Classifying clinical notes with pain assessment using machine learning

The Role and Applications of Artificial Intelligence in the Treatment of Chronic Pain

PURPOSE OF REVIEW

This review aims to explore the interface between artificial intelligence (AI) and chronic pain, seeking to identify areas of focus for enhancing current treatments and yielding novel therapies.

RECENT FINDINGS

In the United States, the prevalence of chronic pain is estimated to be upwards of 40%. Its impact extends to increased healthcare costs, reduced economic productivity, and strain on healthcare resources. Addressing this condition is particularly challenging due to its complexity and the significant variability in how patients respond to treatment. Current options often struggle to provide long-term relief, with their benefits rarely outweighing the risks, such as dependency or other side effects. Currently, AI has impacted four key areas of chronic pain treatment and research: (1) predicting outcomes based on clinical information; (2) extracting features from text, specifically clinical notes; (3) modeling 'omic data to identify meaningful patient subgroups with potential for personalized treatments and improved understanding of disease processes; and (4) disentangling complex neuronal signals responsible for pain, which current therapies attempt to modulate. As AI advances, leveraging state-of-the-art architectures will be essential for improving chronic pain treatment. Current efforts aim to extract meaningful representations from complex data, paving the way for personalized medicine. The identification of unique patient subgroups should reveal targets for tailored chronic pain treatments. Moreover, enhancing current treatment approaches is achievable by gaining a more profound understanding of patient physiology and responses. This can be realized by leveraging AI on the increasing volume of data linked to chronic pain.

Predicting Chronic Pain and Treatment Outcomes Using Machine Learning Models Based on High-dimensional Clinical Data From a Large Retrospective Cohort

PURPOSE

To identify factors and indicators that affect chronic pain and pain relief, and to develop predictive models using machine learning.

METHODS

We analyzed the data of 67,028 outpatient cases and 11,310 valid samples with pain from a large retrospective cohort. We used decision tree, random forest, AdaBoost, neural network, and logistic regression to discover significant indicators and to predict pain and treatment relief.

FINDINGS

The random forest model had the highest accuracy, F1 value, precision, and recall rates for predicting pain relief. The main factors affecting pain and treatment relief included body mass index, blood pressure, age, body temperature, heart rate, pulse, and neutrophil/lymphocyte × platelet ratio. The logistic regression model had high sensitivity and specificity for predicting pain occurrence.

IMPLICATIONS

Machine learning models can be used to analyze the risk factors and predictors of chronic pain and pain relief, and to provide personalized and evidence-based pain management.

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.

Luther S, Heapy A, Brandt C, J. Lisi A. Extracting Pain Care Quality Indicators from U.S. Veterans Health Administration Chiropractic Care Using Natural Language Processing

BACKGROUND

Musculoskeletal pain is common in the Veterans Health Administration (VHA), and there is growing national use of chiropractic services within the VHA. Rapid expansion requires scalable and autonomous solutions, such as natural language processing (NLP), to monitor care quality. Previous work has defined indicators of pain care quality that represent essential elements of guideline-concordant, comprehensive pain assessment, treatment planning, and reassessment.

OBJECTIVE

Our purpose was to identify pain care quality indicators and assess patterns across different clinic visit types using NLP on VHA chiropractic clinic documentation.

METHODS

Notes from ambulatory or in-hospital chiropractic care visits from October 1, 2018 to September 30, 2019 for patients in the Women Veterans Cohort Study were included in the corpus, with visits identified as consultation visits and/or evaluation and management (E&M) visits. Descriptive statistics of pain care quality indicator classes were calculated and compared across visit types.

RESULTS

There were 11,752 patients who received any chiropractic care during FY2019, with 63,812 notes included in the corpus. Consultation notes had more than twice the total number of annotations per note (87.9) as follow-up visit notes (34.7). The mean number of total classes documented per note across the entire corpus was 9.4 (standard deviation [SD]  =  1.5). More total indicator classes were documented during consultation visits with (mean  =  14.8, SD  =  0.9) or without E&M (mean  =  13.9, SD  =  1.2) compared to follow-up visits with (mean  =  9.1, SD  =  1.4) or without E&M (mean  =  8.6, SD  =  1.5). Co-occurrence of pain care quality indicators describing pain assessment was high.

