Combining deep learning with token selection for patient phenotyping from electronic health records

Natural language processing with machine learning methods to analyze unstructured patient-reported outcomes derived from electronic health records: A systematic review

OBJECTIVE

Natural language processing (NLP) combined with machine learning (ML) techniques are increasingly used to process unstructured/free-text patient-reported outcome (PRO) data available in electronic health records (EHRs). This systematic review summarizes the literature reporting NLP/ML systems/toolkits for analyzing PROs in clinical narratives of EHRs and discusses the future directions for the application of this modality in clinical care.

METHODS

We searched PubMed, Scopus, and Web of Science for studies written in English between 1/1/2000 and 12/31/2020. Seventy-nine studies meeting the eligibility criteria were included. We abstracted and summarized information related to the study purpose, patient population, type/source/amount of unstructured PRO data, linguistic features, and NLP systems/toolkits for processing unstructured PROs in EHRs.

RESULTS

Most of the studies used NLP/ML techniques to extract PROs from clinical narratives (n = 74) and mapped the extracted PROs into specific PRO domains for phenotyping or clustering purposes (n = 26). Some studies used NLP/ML to process PROs for predicting disease progression or onset of adverse events (n = 22) or developing/validating NLP/ML pipelines for analyzing unstructured PROs (n = 19). Studies used different linguistic features, including lexical, syntactic, semantic, and contextual features, to process unstructured PROs. Among the 25 NLP systems/toolkits we identified, 15 used rule-based NLP, 6 used hybrid NLP, and 4 used non-neural ML algorithms embedded in NLP.

CONCLUSIONS

This study supports the potential utility of different NLP/ML techniques in processing unstructured PROs available in EHRs for clinical care. Though using annotation rules for NLP/ML to analyze unstructured PROs is dominant, deploying novel neural ML-based methods is warranted.

Improving Diagnostics with Deep Forest Applied to Electronic Health Records

An electronic health record (EHR) is a vital high-dimensional part of medical concepts. Discovering implicit correlations in the information of this data set and the research and informative aspects can improve the treatment and management process. The challenge of concern is the data sources' limitations in finding a stable model to relate medical concepts and use these existing connections. This paper presents Patient Forest, a novel end-to-end approach for learning patient representations from tree-structured data for readmission and mortality prediction tasks. By leveraging statistical features, the proposed model is able to provide an accurate and reliable classifier for predicting readmission and mortality. Experiments on MIMIC-III and eICU datasets demonstrate Patient Forest outperforms existing machine learning models, especially when the training data are limited. Additionally, a qualitative evaluation of Patient Forest is conducted by visualising the learnt representations in 2D space using the t-SNE, which further confirms the effectiveness of the proposed model in learning EHR representations.

Data Challenges for Externally Controlled Trials: Viewpoint

The preferred evidence of a large randomized controlled trial is difficult to adopt in scenarios, such as rare conditions or clinical subgroups with high unmet needs, and evidence from external sources, including real-world data, is being increasingly considered by decision makers. Real-world data originate from many sources, and identifying suitable real-world data that can be used to contextualize a single-arm trial, as an external control arm, has several challenges. In this viewpoint article, we provide an overview of the technical challenges raised by regulatory and health reimbursement agencies when evaluating comparative efficacy, such as identification, outcome, and time selection challenges. By breaking down these challenges, we provide practical solutions for researchers to consider through the approaches of detailed planning, collection, and record linkage to analyze external data for comparative efficacy.

