Leveraging generative AI for clinical evidence synthesis needs to ensure trustworthiness.

Evidence-based medicine promises to improve the quality of healthcare by empowering medical decisions and practices with the best available evidence. The rapid growth of medical evidence, which can be obtained from various sources, poses a challenge in collecting, appraising, and synthesizing the evidential information. Recent advancements in generative AI, exemplified by large language models, hold promise in facilitating the arduous task. However, developing accountable, fair, and inclusive models remains a complicated undertaking. In this perspective, we discuss the trustworthiness of generative AI in the context of automated summarization of medical evidence.

Constructing mesoporous biochar derived from waste carton: Improving multi-site adsorption of dye wastewater and investigating mechanism.

The development of cost-efficient biochar adsorbent with a simple preparation method is essential to constructing efficient wastewater treatment system. Here, a low-cost waste carton biochar (WCB) prepared by a simple two-step carbonization was applied in efficiently removing Rhodamine B (RhB) in aqueous environment. The maximum ability of WCB for RhB adsorption was 222 mg/g, 6 and 10 times higher than both of rice straw biochar (RSB) and broadbean shell biochar (BSB), respectively. It was mainly ascribed to the mesopore structure (3.0-20.4 nm) of WCB possessing more spatial sites compared to RSB (2.2 nm) and BSB (2.4 nm) for RhB (1.4 nm✕1.1 nm✕0.6 nm) adsorption. Furthermore, external mass transfer (EMT) controlled mass transfer resistance (MTR) of the RhB sorption process by WCB which was fitted with the Langmuir model well. Meanwhile, the adsorption process was dominated by physisorption through van der Waals forces and π-π interactions. A mixture of three dyes in river water was well removed by using WCB. This work provides a straightforward method of preparing mesoporous biochar derived from waste carton with high-adsorption capacity for dye wastewater treatment.

Investigations of a 1018 nm gain-switched Yb-doped fiber oscillator.

In this paper, we investigate a 1018 nm gain-switched ytterbium-doped fiber oscillator at a low repetition rate in terms of theory and experiment. Theoretically, a numerical model applicable to a 1018 nm gain-switched ytterbium-doped fiber laser was established. The influence of the pump peak power and active fiber lengths on the 1018 nm gain-switched ytterbium-doped fiber laser was numerically simulated. Experimentally, a compact 1018 nm all-fiber-structured pulsed laser oscillator is constructed, in which a pulse width of 110 ns and a single-pulse energy of 0.1 mJ were obtained. Moreover, the experimental results are in agreement with the numerical simulation ones. To the best of our knowledge, this is the first time that gain-switching technology has been applied to 1018 nm fiber lasers to generate nanosecond pulsed lasers. The model and experimental results can provide a reference for the engineering design of the same type of low repetition rate fiber lasers below the kilohertz level.

Enhancing post-traumatic stress disorder patient assessment: leveraging natural language processing for research of domain criteria identification using electronic medical records.

BACKGROUND: Extracting research of domain criteria (RDoC) from high-risk populations like those with post-traumatic stress disorder (PTSD) is crucial for positive mental health improvements and policy enhancements. The intricacies of collecting, integrating, and effectively leveraging clinical notes for this purpose introduce complexities. METHODS: In our study, we created a natural language processing (NLP) workflow to analyze electronic medical record (EMR) data and identify and extract research of domain criteria using a pre-trained transformer-based natural language model, all-mpnet-base-v2. We subsequently built dictionaries from 100,000 clinical notes and analyzed 5.67 million clinical notes from 38,807 PTSD patients from the University of Pittsburgh Medical Center. Subsequently, we showcased the significance of our approach by extracting and visualizing RDoC information in two use cases: (i) across multiple patient populations and (ii) throughout various disease trajectories. RESULTS: The sentence transformer model demonstrated high F1 macro scores across all RDoC domains, achieving the highest performance with a cosine similarity threshold value of 0.3. This ensured an F1 score of at least 80% across all RDoC domains. The study revealed consistent reductions in all six RDoC domains among PTSD patients after psychotherapy. We found that 60.6% of PTSD women have at least one abnormal instance of the six RDoC domains as compared to PTSD men (51.3%), with 45.1% of PTSD women with higher levels of sensorimotor disturbances compared to men (41.3%). We also found that 57.3% of PTSD patients have at least one abnormal instance of the six RDoC domains based on our records. Also, veterans had the higher abnormalities of negative and positive valence systems (60% and 51.9% of veterans respectively) compared to non-veterans (59.1% and 49.2% respectively). The domains following first diagnoses of PTSD were associated with heightened cue reactivity to trauma, suicide, alcohol, and substance consumption. CONCLUSIONS: The findings provide initial insights into RDoC functioning in different populations and disease trajectories. Natural language processing proves valuable for capturing real-time, context dependent RDoC instances from extensive clinical notes.