CONCLUSION

VHA chiropractors frequently document pain care quality indicators, identifiable using NLP, with variability across different visit types.

Extraction and Quantification of Words Representing Degrees of Diseases: Combining the Fuzzy C-Means Method and Gaussian Membership

Background

Due to the development of medical data, a large amount of clinical data has been generated. These unstructured data contain substantial information. Extracting useful knowledge from this data and making scientific decisions for diagnosing and treating diseases have become increasingly necessary. Unstructured data, such as in the Marketplace for Medical Information in Intensive Care III (MIMIC-III) data set, contain several ambiguous words that demonstrate the subjectivity of doctors, such as descriptions of patient symptoms. These data could be used to further improve the accuracy of medical diagnostic system assessments. To the best of our knowledge, there is currently no method for extracting subjective words that express the extent of these symptoms (hereinafter, “degree words”).

Objective

Therefore, we propose using the fuzzy c-means (FCM) method and Gaussian membership to quantify the degree words in the clinical medical data set MIMIC-III.

Methods

First, we preprocessed the 381,091 radiology reports collected in MIMIC-III, and then we used the FCM method to extract degree words from unstructured text. Thereafter, we used the Gaussian membership method to quantify the extracted degree words, which transform the fuzzy words extracted from the medical text into computer-recognizable numbers.

Results

The results showed that the digitization of ambiguous words in medical texts is feasible. The words representing each degree of each disease had a range of corresponding values. Examples of membership medians were 2.971 (atelectasis), 3.121 (pneumonia), 2.899 (pneumothorax), 3.051 (pulmonary edema), and 2.435 (pulmonary embolus). Additionally, all extracted words contained the same subjective words (low, high, etc), which allows for an objective evaluation method. Furthermore, we will verify the specific impact of the quantification results of ambiguous words such as symptom words and degree words on the use of medical texts in subsequent studies. These same ambiguous words may be used as a new set of feature values to represent the disorders.

Conclusions

This study proposes an innovative method for handling subjective words. We used the FCM method to extract the subjective degree words in the English-interpreted report of the MIMIC-III and then used the Gaussian functions to quantify the subjective degree words. In this method, words containing subjectivity in unstructured texts can be automatically processed and transformed into numerical ranges by digital processing. It was concluded that the digitization of ambiguous words in medical texts is feasible.

Recruitment and retention for chronic pain clinical trials: a narrative review

Opioid misuse is at a crisis level. In response to this epidemic, the National Institutes of Health has funded $945 million in research through the Helping to End Addiction Long-term (HEAL) Pain Management Initiative, including funding to the Vanderbilt Recruitment Innovation Center (RIC) to strategize methods to catalyze participant recruitment. The RIC, recognizing the challenges presented to clinical researchers in recruiting individuals experiencing pain, conducted a review of evidence in the literature on successful participant recruitment methods for chronic pain trials, in preparation for supporting the HEAL Pain trials. Study design as it affects recruitment was reviewed, with issues such as sufficient sample size, impact of placebo, pain symptom instability, and cohort characterization being identified as problems. Potential solutions found in the literature include targeted electronic health record phenotyping, use of alternative study designs, and greater clinician education and involvement. For retention, the literature reports successful strategies that include maintaining a supportive staff, allowing virtual study visits, and providing treatment flexibility within the trial. Community input on study design to identify potential obstacles to recruitment and retention was found to help investigators avoid pitfalls and enhance trust, especially when recruiting underrepresented minority populations. Our report concludes with a description of generalizable resources the RIC has developed or adapted to enhance recruitment and retention in the HEAL Pain studies. These resources include, among others, a Recruitment and Retention Plan Template, a Competing Trials Tool, and MyCap, a mobile research application that interfaces with Research Electronic Data Capture (REDCap).

Application Scenarios for Artificial Intelligence in Nursing Care: Rapid Review

Background

Artificial intelligence (AI) holds the promise of supporting nurses’ clinical decision-making in complex care situations or conducting tasks that are remote from direct patient interaction, such as documentation processes. There has been an increase in the research and development of AI applications for nursing care, but there is a persistent lack of an extensive overview covering the evidence base for promising application scenarios.