How data science and AI-based technologies impact genomics

Advancements in high-throughput sequencing have yielded vast amounts of genomic data, which are studied using genome-wide association study (GWAS)/phenome-wide association study (PheWAS) methods to identify associations between the genotype and phenotype. The associated findings have contributed to pharmacogenomics and improved clinical decision support at the point of care in many healthcare systems. However, the accumulation of genomic data from sequencing and clinical data from electronic health records (EHRs) poses significant challenges for data scientists. Following the rise of artificial intelligence (AI) technology such as machine learning and deep learning, an increasing number of GWAS/PheWAS studies have successfully leveraged this technology to overcome the aforementioned challenges. In this review, we focus on the application of data science and AI technology in three areas, including risk prediction and identification of causal single-nucleotide polymorphisms, EHR-based phenotyping and CRISPR guide RNA design. Additionally, we highlight a few emerging AI technologies, such as transfer learning and multi-view learning, which will or have started to benefit genomic studies.

Practical Considerations for Developing Clinical Natural Language Processing Systems for Population Health Management and Measurement

Experts have noted a concerning gap between clinical natural language processing (NLP) research and real-world applications, such as clinical decision support. To help address this gap, in this viewpoint, we enumerate a set of practical considerations for developing an NLP system to support real-world clinical needs and improve health outcomes. They include determining (1) the readiness of the data and compute resources for NLP, (2) the organizational incentives to use and maintain the NLP systems, and (3) the feasibility of implementation and continued monitoring. These considerations are intended to benefit the design of future clinical NLP projects and can be applied across a variety of settings, including large health systems or smaller clinical practices that have adopted electronic medical records in the United States and globally.

Artificial Intelligence in Rheumatoid Arthritis: Current Status and Future Perspectives: A State-of-the-Art Review

Investigation of the potential applications of artificial intelligence (AI), including machine learning (ML) and deep learning (DL) techniques, is an exponentially growing field in medicine and healthcare. These methods can be critical in providing high-quality care to patients with chronic rheumatological diseases lacking an optimal treatment, like rheumatoid arthritis (RA), which is the second most prevalent autoimmune disease. Herein, following reviewing the basic concepts of AI, we summarize the advances in its applications in RA clinical practice and research. We provide directions for future investigations in this field after reviewing the current knowledge gaps and technical and ethical challenges in applying AI. Automated models have been largely used to improve RA diagnosis since the early 2000s, and they have used a wide variety of techniques, e.g., support vector machine, random forest, and artificial neural networks. AI algorithms can facilitate screening and identification of susceptible groups, diagnosis using omics, imaging, clinical, and sensor data, patient detection within electronic health record (EHR), i.e., phenotyping, treatment response assessment, monitoring disease course, determining prognosis, novel drug discovery, and enhancing basic science research. They can also aid in risk assessment for incidence of comorbidities, e.g., cardiovascular diseases, in patients with RA. However, the proposed models may vary significantly in their performance and reliability. Despite the promising results achieved by AI models in enhancing early diagnosis and management of patients with RA, they are not fully ready to be incorporated into clinical practice. Future investigations are required to ensure development of reliable and generalizable algorithms while they carefully look for any potential source of bias or misconduct. We showed that a growing body of evidence supports the potential role of AI in revolutionizing screening, diagnosis, and management of patients with RA. However, multiple obstacles hinder clinical applications of AI models. Incorporating the machine and/or deep learning algorithms into real-world settings would be a key step in the progress of AI in medicine.

Applying Machine Learning in Distributed Data Networks for Pharmacoepidemiologic and Pharmacovigilance Studies: Opportunities, Challenges, and Considerations

Increasing availability of electronic health databases capturing real-world experiences with medical products has garnered much interest in their use for pharmacoepidemiologic and pharmacovigilance studies. The traditional practice of having numerous groups use single databases to accomplish similar tasks and address common questions about medical products can be made more efficient through well-coordinated multi-database studies, greatly facilitated through distributed data network (DDN) architectures. Access to larger amounts of electronic health data within DDNs has created a growing interest in using data-adaptive machine learning (ML) techniques that can automatically model complex associations in high-dimensional data with minimal human guidance. However, the siloed storage and diverse nature of the databases in DDNs create unique challenges for using ML. In this paper, we discuss opportunities, challenges, and considerations for applying ML in DDNs for pharmacoepidemiologic and pharmacovigilance studies. We first discuss major types of activities performed by DDNs and how ML may be used. Next, we discuss practical data-related factors influencing how DDNs work in practice. We then combine these discussions and jointly consider how opportunities for ML are affected by practical data-related factors for DDNs, leading to several challenges. We present different approaches for addressing these challenges and highlight efforts that real-world DDNs have taken or are currently taking to help mitigate them. Despite these challenges, the time is ripe for the emerging interest to use ML in DDNs, and the utility of these data-adaptive modeling techniques in pharmacoepidemiologic and pharmacovigilance studies will likely continue to increase in the coming years.

