well suited for tasks such as machine translation and text summarization. In this paper, we propose a new BIR system for EHRs that uses transformers for predicting cancer treatment from EHR. Our system can understand the complex relationships between the different entities in an EHR, which allows it to return more relevant results to clinicians. We evaluated our system on a dataset of EHRs and found that it outperformed state-of-the-art BIR systems on various tasks, including medical question answering and information extraction. Our results show that Transformers are a promising approach for BIR in EHRs, reaching an accuracy and an F1-score of 86.46%, and 0.8157, respectively. We believe that our system can help clinicians find the information they need more quickly and easily, leading to improved patient care.

A Review on Electronic Health Record Text-Mining for Biomedical Name Entity Recognition in Healthcare Domain

Biomedical-named entity recognition (bNER) is critical in biomedical informatics. It identifies biomedical entities with special meanings, such as people, places, and organizations, as predefined semantic types in electronic health records (EHR). bNER is essential for discovering novel knowledge using computational methods and Information Technology. Early bNER systems were configured manually to include domain-specific features and rules. However, these systems were limited in handling the complexity of the biomedical text. Recent advances in deep learning (DL) have led to the development of more powerful bNER systems. DL-based bNER systems can learn the patterns of biomedical text automatically, making them more robust and efficient than traditional rule-based systems. This paper reviews the healthcare domain of bNER, using DL techniques and artificial intelligence in clinical records, for mining treatment prediction. bNER-based tools are categorized systematically and represent the distribution of input, context, and tag (encoder/decoder). Furthermore, to create a labeled dataset for our machine learning sentiment analyzer to analyze the sentiment of a set of tweets, we used a manual coding approach and the multi-task learning method to bias the training signals with domain knowledge inductively. To conclude, we discuss the challenges facing bNER systems and future directions in the healthcare field.

Backdoor Attack on Machine Learning Models of Electronic Health Records: Exploiting Missing Value Patterns (Preprint)

Background

A backdoor attack controls the output of a machine learning model in 2 stages. First, the attacker poisons the training data set, introducing a back door into the victim’s trained model. Second, during test time, the attacker adds an imperceptible pattern called a trigger to the input values, which forces the victim’s model to output the attacker’s intended values instead of true predictions or decisions. While backdoor attacks pose a serious threat to the reliability of machine learning–based medical diagnostics, existing backdoor attacks that directly change the input values are detectable relatively easily.

Objective

The goal of this study was to propose and study a robust backdoor attack on mortality-prediction machine learning models that use electronic health records. We showed that our backdoor attack grants attackers full control over classification outcomes for safety-critical tasks such as mortality prediction, highlighting the importance of undertaking safe artificial intelligence research in the medical field.

Methods

We present a trigger generation method based on missing patterns in electronic health record data. Compared to existing approaches, which introduce noise into the medical record, the proposed backdoor attack makes it simple to construct backdoor triggers without prior knowledge. To effectively avoid detection by manual inspectors, we employ variational autoencoders to learn the missing patterns in normal electronic health record data and produce trigger data that appears similar to this data.

Results

We experimented with the proposed backdoor attack on 4 machine learning models (linear regression, multilayer perceptron, long short-term memory, and gated recurrent units) that predict in-hospital mortality using a public electronic health record data set. The results showed that the proposed technique achieved a significant drop in the victim’s discrimination performance (reducing the area under the precision-recall curve by at most 0.45), with a low poisoning rate (2%) in the training data set. In addition, the impact of the attack on general classification performance was negligible (it reduced the area under the precision-recall curve by an average of 0.01025), which makes it difficult to detect the presence of poison.

Conclusions

To the best of our knowledge, this is the first study to propose a backdoor attack that uses missing information from tabular data as a trigger. Through extensive experiments, we demonstrated that our backdoor attack can inflict severe damage on medical machine learning classifiers in practice.

Explainable Uncertainty-Aware Convolutional Recurrent Neural Network for Irregular Medical Time Series

Influenced by the dynamic changes in the severity of illness, patients usually take examinations in hospitals irregularly, producing a large volume of irregular medical time-series data. Performing diagnosis prediction from the irregular medical time series is challenging because the intervals between consecutive records significantly vary along time. Existing methods often handle this problem by generating regular time series from the irregular medical records without considering the uncertainty in the generated data, induced by the varying intervals. Thus, a novel Uncertainty-Aware Convolutional Recurrent Neural Network (UA-CRNN) is proposed in this article, which introduces the uncertainty information in the generated data to boost the risk prediction. To tackle the complex medical time series with subseries of different frequencies, the uncertainty information is further incorporated into the subseries level rather than the whole sequence to seamlessly adjust different time intervals. Specifically, a hierarchical uncertainty-aware decomposition layer (UADL) is designed to adaptively decompose time series into different subseries and assign them proper weights in accordance with their reliabilities. Meanwhile, an Explainable UA-CRNN (eUA-CRNN) is proposed to exploit filters with different passbands to ensure the unity of components in each subseries and the diversity of components in different subseries. Furthermore, eUA-CRNN incorporates with an uncertainty-aware attention module to learn attention weights from the uncertainty information, providing the explainable prediction results. The extensive experimental results on three real-world medical data sets illustrate the superiority of the proposed method compared with the state-of-the-art methods.