Nonlinear spectral compression in high-power narrow-linewidth polarization maintaining fiber amplifiers for SBS suppression.

In this paper, we propose a method for narrowing the spectrum in high-power narrow-linewidth polarization-maintaining (PM) fiber amplifiers and investigate its potential for suppressing the stimulated Brillouin scattering (SBS). In this method, in addition to common phase modulation to suppress SBS, precisely designed amplitude modulation is induced to generate self-phase modulation in a high-power PM fiber amplifier. In this co-modulation way, the spectrum can be gradually compressed along the fiber. Compared to phase modulation alone or fiber-Bragg-gratings (FBGs) based narrow-linewidth fiber oscillator schemes, in which the spectrum remains the same or broadens, this scheme can achieve a higher SBS threshold for the same output spectral linewidth. Experiments on a ∼ 3 kW peak power quasi-continuous wave (QCW) fiber amplifier show that the co-modulation scheme can compress the spectrum from 0.25 nm to 0.084 nm as output peak power increases from 13 W to 3.2 kW and enhances the SBS threshold by ∼1.7 times compared to traditional FBGs-based fiber oscillator schemes, and by ∼1.4 times compared to common phase modulation schemes. This co-modulation scheme has the potential for mitigating SBS in high-power fiber amplifiers.

Linearly polarized fiber amplifier with narrow linewidth of 5†kW exhibiting a record output power and near-diffraction-limited beam quality.

In this work, a narrow-linewidth polarization-maintaining (PM) all-fiber amplifier with near-diffraction-limited beam quality and record output power is presented. First, a 4.45-kW PM fiber amplifier with a 3-dB linewidth of 0.08 nm and root mean square (rms) linewidth of 0.22 nm is achieved based on optimized phase modulation. However, the sideband of the spectrum broadens significantly during the amplification process, which is mainly caused by the additional intensity variation of the injected signal. Meanwhile, an up to 5.04-kW linearly polarized fiber laser with a relatively stable spectral bandwidth is achieved by effectively suppressing spectral broadening. At the maximum output power, the rms linewidth is 0.2 nm, the beam quality factor M2 is less than 1.3, the polarization extinction ratio (PER) is 16.5 dB, and the signal-to-noise ratio (SNR) is approximately 53 dB. The further power scaling of the amplifier is mainly limited by the pump power. To the best of our knowledge, this is the maximum output power of a narrow linewidth linearly polarized fiber amplifier to date.

The importance of social activity to risk of major depression in older adults.

BACKGROUND: Several social determinants of health (SDoH) have been associated with the onset of major depressive disorder (MDD). However, prior studies largely focused on individual SDoH and thus less is known about the relative importance (RI) of SDoH variables, especially in older adults. Given that risk factors for MDD may differ across the lifespan, we aimed to identify the SDoH that was most strongly related to newly diagnosed MDD in a cohort of older adults. METHODS: We used self-reported health-related survey data from 41 174 older adults (50-89 years, median age = 67 years) who participated in the Mayo Clinic Biobank, and linked ICD codes for MDD in the participants' electronic health records. Participants with a history of clinically documented or self-reported MDD prior to survey completion were excluded from analysis (N = 10 938, 27%). We used Cox proportional hazards models with a gradient boosting machine approach to quantify the RI of 30 pre-selected SDoH variables on the risk of future MDD diagnosis. RESULTS: Following biobank enrollment, 2073 older participants were diagnosed with MDD during the follow-up period (median duration = 6.7 years). The most influential SDoH was perceived level of social activity (RI = 0.17). Lower level of social activity was associated with a higher risk of MDD [hazard ratio = 2.27 (95% CI 2.00-2.50) for highest v. lowest level]. CONCLUSION: Across a range of SDoH variables, perceived level of social activity is most strongly related to MDD in older adults. Monitoring changes in the level of social activity may help identify older adults at an increased risk of MDD.

