Topic modeling is one of the most powerful techniques in text mining for data mining, latent data discovery, and finding relationships among data and text documents. Researchers have published many articles in the field of topic modeling and applied in various fields such as software engineering, political science, medical and linguistic science, etc. There are various methods for topic modelling; Latent Dirichlet Allocation (LDA) is one of the most popular in this field. Researchers have proposed various models based on the LDA in topic modeling. According to previous work, this paper will be very useful and valuable for introducing LDA approaches in topic modeling. In this paper, we investigated highly scholarly articles (between 2003 to 2016) related to topic modeling based on LDA to discover the research development, current trends and intellectual structure of topic modeling. In addition, we summarize challenges and introduce famous tools and datasets in topic modeling based on LDA.

Objective Cohort definition is a bottleneck for conducting clinical research and depends on subjective decisions by domain experts. Data-driven cohort definition is appealing but requires substantial knowledge of terminologies and clinical data models. Criteria2Query is a natural language interface that facilitates human-computer collaboration for cohort definition and execution using clinical databases. Materials and Methods Criteria2Query uses a hybrid information extraction pipeline combining machine learning and rule-based methods to systematically parse eligibility criteria text, transforms it first into a structured criteria representation and next into sharable and executable clinical data queries represented as SQL queries conforming to the OMOP Common Data Model. Users can interactively review, refine, and execute queries in the ATLAS web application. To test effectiveness, we evaluated 125 criteria across different disease domains from ClinicalTrials.gov and 52 user-entered criteria. We evaluated F1 score and accuracy against 2 domain experts and calculated the average computation time for fully automated query formulation. We conducted an anonymous survey evaluating usability. Results Criteria2Query achieved 0.795 and 0.805 F1 score for entity recognition and relation extraction, respectively. Accuracies for negation detection, logic detection, entity normalization, and attribute normalization were 0.984, 0.864, 0.514 and 0.793, respectively. Fully automatic query formulation took 1.22 seconds/criterion. More than 80% (11+ of 13) of users would use Criteria2Query in their future cohort definition tasks. Conclusions We contribute a novel natural language interface to clinical databases. It is open source and supports fully automated and interactive modes for autonomous data-driven cohort definition by researchers with minimal human effort. We demonstrate its promising user friendliness and usability.

Integration of detailed phenotype information with genetic data is well established to facilitate accurate diagnosis of hereditary disorders. As a rich source of phenotype information, electronic health records (EHRs) promise to empower diagnostic variant interpretation. However, how to accurately and efficiently extract phenotypes from heterogeneous EHR narratives remains a challenge. Here, we present EHR-Phenolyzer, a high-throughput EHR framework for extracting and analyzing phenotypes. EHR-Phenolyzer extracts and normalizes Human Phenotype Ontology (HPO) concepts from EHR narratives and then prioritizes genes with causal variants on the basis of the HPO-coded phenotype manifestations. We assessed EHR-Phenolyzer on 28 pediatric individuals with confirmed diagnoses of monogenic diseases and found that the genes with causal variants were ranked among the top 100 genes selected by EHR-Phenolyzer for 16/28 individuals (p < 2.2 × 10), supporting the value of phenotype-driven gene prioritization in diagnostic sequence interpretation. To assess the generalizability, we replicated this finding on an independent EHR dataset of ten individuals with a positive diagnosis from a different institution. We then assessed the broader utility by examining two additional EHR datasets, including 31 individuals who were suspected of having a Mendelian disease and underwent different types of genetic testing and 20 individuals with positive diagnoses of specific Mendelian etiologies of chronic kidney disease from exome sequencing. Finally, through several retrospective case studies, we demonstrated how combined analyses of genotype data and deep phenotype data from EHRs can expedite genetic diagnoses. In summary, EHR-Phenolyzer leverages EHR narratives to automate phenotype-driven analysis of clinical exomes or genomes, facilitating the broader implementation of genomic medicine.

Rationale:Philadelphia chromosome positive acute myeloid leukemia (Ph+ AML) is a rare subtype of AML that is now included as a provisional entity in the 2016 revised WHO classification of myeloid malignancies. However, a clear distinction between de novo Ph+ AML and chronic myeloid leukemia blast crisis is challenging. It is still a matter of debate whether Ph+ AML patients should be treated with chemotherapy or tyrosine kinase inhibitors as first-line therapy.Patient concerns:We reported here a case of a 46-year-old man who was diagnosed as Ph+ AML. This diagnosis was confirmed by bone marrow pathology and karyotype analysis of 46, XY, t (9; 22). Further examination, molecular genetic analysis showed BCR/ABL1 (p190) without ABL1 kinase domain mutations, and direct evidence demonstrated in AML by flow cytometry.Diagnosis:The diagnosis of Ph+ AML was made on May 2016 according to morphology, immunology, cytogenetic, and molecular criteria, and multiple organ failure was also diagnosed.Interventions:The patient was treated with dasatinib as the only medication after experiencing multiple organ failure. Then, he received 2 cycles of chemotherapy with IA (idarubicin 8 mg/m2, day 1–3; cytarabine 100 mg/m2, day 1–7) in August, 2016.Outcomes:The patient finally achieved a complete molecular remission.Lessons:This case study suggests that dasatinib can be a safe and effective treatment for Ph+ AML patients with poor physical condition.