Crowdsourcing and machine learning approaches for extracting entities indicating potential foodborne outbreaks from social media

Foodborne outbreaks are a serious but preventable threat to public health that often lead to illness, loss of life, significant economic loss, and the erosion of consumer confidence. Understanding how consumers respond when interacting with foods, as well as extracting information from posts on social media may provide new means of reducing the risks and curtailing the outbreaks. In recent years, Twitter has been employed as a new tool for identifying unreported foodborne illnesses. However, there is a huge gap between the identification of sporadic illnesses and the early detection of a potential outbreak. In this work, the dual-task BERTweet model was developed to identify unreported foodborne illnesses and extract foodborne-illness-related entities from Twitter. Unlike previous methods, our model leveraged the mutually beneficial relationships between the two tasks. The results showed that the F1-score of relevance prediction was 0.87, and the F1-score of entity extraction was 0.61. Key elements such as time, location, and food detected from sentences indicating foodborne illnesses were used to analyze potential foodborne outbreaks in massive historical tweets. A case study on tweets indicating foodborne illnesses showed that the discovered trend is consistent with the true outbreaks that occurred during the same period.

Medical Text Classification Using Hybrid Deep Learning Models with Multihead Attention

To unlock information present in clinical description, automatic medical text classification is highly useful in the arena of natural language processing (NLP). For medical text classification tasks, machine learning techniques seem to be quite effective; however, it requires extensive effort from human side, so that the labeled training data can be created. For clinical and translational research, a huge quantity of detailed patient information, such as disease status, lab tests, medication history, side effects, and treatment outcomes, has been collected in an electronic format, and it serves as a valuable data source for further analysis. Therefore, a huge quantity of detailed patient information is present in the medical text, and it is quite a huge challenge to process it efficiently. In this work, a medical text classification paradigm, using two novel deep learning architectures, is proposed to mitigate the human efforts. The first approach is that a quad channel hybrid long short-term memory (QC-LSTM) deep learning model is implemented utilizing four channels, and the second approach is that a hybrid bidirectional gated recurrent unit (BiGRU) deep learning model with multihead attention is developed and implemented successfully. The proposed methodology is validated on two medical text datasets, and a comprehensive analysis is conducted. The best results in terms of classification accuracy of 96.72% is obtained with the proposed QC-LSTM deep learning model, and a classification accuracy of 95.76% is obtained with the proposed hybrid BiGRU deep learning model.

Lexicon Development for COVID-19-related Concepts Using Open-source Word Embedding Sources: An Intrinsic and Extrinsic Evaluation

BACKGROUND

Scientists are developing new computational methods and prediction models to better clinically understand COVID-19 prevalence, treatment efficacy, and patient outcomes. These efforts could be improved by leveraging documented COVID-19-related symptoms, findings, and disorders from clinical text sources in an electronic health record. Word embeddings can identify terms related to these clinical concepts from both the biomedical and nonbiomedical domains, and are being shared with the open-source community at large. However, it's unclear how useful openly available word embeddings are for developing lexicons for COVID-19-related concepts.

OBJECTIVE

Given an initial lexicon of COVID-19-related terms, this study aims to characterize the returned terms by similarity across various open-source word embeddings and determine common semantic and syntactic patterns between the COVID-19 queried terms and returned terms specific to the word embedding source.