Fair patient model: Mitigating bias in the patient representation learned from the electronic health records.

OBJECTIVE: To pre-train fair and unbiased patient representations from Electronic Health Records (EHRs) using a novel weighted loss function that reduces bias and improves fairness in deep representation learning models. METHODS: We defined a new loss function, called weighted loss function, in the deep representation learning model to balance the importance of different groups of patients and features. We applied the proposed model, called Fair Patient Model (FPM), to a sample of 34,739 patients from the MIMIC-III dataset and learned patient representations for four clinical outcome prediction tasks. RESULTS: FPM outperformed the baseline models in terms of three fairness metrics: demographic parity, equality of opportunity difference, and equalized odds ratio. FPM also achieved comparable predictive performance with the baselines, with an average accuracy of 0.7912. Feature analysis revealed that FPM captured more information from clinical features than the baselines. CONCLUSION: FPM is a novel method to pre-train fair and unbiased patient representations from the EHR data using a weighted loss function. The learned representations can be used for various downstream tasks in healthcare and can be extended to other domains where fairness is important.

Representing and utilizing clinical textual data for real world studies: An OHDSI approach.

Clinical documentation in electronic health records contains crucial narratives and details about patients and their care. Natural language processing (NLP) can unlock the information conveyed in clinical notes and reports, and thus plays a critical role in real-world studies. The NLP Working Group at the Observational Health Data Sciences and Informatics (OHDSI) consortium was established to develop methods and tools to promote the use of textual data and NLP in real-world observational studies. In this paper, we describe a framework for representing and utilizing textual data in real-world evidence generation, including representations of information from clinical text in the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM), the workflow and tools that were developed to extract, transform and load (ETL) data from clinical notes into tables in OMOP CDM, as well as current applications and specific use cases of the proposed OHDSI NLP solution at large consortia and individual institutions with English textual data. Challenges faced and lessons learned during the process are also discussed to provide valuable insights for researchers who are planning to implement NLP solutions in real-world studies.

Classifying the lifestyle status for Alzheimer's disease from clinical notes using deep learning with weak supervision.

BACKGROUND: Since no effective therapies exist for Alzheimer's disease (AD), prevention has become more critical through lifestyle status changes and interventions. Analyzing electronic health records (EHRs) of patients with AD can help us better understand lifestyle's effect on AD. However, lifestyle information is typically stored in clinical narratives. Thus, the objective of the study was to compare different natural language processing (NLP) models on classifying the lifestyle statuses (e.g., physical activity and excessive diet) from clinical texts in English. METHODS: Based on the collected concept unique identifiers (CUIs) associated with the lifestyle status, we extracted all related EHRs for patients with AD from the Clinical Data Repository (CDR) of the University of Minnesota (UMN). We automatically generated labels for the training data by using a rule-based NLP algorithm. We conducted weak supervision for pre-trained Bidirectional Encoder Representations from Transformers (BERT) models and three traditional machine learning models as baseline models on the weakly labeled training corpus. These models include the BERT base model, PubMedBERT (abstracts + full text), PubMedBERT (only abstracts), Unified Medical Language System (UMLS) BERT, Bio BERT, Bio-clinical BERT, logistic regression, support vector machine, and random forest. The rule-based model used for weak supervision was tested on the GSC for comparison. We performed two case studies: physical activity and excessive diet, in order to validate the effectiveness of BERT models in classifying lifestyle status for all models were evaluated and compared on the developed Gold Standard Corpus (GSC) on the two case studies. RESULTS: The UMLS BERT model achieved the best performance for classifying status of physical activity, with its precision, recall, and F-1 scores of 0.93, 0.93, and 0.92, respectively. Regarding classifying excessive diet, the Bio-clinical BERT model showed the best performance with precision, recall, and F-1 scores of 0.93, 0.93, and 0.93, respectively. CONCLUSION: The proposed approach leveraging weak supervision could significantly increase the sample size, which is required for training the deep learning models. By comparing with the traditional machine learning models, the study also demonstrates the high performance of BERT models for classifying lifestyle status for Alzheimer's disease in clinical notes.

