Clinical characteristics and prognostic factors for Crohn's disease relapses using natural language processing and machine learning: a pilot study

Artificial Intelligence in Inflammatory Bowel Disease

Artificial intelligence (AI) is being increasingly studied and implemented in gastroenterology. In inflammatory bowel disease (IBD), numerous AI models are being developed to assist with IBD diagnosis, standardization of endoscopic and radiologic disease activity, and predicting outcomes. Further prospective, multicenter studies representing diverse populations and novel applications are needed prior to routine implementation in clinical practice and expected improved outcomes for clinicians and patients.

Modifiable Factors Influencing Disease Flares in Inflammatory Bowel Disease: A Literature Overview of Lifestyle, Psychological, and Environmental Risk Factors

Background: A significant concern for patients with Inflammatory Bowel Disease (IBD) is predicting and managing disease flares. While healthcare providers rely on biomarkers, providing conclusive patient advice remains challenging. This review explores the role of lifestyle, psychological health, and environmental exposures in the prediction and management of IBD flares. Methods: This review followed PRISMA guidelines (2020). A structured search was conducted in PubMed for articles published between 2012 and 2024, using free and Medical Subject Heading (MeSH) terms for predicting factors in IBD. Inclusion criteria included studies reporting primary data on modifiable clinical or environmental predictors of IBD relapse, excluding studies on post-operative investigations, treatment cessation, and pediatric or pregnant populations. The Mixed Method Appraisal Tool (MMAT) was used to assess the quality of the studies. Results: Out of 2287 identified citations, 58 articles were included. Several modifiable factors influencing disease flares were identified, including psychological stress, sleep disturbances, smoking, and nutrition. Poor sleep quality and mental health were linked to increased flare risks, while smoking was associated with higher relapse rates in Crohn's disease. Environmental exposures, such as heat waves and high-altitude regions, also contributed. Predictive models integrating clinical, lifestyle, and psychological factors showed promising accuracy but require further refinement. Limitations of this review include the potential for publication bias, variability in flare definitions, and limited sample sizes Conclusions: Key predictors of IBD flares include dietary factors, psychological stress, poor sleep quality, and pharmacological influences. Personalized approaches integrating these predictors can optimize disease control and improve patient outcomes.

Accurate, Robust, and Scalable Machine Abstraction of Mayo Endoscopic Subscores From Colonoscopy Reports

BACKGROUND

The Mayo endoscopic subscore (MES) is an important quantitative measure of disease activity in ulcerative colitis. Colonoscopy reports in routine clinical care usually characterize ulcerative colitis disease activity using free text description, limiting their utility for clinical research and quality improvement. We sought to develop algorithms to classify colonoscopy reports according to their MES.

METHODS

We annotated 500 colonoscopy reports from 2 health systems. We trained and evaluated 4 classes of algorithms. Our primary outcome was accuracy in identifying scorable reports (binary) and assigning an MES (ordinal). Secondary outcomes included learning efficiency, generalizability, and fairness.

RESULTS

Automated machine learning models achieved 98% and 97% accuracy on the binary and ordinal prediction tasks, outperforming other models. Binary models trained on the University of California, San Francisco data alone maintained accuracy (96%) on validation data from Zuckerberg San Francisco General. When using 80% of the training data, models remained accurate for the binary task (97% [n = 320]) but lost accuracy on the ordinal task (67% [n = 194]). We found no evidence of bias by gender (P = .65) or area deprivation index (P = .80).

CONCLUSIONS

We derived a highly accurate pair of models capable of classifying reports by their MES and recognizing when to abstain from prediction. Our models were generalizable on outside institution validation. There was no evidence of algorithmic bias. Our methods have the potential to enable retrospective studies of treatment effectiveness, prospective identification of patients meeting study criteria, and quality improvement efforts in inflammatory bowel diseases.

A foundation systematic review of natural language processing applied to gastroenterology & hepatology

OBJECTIVE

This review assesses the progress of NLP in gastroenterology to date, grades the robustness of the methodology, exposes the field to a new generation of authors, and highlights opportunities for future research.

