Natural language processing in clinical neuroscience and psychiatry: A review

Medical Information Extraction With NLP-Powered QABots: A Real-World Scenario

The advent of computerized medical recording systems in healthcare facilities has made data retrieval tasks easier, compared to manual recording. Nevertheless, the potential of the information contained within medical records remains largely untapped, mostly due to the time and effort required to extract data from unstructured documents. Natural Language Processing (NLP) represents a promising solution to this challenge, as it enables the use of automated text-mining tools for clinical practitioners. In this work, we present the architecture of the Virtual Dementia Institute (IVD), a consortium of sixteen Italian hospitals, using the NLP Extraction and Management Tool (NEMT), a (semi-) automated end-to-end pipeline that extracts relevant information from clinical documents and stores it in a centralized REDCap database. After defining a common Case Report Form (CRF) across the IVD hospitals, we implemented NEMT, the core of which is a Question Answering Bot (QABot) based on a modern NLP model. This QABot is fine-tuned on thousands of examples from IVD centers. Detailed descriptions of the process to define a common minimum dataset, Inter-Annotator Agreement calculated on clinical documents, and NEMT results are provided. The best QABot performance show an Exact Match score (EM) of 78.1%, a F1-score of 84.7%, a Lenient Accuracy (LAcc) of 0.834, and a Mean Reciprocal Rank (MRR) of 0.810. EM and F1 scores outperform the same metrics obtained with ChatGPTv3.5 (68.9% and 52.5%, respectively). With NEMT the IVD has been able to populate a database that will contain data from thousands of Italian patients, all screened with the same procedure. NEMT represents an efficient tool that paves the way for medical information extraction and exploitation for new research studies.

Perceived Impact of COVID-19 in an Underserved Community: A Natural Language Processing Approach

AIM

To utilise natural language processing (NLP) to analyse interviews about the impact of COVID-19 in underserved communities and to compare it to traditional thematic analysis in a small subset of interviews.

DESIGN

NLP and thematic analysis were used together to comprehensively examine the interview data.

METHODS

Fifty transcribed interviews with purposively sampled adults living in underserved communities in the United States, conducted from June 2021 to May 2022, were analysed to explore the impact of the COVID-19 pandemic on social activities, mental and emotional stress and physical and spiritual well-being. NLP includes several stages: data extraction, preprocessing, processing using word embeddings and topic modelling and visualisation. This was compared to thematic analysis in a random sample of 10 interviews.

RESULTS

Six themes emerged from thematic analysis: The New Normal, Juxtaposition of Emotions, Ripple Effects on Health, Brutal yet Elusive Reality, Evolving Connections and Journey of Spirituality and Self-Realisation. With NLP, four clusters of similar context words for each approach were analysed visually and numerically. The frequency-based word embedding approach was most interpretable and well aligned with the thematic analysis.

CONCLUSION

The NLP results complemented the thematic analysis and offered new insights regarding the passage of time, the interconnectedness of impacts and the semantic connections among words. This research highlights the interdependence of pandemic impacts, simultaneously positive and negative effects and deeply individual COVID-19 experiences in underserved communities.

IMPLICATIONS

The iterative integration of NLP and thematic analysis was efficient and effective, facilitating the analysis of many transcripts and expanding nursing research methodology.

IMPACT

While thematic analysis provided richer, more detailed themes, NLP captured new elements and combinations of words, making it a promising tool in qualitative analysis.

REPORTING METHOD

Not applicable.

PATIENT OR PUBLIC CONTRIBUTION

No patient or public contribution.

Using a natural language processing toolkit to classify electronic health records by psychiatric diagnosis

Objective: We analyzed a natural language processing (NLP) toolkit's ability to classify unstructured EHR data by psychiatric diagnosis. Expertise can be a barrier to using NLP. We employed an NLP toolkit (CLARK) created to support studies led by investigators with a range of informatics knowledge. Methods: The EHR of 652 patients were manually reviewed to establish Depression and Substance Use Disorder (SUD) labeled datasets, which were split into training and evaluation datasets. We used CLARK to train depression and SUD classification models using training datasets; model performance was analyzed against evaluation datasets. Results: The depression model accurately classified 69% of records (sensitivity = 0.68, specificity = 0.70, F1 = 0.68). The SUD model accurately classified 84% of records (sensitivity = 0.56, specificity = 0.92, F1 = 0.57). Conclusion: The depression model performed a more balanced job, while the SUD model's high specificity was paired with a low sensitivity. NLP applications may be especially helpful when combined with a confidence threshold for manual review.