An aberration detection-based approach for sentinel syndromic surveillance of COVID-19 and other novel influenza-like illnesses.

Coronavirus Disease 2019 has emerged as a significant global concern, triggering harsh public health restrictions in a successful bid to curb its exponential growth. As discussion shifts towards relaxation of these restrictions, there is significant concern of second-wave resurgence. The key to managing these outbreaks is early detection and intervention, and yet there is a significant lag time associated with usage of laboratory confirmed cases for surveillance purposes. To address this, syndromic surveillance can be considered to provide a timelier alternative for first-line screening. Existing syndromic surveillance solutions are however typically focused around a known disease and have limited capability to distinguish between outbreaks of individual diseases sharing similar syndromes. This poses a challenge for surveillance of COVID-19 as its active periods tend to overlap temporally with other influenza-like illnesses. In this study we explore performing sentinel syndromic surveillance for COVID-19 and other influenza-like illnesses using a deep learning-based approach. Our methods are based on aberration detection utilizing autoencoders that leverages symptom prevalence distributions to distinguish outbreaks of two ongoing diseases that share similar syndromes, even if they occur concurrently. We first demonstrate that this approach works for detection of outbreaks of influenza, which has known temporal boundaries. We then demonstrate that the autoencoder can be trained to not alert on known and well-managed influenza-like illnesses such as the common cold and influenza. Finally, we applied our approach to 2019-2020 data in the context of a COVID-19 syndromic surveillance task to demonstrate how implementation of such a system could have provided early warning of an outbreak of a novel influenza-like illness that did not match the symptom prevalence profile of influenza and other known influenza-like illnesses.

3.25 kW all-fiberized and polarization-maintained Yb-doped amplifier with a 20 GHz linewidth and near-diffraction-limited beam quality.

In this paper, we demonstrate a high-power, narrow-linewidth, polarization-maintaining fiber amplifier with near-diffraction-limited beam quality. By optimizing the phase modulation signal, a nearly top-hat-shaped spectrum was generated for self-pulsing suppressing. That results in doubling the self-pulsing threshold we got from conventional white noise signal phase modulation with the same optical linewidth. Based on an optimized signal and a high power, polarization-maintaining, counter-pumped fiber amplifier, we obtain a 3.25 kW narrow-linewidth linearly polarized laser output with a linewidth of ∼20GHz, the polarization extinction ratio is about 15 dB, and the M2 is less than 1.22 at the maximum output power. To the best of our knowledge, this is the first demonstration of a narrow-linewidth, linear polarization, all-fiber amplifier with 3.25 kW laser output.

Unraveling the mechanism of efficient adsorption of riboflavin onto activated biochar derived from algal blooms.

Riboflavin is commercially produced primarily by bio-fermentation. Nonetheless, purification and separation are particularly complex and costly. Adsorption from the fermentation liquor is an alternative riboflavin separation technology during which a cost-efficient adsorbent is highly desired. In this study, a low-cost activated algal biomass-derived biochar (AABB) was applied as an adsorbent to efficiently adsorb riboflavin from an aqueous solution. The adsorption capacity of riboflavin on AABB increased with the increase in pyrolysis temperature and initial riboflavin concentration. The adsorption isotherms were well described by the Freundlich and Langmuir models. The AABB displayed excellent adsorption performance and its maximum adsorption capacity was 476.9 mg/g, which was 6.8, 6.8, and 5.2 times higher than that of laboratory-prepared activated rape straw biochar, activated broadbean shell biochar and commercial activated carbon, respectively, which was mainly ascribed to its larger specific surface area and abundant functional groups. The mass transfer model results showed that mass transfer resistance was dependent on both the film mass transfer and porous diffusion. Raman and Fourier transform-infrared spectra confirmed the presence of π-π interactions and hydrogen bonding between riboflavin and the AABB. The adsorption of riboflavin onto AABB was a spontaneous process, which was dominated by van der Waals forces. These results will be beneficial for developing effective riboflavin recovery technologies and simultaneously utilizing waste algal blooms.