Objective

This study synthesizes literature on application scenarios for AI in nursing care settings as well as highlights adjacent aspects in the ethical, legal, and social discourse surrounding the application of AI in nursing care.

Methods

Following a rapid review design, PubMed, CINAHL, Association for Computing Machinery Digital Library, Institute of Electrical and Electronics Engineers Xplore, Digital Bibliography & Library Project, and Association for Information Systems Library, as well as the libraries of leading AI conferences, were searched in June 2020. Publications of original quantitative and qualitative research, systematic reviews, discussion papers, and essays on the ethical, legal, and social implications published in English were included. Eligible studies were analyzed on the basis of predetermined selection criteria.

Results

The titles and abstracts of 7016 publications and 704 full texts were screened, and 292 publications were included. Hospitals were the most prominent study setting, followed by independent living at home; fewer application scenarios were identified for nursing homes or home care. Most studies used machine learning algorithms, whereas expert or hybrid systems were entailed in less than every 10th publication. The application context of focusing on image and signal processing with tracking, monitoring, or the classification of activity and health followed by care coordination and communication, as well as fall detection, was the main purpose of AI applications. Few studies have reported the effects of AI applications on clinical or organizational outcomes, lacking particularly in data gathered outside laboratory conditions. In addition to technological requirements, the reporting and inclusion of certain requirements capture more overarching topics, such as data privacy, safety, and technology acceptance. Ethical, legal, and social implications reflect the discourse on technology use in health care but have mostly not been discussed in meaningful and potentially encompassing detail.

Conclusions

The results highlight the potential for the application of AI systems in different nursing care settings. Considering the lack of findings on the effectiveness and application of AI systems in real-world scenarios, future research should reflect on a more nursing care–specific perspective toward objectives, outcomes, and benefits. We identify that, crucially, an advancement in technological-societal discourse that surrounds the ethical and legal implications of AI applications in nursing care is a necessary next step. Further, we outline the need for greater participation among all of the stakeholders involved.

Development of a generalizable natural language processing pipeline to extract physician-reported pain from clinical reports: Generated using publicly-available datasets and tested on institutional clinical reports for cancer patients with bone metastases

OBJECTIVE

The majority of cancer patients suffer from severe pain at the advanced stage of their illness. In most cases, cancer pain is underestimated by clinical staff and is not properly managed until it reaches a critical stage. Therefore, detecting and addressing cancer pain early can potentially improve the quality of life of cancer patients. The objective of this research project was to develop a generalizable Natural Language Processing (NLP) pipeline to find and classify physician-reported pain in the radiation oncology consultation notes of cancer patients with bone metastases.

MATERIALS AND METHODS

The texts of 1249 publicly-available hospital discharge notes in the i2b2 database were used as a training and validation set. The MetaMap and NegEx algorithms were implemented for medical terms extraction. Sets of NLP rules were developed to score pain terms in each note. By averaging pain scores, each note was assigned to one of the three verbally-declared pain (VDP) labels, including no pain, pain, and no mention of pain. Without further training, the generalizability of our pipeline in scoring individual pain terms was tested independently using 30 hospital discharge notes from the MIMIC-III database and 30 consultation notes of cancer patients with bone metastasis from our institution's radiation oncology electronic health record. Finally, 150 notes from our institution were used to assess the pipeline's performance at assigning VDP.

RESULTS

Our NLP pipeline successfully detected and quantified pain in the i2b2 summary notes with 93% overall precision and 92% overall recall. Testing on the MIMIC-III database achieved precision and recall of 91% and 86% respectively. The pipeline successfully detected pain with 89% precision and 82% recall on our institutional radiation oncology corpus. Finally, our pipeline assigned a VDP to each note in our institutional corpus with 84% and 82% precision and recall, respectively.

CONCLUSION

Our NLP pipeline enables the detection and classification of physician-reported pain in our radiation oncology corpus. This portable and ready-to-use pipeline can be used to automatically extract and classify physician-reported pain from clinical notes where the pain is not otherwise documented through structured data entry.