DESIGN

Seven scholarly databases (ACM Digital Library, Arxiv, Embase, IEEE Explore, Pubmed, Scopus and Google Scholar) were searched for studies published between 2015 and 2023 that met the inclusion criteria. Studies lacking a description of appropriate validation or NLP methods were excluded, as were studies ufinavailable in English, those focused on non-gastrointestinal diseases and those that were duplicates. Two independent reviewers extracted study information, clinical/algorithm details, and relevant outcome data. Methodological quality and bias risks were appraised using a checklist of quality indicators for NLP studies.

RESULTS

Fifty-three studies were identified utilising NLP in endoscopy, inflammatory bowel disease, gastrointestinal bleeding, liver and pancreatic disease. Colonoscopy was the focus of 21 (38.9%) studies; 13 (24.1%) focused on liver disease, 7 (13.0%) on inflammatory bowel disease, 4 (7.4%) on gastroscopy, 4 (7.4%) on pancreatic disease and 2 (3.7%) on endoscopic sedation/ERCP and gastrointestinal bleeding. Only 30 (56.6%) of the studies reported patient demographics, and only 13 (24.5%) had a low risk of validation bias. Thirty-five (66%) studies mentioned generalisability, but only 5 (9.4%) mentioned explainability or shared code/models.

CONCLUSION

NLP can unlock substantial clinical information from free-text notes stored in EPRs and is already being used, particularly to interpret colonoscopy and radiology reports. However, the models we have thus far lack transparency, leading to duplication, bias, and doubts about generalisability. Therefore, greater clinical engagement, collaboration, and open sharing of appropriate datasets and code are needed.

Development of Time-Aggregated Machine Learning Model for Relapse Prediction in Pediatric Crohn's Disease

INTRODUCTION

Pediatric Crohn's disease (CD) easily progresses to an active disease compared with adult CD, making it important to predict and minimize CD relapses. However, prediction of relapse at various time points (TPs) during pediatric CD remains understudied. We aimed to develop a real-time aggregated model to predict pediatric CD relapse in different TPs and time windows (TWs).

METHODS

This retrospective study was conducted on children diagnosed with CD between 2015 and 2022 at Severance Hospital. Laboratory test results and demographic data were collected starting at 3 months after diagnosis, and cohorts were formed using data from 6 different TPs at 1-month intervals. Relapse-defined as a pediatric CD activity index ≥ 30 points-was predicted, and TWs were 3-7 months with 1-month intervals. The feature importance of the variables in each setting was determined.

RESULTS

Data from 180 patients were used to construct cohorts corresponding to the TPs. We identified the optimal TP and TW to reliably predict pediatric CD relapse with an area under the receiver operating characteristic curve score of 0.89 when predicting with a 3-month TW at a 3-month TP. Variables such as C-reactive protein levels and lymphocyte fraction were found to be important factors.

DISCUSSION

We developed a time-aggregated model to predict pediatric CD relapse in multiple TPs and TWs. This model identified important variables that predicted relapse in pediatric CD to support real-time clinical decision making.

Chronic liver disease-associated severe thrombocytopenia in Spain: Results from a retrospective study using machine learning and natural language processing

BACKGROUND

Patients with chronic liver disease (CLD) often develop thrombocytopenia (TCP) as a complication. Severe TCP (platelet count<50×109/L) can increase morbidity and complicate CLD management, increasing bleeding risk during invasive procedures.

OBJECTIVES

To describe the real-world scenario of CLD-associated severe TCP patients' clinical characteristics. To evaluate the association between invasive procedures, prophylactic treatments, and bleeding events in this group of patients. To describe their need of medical resource use in Spain.

METHODS

This is a retrospective, multicenter study including patients who had confirmed diagnosis of CLD and severe TCP in four hospitals within the Spanish National Healthcare Network from January 2014 to December 2018. We analyzed the free-text information from Electronic Health Records (EHRs) of patients using Natural Language Processing (NLP), machine learning techniques, and SNOMED-CT terminology. Demographics, comorbidities, analytical parameters and characteristics of CLD were extracted at baseline and need for invasive procedures, prophylactic treatments, bleeding events and medical resources used in the follow up period. Frequency tables were generated for categorical variables, whereas continuous variables were described in summary tables as mean (SD) and median (Q1-Q3).