Clinical concept extraction: A methodology review.

BACKGROUND: Concept extraction, a subdomain of natural language processing (NLP) with a focus on extracting concepts of interest, has been adopted to computationally extract clinical information from text for a wide range of applications ranging from clinical decision support to care quality improvement. OBJECTIVES: In this literature review, we provide a methodology review of clinical concept extraction, aiming to catalog development processes, available methods and tools, and specific considerations when developing clinical concept extraction applications. METHODS: Based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, a literature search was conducted for retrieving EHR-based information extraction articles written in English and published from January 2009 through June 2019 from Ovid MEDLINE In-Process & Other Non-Indexed Citations, Ovid MEDLINE, Ovid EMBASE, Scopus, Web of Science, and the ACM Digital Library. RESULTS: A total of 6,686 publications were retrieved. After title and abstract screening, 228 publications were selected. The methods used for developing clinical concept extraction applications were discussed in this review.

Unsupervised machine learning for the discovery of latent disease clusters and patient subgroups using electronic health records.

Machine learning has become ubiquitous and a key technology on mining electronic health records (EHRs) for facilitating clinical research and practice. Unsupervised machine learning, as opposed to supervised learning, has shown promise in identifying novel patterns and relations from EHRs without using human created labels. In this paper, we investigate the application of unsupervised machine learning models in discovering latent disease clusters and patient subgroups based on EHRs. We utilized Latent Dirichlet Allocation (LDA), a generative probabilistic model, and proposed a novel model named Poisson Dirichlet Model (PDM), which extends the LDA approach using a Poisson distribution to model patients' disease diagnoses and to alleviate age and sex factors by considering both observed and expected observations. In the empirical experiments, we evaluated LDA and PDM on three patient cohorts, namely Osteoporosis, Delirium/Dementia, and Chronic Obstructive Pulmonary Disease (COPD)/Bronchiectasis Cohorts, with their EHR data retrieved from the Rochester Epidemiology Project (REP) medical records linkage system, for the discovery of latent disease clusters and patient subgroups. We compared the effectiveness of LDA and PDM in identifying disease clusters through the visualization of disease representations. We tested the performance of LDA and PDM in differentiating patient subgroups through survival analysis, as well as statistical analysis of demographics and Elixhauser Comorbidity Index (ECI) scores in those subgroups. The experimental results show that the proposed PDM could effectively identify distinguished disease clusters based on the latent patterns hidden in the EHR data by alleviating the impact of age and sex, and that LDA could stratify patients into differentiable subgroups with larger p-values than PDM. However, those subgroups identified by LDA are highly associated with patients' age and sex. The subgroups discovered by PDM might imply the underlying patterns of diseases of greater interest in epidemiology research due to the alleviation of age and sex. Both unsupervised machine learning approaches could be leveraged to discover patient subgroups using EHRs but with different foci.

HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology.