METHODS

We compared seven openly available word embedding sources. Using a series of COVID-19-related terms for associated symptoms, findings, and disorders, we conducted an interannotator agreement study to determine how accurately the most similar returned terms could be classified according to semantic types by three annotators. We conducted a qualitative study of COVID-19 queried terms and their returned terms to detect informative patterns for constructing lexicons. We demonstrated the utility of applying such learned synonyms to discharge summaries by reporting the proportion of patients identified by concept among three patient cohorts: pneumonia (n=6410), acute respiratory distress syndrome (n=8647), and COVID-19 (n=2397).

RESULTS

We observed high pairwise interannotator agreement (Cohen kappa) for symptoms (0.86-0.99), findings (0.93-0.99), and disorders (0.93-0.99). Word embedding sources generated based on characters tend to return more synonyms (mean count of 7.2 synonyms) compared to token-based embedding sources (mean counts range from 2.0 to 3.4). Word embedding sources queried using a qualifier term (eg, dry cough or muscle pain) more often returned qualifiers of the similar semantic type (eg, "dry" returns consistency qualifiers like "wet" and "runny") compared to a single term (eg, cough or pain) queries. A higher proportion of patients had documented fever (0.61-0.84), cough (0.41-0.55), shortness of breath (0.40-0.59), and hypoxia (0.51-0.56) retrieved than other clinical features. Terms for dry cough returned a higher proportion of patients with COVID-19 (0.07) than the pneumonia (0.05) and acute respiratory distress syndrome (0.03) populations.

CONCLUSIONS

Word embeddings are valuable technology for learning related terms, including synonyms. When leveraging openly available word embedding sources, choices made for the construction of the word embeddings can significantly influence the words learned.

Learning fine-grained estimation of physiological states from coarse-grained labels by distribution restoration

Due to its importance in clinical science, the estimation of physiological states (e.g., the severity of pathological tremor) has aroused growing interest in machine learning community. While the physiological state is a continuous variable, its continuity is lost when the physiological state is quantized into a few discrete classes during recording and labeling. The discreteness introduces misalignment between the true value and its label, meaning that these labels are unfortunately imprecise and coarse-grained. Most previous work did not consider the inaccuracy and directly utilized the coarse labels to train the machine learning algorithms, whose predictions are also coarse-grained. In this work, we propose to learn a precise, fine-grained estimation of physiological states using these coarse-grained ground truths. Established on mathematical rigorous proof, we utilize imprecise labels to restore the probabilistic distribution of precise labels in an approximate order-preserving fashion, then the deep neural network learns from this distribution and offers fine-grained estimation. We demonstrate the effectiveness of our approach in assessing the pathological tremor in Parkinson's Disease and estimating the systolic blood pressure from bioelectrical signals.

Clinical Characteristics and Prognostic Factors for Intensive Care Unit Admission of Patients With COVID-19: Retrospective Study Using Machine Learning and Natural Language Processing

BACKGROUND

Many factors involved in the onset and clinical course of the ongoing COVID-19 pandemic are still unknown. Although big data analytics and artificial intelligence are widely used in the realms of health and medicine, researchers are only beginning to use these tools to explore the clinical characteristics and predictive factors of patients with COVID-19.

OBJECTIVE

Our primary objectives are to describe the clinical characteristics and determine the factors that predict intensive care unit (ICU) admission of patients with COVID-19. Determining these factors using a well-defined population can increase our understanding of the real-world epidemiology of the disease.

METHODS

We used a combination of classic epidemiological methods, natural language processing (NLP), and machine learning (for predictive modeling) to analyze the electronic health records (EHRs) of patients with COVID-19. We explored the unstructured free text in the EHRs within the Servicio de Salud de Castilla-La Mancha (SESCAM) Health Care Network (Castilla-La Mancha, Spain) from the entire population with available EHRs (1,364,924 patients) from January 1 to March 29, 2020. We extracted related clinical information regarding diagnosis, progression, and outcome for all COVID-19 cases.