RESULTS

Out of 1,765,675 patients, 1787 had CLD and severe TCP; 65.2% were male with a mean age of 54.7 years old. Cirrhosis was detected in 46% (n=820) of patients and 9.1% (n=163) had hepatocellular carcinoma. Invasive procedures were needed in 85.6% of patients during the follow up period. Patients undergoing procedures compared to those patients without invasive procedures presented higher rates of bleeding events (33% vs 8%, p<0.0001) and higher number of bleedings. While prophylactic platelet transfusions were given to 25.6% of patients undergoing procedures, TPO receptor agonist use was only detected in 3.1% of them. Most patients (60.9%) required at least one hospital admission during the follow up and 14.4% of admissions were due to bleeding events with a hospital length of stay of 6 (3, 9) days.

CONCLUSIONS

NLP and machine learning are useful tools to describe real-world data in patients with CLD and severe TCP in Spain. Bleeding events are frequent in those patients who need invasive procedures, even receiving platelet transfusions as a prophylactic treatment, increasing the further use of medical resources. Because that, new prophylactic treatments that are not yet generalized, are needed.

Using natural language processing to explore characteristics and management of patients with axial spondyloarthritis and psoriatic arthritis treated under real-world conditions in Spain: SpAINET study

Background

Spondyloarthritis (SpA) is a group of related but phenotypically distinct inflammatory disorders that include axial SpA (axSpA) and psoriatic arthritis (PsA). Information on the characteristics and management of these patients in the real world remains scarce.

Objectives

To explore the characteristics and management [disease activity assessment and treatment with secukinumab (SEC) or other biologic disease-modifying antirheumatic drugs (bDMARDs)] of axSpA and PsA patients using natural language processing (NLP) in Electronic Health Records (EHRs).

Design

National, multicenter, observational, and retrospective study.

Methods

We analyzed free-text and structured clinical information from EHR at three hospitals. All adult patients with axSpA, PsA or non-classified SpA from 2018 to 2021 with minimum follow-up of three months were included when starting SEC or other bDMARDs. Clinical variables were extracted using EHRead® technology based on Systemized Nomenclature of Medicine-Clinical Terms (SNOMED CT) terminology.

Results

Out of 887,735 patients, 758 were included, of which 328 had axSpA [58.5% male; mean (SD) age of 50.7 (12.7) years], 365 PsA [54.8% female, 53.9 (12.4) years], and 65 non-classified SpA. Mean (SD) time since diagnosis was 36.8 (61.0) and 24.1 (35.2) months for axSpA and PsA, respectively. Only 116 axSpA patients (35.3%) had available Ankylosing Spondylitis Disease Activity Score (ASDAS) or Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) at bDMARD onset, of which 61 presented active disease. Disease Activity in PSoriatic Arthritis (DAPSA) or Disease Assessment Score - 28 joints (DAS-28) values at bDMARD onset were available for only 61 PsA (16.7%) patients, with 23 of them having active disease. The number of patients with available tender joint count or swollen joint count assessment was 68 (20.7%) and 59 (18%) for axSpA, and 115 (31.5%) and 119 (32.6%) for PsA, respectively. SEC was used in 63 (19.2%) axSpA patients and in 63 (17.3%) PsA patients.

Conclusion

Using NLP, the study showed that around one-third of axSpA and one-sixth of PsA patients have disease activity assessments with ASDAS/BASDAI or DAPSA/DAS-28, respectively, highlighting an area of improvement in these patients' management.

Prevalence of cancer in patients with hypothyroidism: Analysis using big data tools

OBJECTIVE

To evaluate the frequency of different types of cancer in patients diagnosed with hypothyroidism using big data methodology on the Savana Manager platform.

METHODS

An observational, retrospective study was carried out using electronic medical record (EMR) data from the Hospital Universitario Puerta de Hierro Majadahonda (Madrid). Information from the EMRs was extracted using artificial intelligence techniques and analysed using the Savana Manager v3.0 software. Searches were performed using the term "hypothyroidism" and the terms corresponding to the tumours analysed.

RESULTS

Of a total population of 506,749 patients, 23,570 (4.7%) were diagnosed with hypothyroidism. Patients with this diagnosis had a significantly higher frequency of cancer than that found in non-hypothyroid subjects (OR 2.09, 95% confidence interval [CI] 2.01-2.17). This higher frequency was found both in women (OR 1.99, 95% CI 1.90-2.08) and in men (OR 2.83, 95% CI 2.63-3.05). However, this higher frequency of cancer was not observed in hypothyroid patients older than 60 years (OR 0.97, 95% CI 0.92-1.02). Although the frequency of most of the neoplasms studied individually was higher in the population with hypothyroidism, we observed that hypothyroid patients over 60 years of age had a significant decrease in the frequency of prostate, lung, colorectal, and liver cancer.