BACKGROUND: In precision medicine, deep phenotyping is defined as the precise and comprehensive analysis of phenotypic abnormalities, aiming to acquire a better understanding of the natural history of a disease and its genotype-phenotype associations. Detecting phenotypic relevance is an important task when translating precision medicine into clinical practice, especially for patient stratification tasks based on deep phenotyping. In our previous work, we developed node embeddings for the Human Phenotype Ontology (HPO) to assist in phenotypic relevance measurement incorporating distributed semantic representations. However, the derived HPO embeddings hold only distributed representations for IS-A relationships among nodes, hampering the ability to fully explore the graph. METHODS: In this study, we developed a framework, HPO2Vec+, to enrich the produced HPO embeddings with heterogeneous knowledge resources (i.e., DECIPHER, OMIM, and Orphanet) for detecting phenotypic relevance. Specifically, we parsed disease-phenotype associations contained in these three resources to enrich non-inheritance relationships among phenotypic nodes in the HPO. To generate node embeddings for the HPO, node2vec was applied to perform node sampling on the enriched HPO graphs based on random walk followed by feature learning over the sampled nodes to generate enriched node embeddings. Four HPO embeddings were generated based on different graph structures, which we hereafter label as HPOEmb-Original, HPOEmb-DECIPHER, HPOEmb-OMIM, and HPOEmb-Orphanet. We evaluated the derived embeddings quantitatively through an HPO link prediction task with four edge embeddings operations and six machine learning algorithms. The resulting best embeddings were then evaluated for patient stratification of 10 rare diseases using electronic health records (EHR) collected at Mayo Clinic. We assessed our framework qualitatively by visualizing phenotypic clusters and conducting a use case study on primary hyperoxaluria (PH), a rare disease, on the task of inferring relevant phenotypes given 22 annotated PH related phenotypes. RESULTS: The quantitative link prediction task shows that HPOEmb-Orphanet achieved an optimal AUROC of 0.92 and an average precision of 0.94. In addition, HPOEmb-Orphanet achieved an optimal F1 score of 0.86. The quantitative patient similarity measurement task indicates that HPOEmb-Orphanet achieved the highest average detection rate for similar patients over 10 rare diseases and performed better than other similarity measures implemented by an existing tool, HPOSim, especially for pairwise patients with fewer shared common phenotypes. The qualitative evaluation shows that the enriched HPO embeddings are generally able to detect relationships among nodes with fine granularity and HPOEmb-Orphanet is particularly good at associating phenotypes across different disease systems. For the use case of detecting relevant phenotypic characterizations for given PH related phenotypes, HPOEmb-Orphanet outperformed the other three HPO embeddings by achieving the highest average P@5 of 0.81 and the highest P@10 of 0.79. Compared to seven conventional similarity measurements provided by HPOSim, HPOEmb-Orphanet is able to detect more relevant phenotypic pairs, especially for pairs not in inheritance relationships. CONCLUSION: We drew the following conclusions based on the evaluation results. First, with additional non-inheritance edges, enriched HPO embeddings can detect more associations between fine granularity phenotypic nodes regardless of their topological structures in the HPO graph. Second, HPOEmb-Orphanet not only can achieve the optimal performance through link prediction and patient stratification based on phenotypic similarity, but is also able to detect relevant phenotypes closer to domain expert's judgments than other embeddings and conventional similarity measurements. Third, incorporating heterogeneous knowledge resources do not necessarily result in better performance for detecting relevant phenotypes. From a clinical perspective, in our use case study, clinical-oriented knowledge resources (e.g., Orphanet) can achieve better performance in detecting relevant phenotypic characterizations compared to biomedical-oriented knowledge resources (e.g., DECIPHER and OMIM).

1.5 kW polarization-maintained Yb-doped amplifier with 13 GHz linewidth by suppressing the self-pulsing and stimulated Brillouin scattering.

In this work, we study the characteristics of self-pulsing in a polarization-maintained fiber amplifier operated with different linewidths based on white noise source phase modulation. It indicates that the self-pulsing is almost simultaneous with the stimulated Brillouin scattering process, and its threshold is increasing near-linearly with the linewidth. By optimizing the laser structure, the threshold of self-pulsing increases by a factor of 1.5. We demonstrate a high-power linear polarization and all-fiberized amplifier with narrow linewidth and near-diffraction-limited beam quality. The output power scales to 1.5 kW with the pumping efficiency of 83%. The full width at half-maximum linewidth was measured to be 13 GHz. The polarization extinction ratio was larger than 13 dB. The beam quality M2 was about 1.14 at the maximum laser power.

Discovering associations between problem list and practice setting.