The Role of Virtual Reality and Artificial Intelligence in Cognitive Pain Therapy: A Narrative Review

PURPOSE OF REVIEW

This review investigates the roles of artificial intelligence (AI) and virtual reality (VR) in enhancing cognitive pain therapy for chronic pain management. The work assesses current research, outlines benefits and limitations and examines their potential integration into existing pain management methods.

RECENT FINDINGS

Advances in VR have shown promise in chronic pain management through immersive cognitive therapy exercises, with evidence supporting VR's effectiveness in symptom reduction. AI's personalization of treatment plans and its support for mental health through AI-driven avatars are emerging trends. The integration of AI in hybrid programs indicates a future with real-time adaptive technology tailored to individual needs in chronic pain management. Incorporating AI and VR into chronic pain cognitive therapy represents a promising approach to enhance management by leveraging VR's immersive experiences and AI's personalized tactics, aiming to improve patient engagement and outcomes. Nonetheless, further empirical studies are needed to standardized methodologies, compare these technologies to traditional therapies and fully realize their clinical potential.

Natural Language Processing Applied to Spontaneous Recall of Famous Faces Reveals Memory Dysfunction in Temporal Lobe Epilepsy Patients

Objective and Background

Epilepsy patients rank memory problems as their most significant cognitive comorbidity. Current clinical assessments are laborious to administer and score and may not always detect subtle memory decline. The Famous Faces Task (FF) has robustly demonstrated that left temporal lobe epilepsy (LTLE) patients remember fewer names and biographical details compared to right TLE (RTLE) patients and healthy controls (HCs). We adapted the FF task to capture subjects' entire spontaneous spoken recall, then scored responses using manual and natural language processing (NLP) methods. We expected to replicate previous group level differences using spontaneous speech and semi-automated analysis.

Methods

Seventy-three (N=73) adults (28 LTLE, 18 RTLE, and 27 HCs) were included in a case-control prospective study design. Twenty FF in politics, sports, and entertainment (active 2008-2017) were shown to subjects, who were asked if they could recognize and spontaneously recall as much biographical detail as possible. We created human-generated and automatically-generated keyword dictionaries for each celebrity, based on a randomly selected training set of half of the HC transcripts. To control for speech output, we measured the speech duration, total word count and content word count for the FF task and a Cookie Theft Control Task (CTT), in which subjects were merely asked to describe a visual scene. Subjects' responses to FF and CTT tasks were recorded, transcribed, and analyzed in a blinded manner with a combination of manual and automated NLP approaches.

Results

Famous face recognition accuracy was similar between groups. LTLE patients recalled fewer biographical details compared to HCs and RTLEs using both the gold-standard human-generated dictionary (24%±12% vs. 31%±12% and 30%±12%, p=0.007) and the automated dictionary (24%±12% vs. 31%±12% and 32%±13%, p=0.007). There were no group level differences in speech duration, total word count, or content word count for either the FF and CTT to explain difference in recall performance. There was a positive, statistically significant relationship between MOCA score and FF recall performance as scored by the human-generated (ρ= .327, p= .029) and automatically-generated dictionaries (ρ= .422, p= .004) for TLE subjects, but not HCs, an effect that was driven by LTLE subjects.

Discussion

LTLE patients remember fewer details of famous people than HCs or RTLE patients, as discovered by NLP analysis of spontaneous recall. Decreased biographical memory was not due to decreased speech output and correlated with lower MOCA scores. NLP analysis of spontaneous recall can detect memory dysfunction in clinical populations in a semi-automated, objective, and sensitive manner.