CONCLUSION

Data from this hospital cohort suggest that there is a significant association between the diagnosis of hypothyroidism and cancer. However, this association is less evident in hypothyroid patients older than 60 years.

Symptoms timeline and outcomes in amyotrophic lateral sclerosis using artificial intelligence

Amyotrophic lateral sclerosis (ALS) is a fatal, neurodegenerative motor neuron disease. Although an early diagnosis is crucial to provide adequate care and improve survival, patients with ALS experience a significant diagnostic delay. This study aimed to use real-world data to describe the clinical profile and timing between symptom onset, diagnosis, and relevant outcomes in ALS. Retrospective and multicenter study in 5 representative hospitals and Primary Care services in the SESCAM Healthcare Network (Castilla-La Mancha, Spain). Using Natural Language Processing (NLP), the clinical information in electronic health records of all patients with ALS was extracted between January 2014 and December 2018. From a source population of all individuals attended in the participating hospitals, 250 ALS patients were identified (61.6% male, mean age 64.7 years). Of these, 64% had spinal and 36% bulbar ALS. For most defining symptoms, including dyspnea, dysarthria, dysphagia and fasciculations, the overall diagnostic delay from symptom onset was 11 (6-18) months. Prior to diagnosis, only 38.8% of patients had visited the neurologist. In a median post-diagnosis follow-up of 25 months, 52% underwent gastrostomy, 64% non-invasive ventilation, 16.4% tracheostomy, and 87.6% riluzole treatment; these were more commonly reported (all Ps < 0.05) and showed greater probability of occurrence (all Ps < 0.03) in bulbar ALS. Our results highlight the diagnostic delay in ALS and revealed differences in the clinical characteristics and occurrence of major disease-specific events across ALS subtypes. NLP holds great promise for its application in the wider context of rare neurological diseases.

Clinical Characterization of Inpatients with Acute Conjunctivitis: A Retrospective Analysis by Natural Language Processing and Machine Learning

Background Acute bacterial conjunctivitis (ABC) is a relatively common medical condition caused by different pathogens. Although it rarely threatens vision, it is one of the most common conditions that cause red eyes and may be accompanied by discomfort and discharge. The study aimed to identify and characterize inpatients with ABC treated with topical antibiotics. Methods The EHRead® technology, based on natural language processing (NLP) and machine learning, was used to extract and analyze the clinical information in the electronic health records (EHRs) of antibiotic-treated patients with conjunctivitis and admitted to five hospitals in Spain between January 2014 and December 2018. Categorical variables were described by frequency, whereas numerical variables included the mean, standard deviation, median, and quartiles. Results From a source population of 2,071,812 adult patients who attended the participating hospitals in the study period, 11,110 patients diagnosed with acute conjunctivitis were identified. Six thousand five hundred eighty-three patients were treated with antibiotics, comprising the final study population. Microbiology was tested only on 12.1% of patients. Antibiotics, mainly tobramycin, and corticosteroids, mainly dexamethasone, were usually prescribed. NSAIDs were also used in about 50% of patients, always combined with antibiotics. Conclusions The present study provided a realistic representation of the hospital practice concerning managing patients with acute antibiotic-treated conjunctivitis. The diagnosis is usually based on the clinical ground, microbiology is rarely tested, few bacteria species are involved, and local antibiotics are frequently associated with corticosteroids and/or NSAIDs. Moreover, this study provided clinically relevant outcomes, based on new technology, that could be applied in clinical practice.

How can artificial intelligence optimize value-based contracting?