Machine Learning in Chronic Pain Research: A Scoping Review

Given the high prevalence and associated cost of chronic pain, it has a significant impact on individuals and society. Improvements in the treatment and management of chronic pain may increase patients’ quality of life and reduce societal costs. In this paper, we evaluate state-of-the-art machine learning approaches in chronic pain research. A literature search was conducted using the PubMed, IEEE Xplore, and the Association of Computing Machinery (ACM) Digital Library databases. Relevant studies were identified by screening titles and abstracts for keywords related to chronic pain and machine learning, followed by analysing full texts. Two hundred and eighty-seven publications were identified in the literature search. In total, fifty-three papers on chronic pain research and machine learning were reviewed. The review showed that while many studies have emphasised machine learning-based classification for the diagnosis of chronic pain, far less attention has been paid to the treatment and management of chronic pain. More research is needed on machine learning approaches to the treatment, rehabilitation, and self-management of chronic pain. As with other chronic conditions, patient involvement and self-management are crucial. In order to achieve this, patients with chronic pain need digital tools that can help them make decisions about their own treatment and care.

ETM: Enrichment by topic modeling for automated clinical sentence classification to detect patients’ disease history

Given the rapid rate at which text data are being digitally gathered in the medical domain, there is growing need for automated tools that can analyze clinical notes and classify their sentences in electronic health records (EHRs). This study uses EHR texts to detect patients’ disease history from clinical sentences. However, in EHRs, sentences are less topic-focused and shorter than that in general domain, which leads to the sparsity of co-occurrence patterns and the lack of semantic features. To tackle this challenge, current approaches for clinical sentence classification are dependent on external information to improve classification performance. However, this is implausible owing to a lack of universal medical dictionaries. This study proposes the ETM (enrichment by topic modeling) algorithm, based on latent Dirichlet allocation, to smoothen the semantic representations of short sentences. The ETM enriches text representation by incorporating probability distributions generated by an unsupervised algorithm into it. It considers the length of the original texts to enhance representation by using an internal knowledge acquisition procedure. When it comes to clinical predictive modeling, interpretability improves the acceptance of the model. Thus, for clinical sentence classification, the ETM approach employs an initial TFiDF (term frequency inverse document frequency) representation, where we use the support vector machine and neural network algorithms for the classification task. We conducted three sets of experiments on a data set consisting of clinical cardiovascular notes from the Netherlands to test the sentence classification performance of the proposed method in comparison with prevalent approaches. The results show that the proposed ETM approach outperformed state-of-the-art baselines.

Clinical Text Data in Machine Learning: Systematic Review

Background

Clinical narratives represent the main form of communication within health care, providing a personalized account of patient history and assessments, and offering rich information for clinical decision making. Natural language processing (NLP) has repeatedly demonstrated its feasibility to unlock evidence buried in clinical narratives. Machine learning can facilitate rapid development of NLP tools by leveraging large amounts of text data.

Objective

The main aim of this study was to provide systematic evidence on the properties of text data used to train machine learning approaches to clinical NLP. We also investigated the types of NLP tasks that have been supported by machine learning and how they can be applied in clinical practice.

Methods

Our methodology was based on the guidelines for performing systematic reviews. In August 2018, we used PubMed, a multifaceted interface, to perform a literature search against MEDLINE. We identified 110 relevant studies and extracted information about text data used to support machine learning, NLP tasks supported, and their clinical applications. The data properties considered included their size, provenance, collection methods, annotation, and any relevant statistics.

Results

The majority of datasets used to train machine learning models included only hundreds or thousands of documents. Only 10 studies used tens of thousands of documents, with a handful of studies utilizing more. Relatively small datasets were utilized for training even when much larger datasets were available. The main reason for such poor data utilization is the annotation bottleneck faced by supervised machine learning algorithms. Active learning was explored to iteratively sample a subset of data for manual annotation as a strategy for minimizing the annotation effort while maximizing the predictive performance of the model. Supervised learning was successfully used where clinical codes integrated with free-text notes into electronic health records were utilized as class labels. Similarly, distant supervision was used to utilize an existing knowledge base to automatically annotate raw text. Where manual annotation was unavoidable, crowdsourcing was explored, but it remains unsuitable because of the sensitive nature of data considered. Besides the small volume, training data were typically sourced from a small number of institutions, thus offering no hard evidence about the transferability of machine learning models. The majority of studies focused on text classification. Most commonly, the classification results were used to support phenotyping, prognosis, care improvement, resource management, and surveillance.