BACKGROUND: The Health Information Technology for Economic and Clinical Health Act (HITECH) has greatly accelerated the adoption of electronic health records (EHRs) with the promise of better clinical decisions and patients' outcomes. One of the core criteria for "Meaningful Use" of EHRs is to have a problem list that shows the most important health problems faced by a patient. The implementation of problem lists in EHRs has a potential to help practitioners to provide customized care to patients. However, it remains an open question on how to leverage problem lists in different practice settings to provide tailored care, of which the bottleneck lies in the associations between problem list and practice setting. METHODS: In this study, using sampled clinical documents associated with a cohort of patients who received their primary care at Mayo Clinic, we investigated the associations between problem list and practice setting through natural language processing (NLP) and topic modeling techniques. Specifically, after practice settings and problem lists were normalized, statistical χ2 test, term frequency-inverse document frequency (TF-IDF) and enrichment analysis were used to choose representative concepts for each setting. Then Latent Dirichlet Allocations (LDA) were used to train topic models and predict potential practice settings using similarity metrics based on the problem concepts representative of practice settings. Evaluation was conducted through 5-fold cross validation and Recall@k, Precision@k and F1@k were calculated. RESULTS: Our method can generate prioritized and meaningful problem lists corresponding to specific practice settings. For practice setting prediction, recall increases from 0.719 (k = 2) to 0.931 (k = 10), precision increases from 0.882 (k = 2) to 0.931 (k = 10) and F1 increases from 0.790 (k = 2) to 0.931 (k = 10). CONCLUSION: To our best knowledge, our study is the first attempting to discover the association between the problem lists and hospital practice settings. In the future, we plan to investigate how to provide more tailored care by utilizing the association between problem list and practice setting revealed in this study.

Natural language processing for populating lung cancer clinical research data.

BACKGROUND: Lung cancer is the second most common cancer for men and women; the wide adoption of electronic health records (EHRs) offers a potential to accelerate cohort-related epidemiological studies using informatics approaches. Since manual extraction from large volumes of text materials is time consuming and labor intensive, some efforts have emerged to automatically extract information from text for lung cancer patients using natural language processing (NLP), an artificial intelligence technique. METHODS: In this study, using an existing cohort of 2311 lung cancer patients with information about stage, histology, tumor grade, and therapies (chemotherapy, radiotherapy and surgery) manually ascertained, we developed and evaluated an NLP system to extract information on these variables automatically for the same patients from clinical narratives including clinical notes, pathology reports and surgery reports. RESULTS: Evaluation showed promising results with the recalls for stage, histology, tumor grade, and therapies achieving 89, 98, 78, and 100% respectively and the precisions were 70, 88, 90, and 100% respectively. CONCLUSION: This study demonstrated the feasibility and accuracy of automatically extracting pre-defined information from clinical narratives for lung cancer research.

Natural language processing of radiology reports for identification of skeletal site-specific fractures.

BACKGROUND: Osteoporosis has become an important public health issue. Most of the population, particularly elderly people, are at some degree of risk of osteoporosis-related fractures. Accurate identification and surveillance of patient populations with fractures has a significant impact on reduction of cost of care by preventing future fractures and its corresponding complications. METHODS: In this study, we developed a rule-based natural language processing (NLP) algorithm for identification of twenty skeletal site-specific fractures from radiology reports. The rule-based NLP algorithm was based on regular expressions developed using MedTagger, an NLP tool of the Apache Unstructured Information Management Architecture (UIMA) pipeline to facilitate information extraction from clinical narratives. Radiology notes were retrieved from the Mayo Clinic electronic health records data warehouse. We developed rules for identifying each fracture type according to physicians' knowledge and experience, and refined these rules via verification with physicians. This study was approved by the institutional review board (IRB) for human subject research. RESULTS: We validated the NLP algorithm using the radiology reports of a community-based cohort at Mayo Clinic with the gold standard constructed by medical experts. The micro-averaged results of sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and F1-score of the proposed NLP algorithm are 0.930, 1.0, 1.0, 0.941, 0.961, respectively. The F1-score is 1.0 for 8 fractures, and above 0.9 for a total of 17 out of 20 fractures (85%). CONCLUSIONS: The results verified the effectiveness of the proposed rule-based NLP algorithm in automatic identification of osteoporosis-related skeletal site-specific fractures from radiology reports. The NLP algorithm could be utilized to accurately identify the patients with fractures and those who are also at high risk of future fractures due to osteoporosis. Appropriate care interventions to those patients, not only the most at-risk patients but also those with emerging risk, would significantly reduce future fractures.