Efforts in the pharmaceutical market have been aimed at ensuring that the benefits obtained from the introduction of new therapies justify the associated costs. In recent years, drug payment models in healthcare have undergone a dramatic shift from focusing on volume (i.e., size of the target clinical population) to focusing on value (i.e., drug performance in real-world settings). In this context, value-based contracts (VBCs) were designed to align the payment of a drug to its clinical performance outside clinical trials by evaluating the effectiveness using real-word evidence (RWE). Despite their widespread implementation, different factors jeopardize the application of VBCs to most marketed drugs in a near future, including the need for easily measurable and relevant outcomes associated with clinical improvements, and access to a large patient population to assess said outcomes. Here, we argue that the extraction and analysis of massive amounts of RWE captured in patients' electronic health records (EHRs) will circumvent these issues and optimize negotiations in VBCs. Particularly, the use of Natural Language Processing (NLP) has proven successful in the analysis of structured and unstructured clinical information in EHRs in multicenter research studies. Thus, the application of NLP to analyze patient-centered information in EHRs in the context of innovative contracting can be utterly beneficial as it enables the real-time evaluation of treatment response and financial impact in real-world settings.

Major Adverse Cardiovascular Events in Coronary Type 2 Diabetic Patients: Identification of Associated Factors Using Electronic Health Records and Natural Language Processing

Patients with Type 2 diabetes mellitus (T2DM) and coronary artery disease (CAD) are at high risk of developing major adverse cardiovascular events (MACE). This is a multicenter, retrospective, and observational study performed in Spain aimed to characterize these patients in a real-world setting. Unstructured data from the Electronic Health Records were extracted by EHRead^®, a technology based on Natural Language Processing and machine learning. The association between new MACE and the variables of interest were investigated by univariable and multivariable analyses. From a source population of 2,184,662 patients, we identified 4072 adults diagnosed with T2DM and CAD (62.2% male, mean age 70 ± 11). The main comorbidities observed included arterial hypertension, hyperlipidemia, and obesity, with metformin and statins being the treatments most frequently prescribed. MACE development was associated with multivessel (Hazard Ratio (HR) = 2.49) and single coronary vessel disease (HR = 1.71), transient ischemic attack (HR = 2.01), heart failure (HR = 1.32), insulin treatment (HR = 1.40), and percutaneous coronary intervention (PCI) (HR = 2.27), whilst statins (HR = 0.73) were associated with a lower risk of MACE occurrence. In conclusion, we found six risk factors associated with the development of MACE which were related with cardiovascular diseases and T2DM severity, and treatment with statins was identified as a protective factor for new MACE in this study.

Assessment of medical management in Coronary Type 2 Diabetic patients with previous percutaneous coronary intervention in Spain: A retrospective analysis of electronic health records using Natural Language Processing

INTRODUCTION AND OBJECTIVES

Patients with type 2 diabetes (T2D) and stable coronary artery disease (CAD) previously revascularized with percutaneous coronary intervention (PCI) are at high risk of recurrent ischemic events. We aimed to provide real-world insights into the clinical characteristics and management of this clinical population, excluding patients with a history of myocardial infarction (MI) or stroke, using Natural Language Processing (NLP) technology.

METHODS

This is a multicenter, retrospective study based on the secondary use of 2014-2018 real-world data captured in the Electronic Health Records (EHRs) of 1,579 patients (0.72% of the T2D population analyzed; n = 217,632 patients) from 12 representative hospitals in Spain. To access the unstructured clinical information in EHRs, we used the EHRead® technology, based on NLP and machine learning. Major adverse cardiovascular events (MACE) were considered: MI, ischemic stroke, urgent coronary revascularization, and hospitalization due to unstable angina. The association between MACE rates and the variables included in this study was evaluated following univariate and multivariate approaches.

RESULTS

Most patients were male (72.13%), with a mean age of 70.5±10 years. Regarding T2D, most patients were non-insulin-dependent T2D (61.75%) with high prevalence of comorbidities. The median (Q1-Q3) duration of follow-up was 1.2 (0.3-4.5) years. Overall, 35.66% of patients suffered from at least one MACE during follow up. Using a Cox Proportional Hazards regression model analysis, several independent factors were associated with MACE during follow up: CAD duration (p < 0.001), COPD/Asthma (p = 0.021), heart valve disease (p = 0.031), multivessel disease (p = 0.005), insulin treatment (p < 0.001), statins treatment (p < 0.001), and clopidogrel treatment (p = 0.039).

CONCLUSIONS

Our results showed high rates of MACE in a large real-world series of PCI-revascularized patients with T2D and CAD with no history of MI or stroke. These data represent a potential opportunity to improve the clinical management of these patients.