RESULTS

A total of 10,504 patients with a clinical or polymerase chain reaction-confirmed diagnosis of COVID-19 were identified; 5519 (52.5%) were male, with a mean age of 58.2 years (SD 19.7). Upon admission, the most common symptoms were cough, fever, and dyspnea; however, all three symptoms occurred in fewer than half of the cases. Overall, 6.1% (83/1353) of hospitalized patients required ICU admission. Using a machine-learning, data-driven algorithm, we identified that a combination of age, fever, and tachypnea was the most parsimonious predictor of ICU admission; patients younger than 56 years, without tachypnea, and temperature <39 degrees Celsius (or >39 ºC without respiratory crackles) were not admitted to the ICU. In contrast, patients with COVID-19 aged 40 to 79 years were likely to be admitted to the ICU if they had tachypnea and delayed their visit to the emergency department after being seen in primary care.

CONCLUSIONS

Our results show that a combination of easily obtainable clinical variables (age, fever, and tachypnea with or without respiratory crackles) predicts whether patients with COVID-19 will require ICU admission.

Named Entity Recognition and Relation Detection for Biomedical Information Extraction

The number of scientific publications in the literature is steadily growing, containing our knowledge in the biomedical, health, and clinical sciences. Since there is currently no automatic archiving of the obtained results, much of this information remains buried in textual details not readily available for further usage or analysis. For this reason, natural language processing (NLP) and text mining methods are used for information extraction from such publications. In this paper, we review practices for Named Entity Recognition (NER) and Relation Detection (RD), allowing, e.g., to identify interactions between proteins and drugs or genes and diseases. This information can be integrated into networks to summarize large-scale details on a particular biomedical or clinical problem, which is then amenable for easy data management and further analysis. Furthermore, we survey novel deep learning methods that have recently been introduced for such tasks.

An Introductory Review of Deep Learning for Prediction Models With Big Data

Deep learning models stand for a new learning paradigm in artificial intelligence (AI) and machine learning. Recent breakthrough results in image analysis and speech recognition have generated a massive interest in this field because also applications in many other domains providing big data seem possible. On a downside, the mathematical and computational methodology underlying deep learning models is very challenging, especially for interdisciplinary scientists. For this reason, we present in this paper an introductory review of deep learning approaches including Deep Feedforward Neural Networks (D-FFNN), Convolutional Neural Networks (CNNs), Deep Belief Networks (DBNs), Autoencoders (AEs), and Long Short-Term Memory (LSTM) networks. These models form the major core architectures of deep learning models currently used and should belong in any data scientist's toolbox. Importantly, those core architectural building blocks can be composed flexibly-in an almost Lego-like manner-to build new application-specific network architectures. Hence, a basic understanding of these network architectures is important to be prepared for future developments in AI.

An Introductory Review of Deep Learning for Prediction Models With Big Data

Deep learning models stand for a new learning paradigm in artificial intelligence (AI) and machine learning. Recent breakthrough results in image analysis and speech recognition have generated a massive interest in this field because also applications in many other domains providing big data seem possible. On a downside, the mathematical and computational methodology underlying deep learning models is very challenging, especially for interdisciplinary scientists. For this reason, we present in this paper an introductory review of deep learning approaches including Deep Feedforward Neural Networks (D-FFNN), Convolutional Neural Networks (CNNs), Deep Belief Networks (DBNs), Autoencoders (AEs), and Long Short-Term Memory (LSTM) networks. These models form the major core architectures of deep learning models currently used and should belong in any data scientist's toolbox. Importantly, those core architectural building blocks can be composed flexibly-in an almost Lego-like manner-to build new application-specific network architectures. Hence, a basic understanding of these network architectures is important to be prepared for future developments in AI.