Natural Language Processing and Schizophrenia: A Scoping Review of Uses and Challenges

(1) Background: Approximately 1% of the global population is affected by schizophrenia, a disorder marked by cognitive deficits, delusions, hallucinations, and language issues. It is associated with genetic, neurological, and environmental factors, and linked to dopaminergic hyperactivity and neurotransmitter imbalances. Recent research reveals that patients exhibit significant language impairments, such as reduced verbal output and fluency. Advances in machine learning and natural language processing show potential for early diagnosis and personalized treatments, but additional research is required for the practical application and interpretation of such technology. The objective of this study is to explore the applications of natural language processing in patients diagnosed with schizophrenia. (2) Methods: A scoping review was conducted across multiple electronic databases, including Medline, PubMed, Embase, and PsycInfo. The search strategy utilized a combination of text words and subject headings, focusing on schizophrenia and natural language processing. Systematically extracted information included authors, population, primary uses of the natural language processing algorithms, main outcomes, and limitations. The quality of the identified studies was assessed. (3) Results: A total of 516 eligible articles were identified, from which 478 studies were excluded based on the first analysis of titles and abstracts. Of the remaining 38 studies, 18 were selected as part of this scoping review. The following six main uses of natural language processing were identified: diagnostic and predictive modeling, followed by specific linguistic phenomena, speech and communication analysis, social media and online content analysis, clinical and cognitive assessment, and linguistic feature analysis. (4) Conclusions: This review highlights the main uses of natural language processing in the field of schizophrenia and the need for more studies to validate the effectiveness of natural language processing in diagnosing and treating schizophrenia.

Characterizing Myasthenia Gravis Symptoms, Exacerbations, and Crises From Neurologist's Clinical Notes Using Natural Language Processing

Background Myasthenia gravis (MG) is a rare, autoantibody neuromuscular disorder characterized by fatigable weakness. Real-world evidence based on administrative and structured datasets regarding MG may miss important details related to the clinical encounter. Examination of free-text clinical progress notes has the potential to illuminate aspects of MG care. Objective The primary objective was to examine and characterize neurologist progress notes in the care of individuals with MG regarding the prevalence of documentation of clinical subtypes, antibody status, symptomatology, and MG deteriorations, including exacerbations and crises. The secondary objectives were to categorize MG deteriorations into practical, objective states as well as examine potential sources of clinical inertia in MG care. Methods We performed a retrospective, cross-sectional analysis of de-identified neurologist clinical notes from 2017 to 2022. A qualitative analysis of physician descriptions of MG deteriorations and a discussion of risks in MG care (risk for adverse effects, risk for clinical decompensation, etc.) was performed. Results Of the 3,085 individuals with MG, clinical subtypes and antibody status identified included gMG (n = 400; 13.0%), ocular MG (n = 253; 8.2%), MG unspecified (2,432; 78.8%), seropositivity for acetylcholine receptor antibody (n = 441; 14.3%), and MuSK antibody (n = 29; 0.9%). The most common gMG manifestations were dysphagia (n = 712; 23.0%), dyspnea (n = 626; 20.3%), and dysarthria (n = 514; 16.7%). In MG crisis patients, documentation of difficulties with MG standard therapies was common (n = 62; 45.2%). The qualitative analysis of MG deterioration types includes symptom fluctuation, symptom worsening with treatment intensification, MG deterioration with rescue therapy, and MG crisis. Qualitative analysis of MG-related risks included the toxicity of new therapies and concern for worsening MG because of changing therapies. Conclusions This study of neurologist progress notes demonstrates the potential for real-world evidence generation in the care of individuals with MG. MG patients suffer fluctuating symptomatology and a spectrum of clinical deteriorations. Adverse effects of MG therapies are common, highlighting the need for effective, less toxic treatments.

GPT-4 Performance for Neurologic Localization

Background and Objectives

In health care, large language models such as Generative Pretrained Transformers (GPTs), trained on extensive text datasets, have potential applications in reducing health care disparities across regions and populations. Previous software developed for lesion localization has been limited in scope. This study aims to evaluate the capability of GPT-4 for lesion localization based on clinical presentation.

Methods

GPT-4 was prompted using history and neurologic physical examination (H&P) from published cases of acute stroke followed by questions for clinical reasoning with answering for "single or multiple lesions," "side," and "brain region" using Zero-Shot Chain-of-Thought and Text Classification prompting. GPT-4 output on 3 separate trials for each of 46 cases was compared with imaging-based localization.