Conclusions

We identified the data annotation bottleneck as one of the key obstacles to machine learning approaches in clinical NLP. Active learning and distant supervision were explored as a way of saving the annotation efforts. Future research in this field would benefit from alternatives such as data augmentation and transfer learning, or unsupervised learning, which do not require data annotation.

Framework for improving outcome prediction for acute to chronic low back pain transitions

Clinical practice guidelines and the Federal Pain Research Strategy (United States) have recently highlighted research priorities to lessen the public health impact of low back pain (LBP). It may be necessary to improve existing predictive approaches to meet these research priorities for the transition from acute to chronic LBP. In this article, we first present a mapping review of previous studies investigating this transition and, from the characterization of the mapping review, present a predictive framework that accounts for limitations in the identified studies. Potential advantages of implementing this predictive framework are further considered. These advantages include (1) leveraging routinely collected health care data to improve prediction of the development of chronic LBP and (2) facilitating use of advanced analytical approaches that may improve prediction accuracy. Furthermore, successful implementation of this predictive framework in the electronic health record would allow for widespread testing of accuracy resulting in validated clinical decision aids for predicting chronic LBP development.

Sensor Technologies to Manage the Physiological Traits of Chronic Pain: A Review

Non-oncologic chronic pain is a common high-morbidity impairment worldwide and acknowledged as a condition with significant incidence on quality of life. Pain intensity is largely perceived as a subjective experience, what makes challenging its objective measurement. However, the physiological traces of pain make possible its correlation with vital signs, such as heart rate variability, skin conductance, electromyogram, etc., or health performance metrics derived from daily activity monitoring or facial expressions, which can be acquired with diverse sensor technologies and multisensory approaches. As the assessment and management of pain are essential issues for a wide range of clinical disorders and treatments, this paper reviews different sensor-based approaches applied to the objective evaluation of non-oncological chronic pain. The space of available technologies and resources aimed at pain assessment represent a diversified set of alternatives that can be exploited to address the multidimensional nature of pain.

Task definition, annotated dataset, and supervised natural language processing models for symptom extraction from unstructured clinical notes

INTRODUCTION

Machine learning (ML) and natural language processing have great potential to improve information extraction (IE) within electronic medical records (EMRs) for a wide variety of clinical search and summarization tools. Despite ML advancements, clinical adoption of real time IE tools for patient care remains low. Clinically motivated IE task definitions, publicly available annotated clinical datasets, and inclusion of subtasks such as coreference resolution and named entity normalization are critical for the development of useful clinical tools.

MATERIALS AND METHODS

We provide a task definition and comprehensive annotation requirements for a clinically motivated symptom extraction task. Four annotators labeled symptom mentions within 1108 discharge summaries from two public clinical note datasets for the tasks of named entity recognition, coreference resolution, and named entity normalization; these annotations will be released to the public. Baseline human performance was assessed and two ML models were evaluated on the symptom extraction task.

RESULTS

16,922 symptom mentions were identified within the discharge summaries, with 11,944 symptom instances after coreference resolution and 1255 unique normalized answer forms. Human annotator performance averaged 92.2% F1. Recurrent network model performance was 85.6% F1 (recall 85.8%, precision 85.4%), and Transformer-based model performance was 86.3% F1 (recall 86.6%, precision 86.1%). Our models extracted vague symptoms, acronyms, typographical errors, and grouping statements. The models generalized effectively to a separate clinical note corpus and can run in real time.

CONCLUSION

To our knowledge, this dataset will be the largest and most comprehensive publicly released, annotated dataset for clinically motivated symptom extraction, as it includes annotations for named entity recognition, coreference, and normalization for more than 1000 clinical documents. Our neural network models extracted symptoms from unstructured clinical free text at near human performance in real time. In this paper, we present a clinically motivated task definition, dataset, and simple supervised natural language processing models to demonstrate the feasibility of building clinically applicable information extraction tools.