Results

GPT-4 successfully processed raw text from H&P to generate accurate neuroanatomical localization and detailed clinical reasoning. Performance metrics across trial-based analysis for specificity, sensitivity, precision, and F1-score were 0.87, 0.74, 0.75, and 0.74, respectively, for side; 0.94, 0.85, 0.84, and 0.85, respectively, for brain region. Class labels within the brain region were similarly high for all regions except the cerebellum and were also similar when considering all 3 trials to examine metrics by case. Errors were due to extrinsic causes-inadequate information in the published cases, and intrinsic causes-failures of logic or inadequate knowledge base.

Discussion

This study reveals capabilities of GPT-4 in the localization of acute stroke lesions, showing a potential future role as a clinical tool in neurology.

A Health Care Clinical Data Platform for Rapid Deployment of Artificial Intelligence and Machine Learning Algorithms for Cancer Care and Oncology Clinical Trials

The xCures platform aggregates, organizes, structures, and normalizes clinical EMR data across care sites, utilizing advanced technologies for near real-time access. The platform generates data in a format to support clinical care, accelerate research, and promote artificial intelligence/ machine learning algorithm development, highlighted by a clinical decision support algorithm for precision oncology.

Large Language Models in Neurology Research and Future Practice

Recent advancements in generative artificial intelligence, particularly using large language models (LLMs), are gaining increased public attention. We provide a perspective on the potential of LLMs to analyze enormous amounts of data from medical records and gain insights on specific topics in neurology. In addition, we explore use cases for LLMs, such as early diagnosis, supporting patient and caregivers, and acting as an assistant for clinicians. We point to the potential ethical and technical challenges raised by LLMs, such as concerns about privacy and data security, potential biases in the data for model training, and the need for careful validation of results. Researchers must consider these challenges and take steps to address them to ensure that their work is conducted in a safe and responsible manner. Despite these challenges, LLMs offer promising opportunities for improving care and treatment of various neurologic disorders.

Identifying encephalopathy in patients admitted to an intensive care unit: Going beyond structured information using natural language processing

Background

Encephalopathy is a severe co-morbid condition in critically ill patients that includes different clinical constellation of neurological symptoms. However, even for the most recognised form, delirium, this medical condition is rarely recorded in structured fields of electronic health records precluding large and unbiased retrospective studies. We aimed to identify patients with encephalopathy using a machine learning-based approach over clinical notes in electronic health records.

Methods

We used a list of ICD-9 codes and clinical concepts related to encephalopathy to define a cohort of patients from the MIMIC-III dataset. Clinical notes were annotated with MedCAT and vectorized with a bag-of-word approach or word embedding using clinical concepts normalised to standard nomenclatures as features. Machine learning algorithms (support vector machines and random forest) trained with clinical notes from patients who had a diagnosis of encephalopathy (defined by ICD-9 codes) were used to classify patients with clinical concepts related to encephalopathy in their clinical notes but without any ICD-9 relevant code. A random selection of 50 patients were reviewed by a clinical expert for model validation.

Results

Among 46,520 different patients, 7.5% had encephalopathy related ICD-9 codes in all their admissions (group 1, definite encephalopathy), 45% clinical concepts related to encephalopathy only in their clinical notes (group 2, possible encephalopathy) and 38% did not have encephalopathy related concepts neither in structured nor in clinical notes (group 3, non-encephalopathy). Length of stay, mortality rate or number of co-morbid conditions were higher in groups 1 and 2 compared to group 3. The best model to classify patients from group 2 as patients with encephalopathy (SVM using embeddings) had F1 of 85% and predicted 31% patients from group 2 as having encephalopathy with a probability >90%. Validation on new cases found a precision ranging from 92% to 98% depending on the criteria considered.

Conclusions

Natural language processing techniques can leverage relevant clinical information that might help to identify patients with under-recognised clinical disorders such as encephalopathy. In the MIMIC dataset, this approach identifies with high probability thousands of patients that did not have a formal diagnosis in the structured information of the EHR.