Unified Medical Language System Metathesaurus Research Articles

A Large Language Model to Detect Negated Expressions in Radiology Reports.

Natural language processing (NLP) is crucial to extract information accurately from unstructured text to provide insights for clinical decision-making, quality improvement, and medical research. This study compared the performance of a rule-based NLP system and a medical-domain transformer-based model to detect negated concepts in radiology reports. Using a corpus of 984 de-identified radiology reports from a large U.S.-based academic health system (1000 consecutive reports, excluding 16 duplicates), the investigators compared the rule-based medspaCy system and the Clinical Assertion and Negation Classification Bidirectional Encoder Representations from Transformers (CAN-BERT) system to detect negated expressions of terms from RadLex, the Unified Medical Language System Metathesaurus, and the Radiology Gamuts Ontology. Power analysis determined a sample size of 382 terms to achieve α = 0.05 and β = 0.8 for McNemar's test; based on an estimate of 15% negated terms, 2800 randomly selected terms were annotated manually as negated or not negated. Precision, recall, and F1 of the two models were compared using McNemar's test. Of the 2800 terms, 387 (13.8%) were negated. For negation detection, medspaCy attained a recall of 0.795, precision of 0.356, and F1 of 0.492. CAN-BERT achieved a recall of 0.785, precision of 0.768, and F1 of 0.777. Although recall was not significantly different, CAN-BERT had significantly better precision (χ2 = 304.64; p < 0.001). The transformer-based CAN-BERT model detected negated terms in radiology reports with high precision and recall; its precision significantly exceeded that of the rule-based medspaCy system. Use of this system will improve data extraction from textual reports to support information retrieval, AI model training, and discovery of causal relationships.

Toward Reliable Symptom Coding in Electronic Health Records for Symptom Assessment and Research: Identification and Categorization of International Classification of Diseases, Ninth Revision, Clinical Modification Symptom Codes.

To date, symptom documentation has mostly relied on clinical notes in electronic health records or patient-reported outcomes using disease-specific symptom inventories. To provide a common and precise language for symptom recording, assessment, and research, a comprehensive list of symptom codes is needed. The International Classification of Diseases, Ninth Revision or its clinical modification ( International Classification of Diseases, Ninth Revision, Clinical Modification ) has a range of codes designated for symptoms, but it does not contain codes for all possible symptoms, and not all codes in that range are symptom related. This study aimed to identify and categorize the first list of International Classification of Diseases, Ninth Revision, Clinical Modification symptom codes for a general population and demonstrate their use to characterize symptoms of patients with type 2 diabetes mellitus in the Cerner database. A list of potential symptom codes was automatically extracted from the Unified Medical Language System Metathesaurus. Two clinical experts in symptom science and diabetes manually reviewed this list to identify and categorize codes as symptoms. A total of 1888 International Classification of Diseases, Ninth Revision, Clinical Modification symptom codes were identified and categorized into 65 categories. The symptom characterization using the newly obtained symptom codes and categories was found to be more reasonable than that using the previous symptom codes and categories on the same Cerner diabetes cohort.

Retrieval-Based Diagnostic Decision Support: Mixed Methods Study.

Diagnostic errors pose significant health risks and contribute to patient mortality. With the growing accessibility of electronic health records, machine learning models offer a promising avenue for enhancing diagnosis quality. Current research has primarily focused on a limited set of diseases with ample training data, neglecting diagnostic scenarios with limited data availability. This study aims to develop an information retrieval (IR)-based framework that accommodates data sparsity to facilitate broader diagnostic decision support. We introduced an IR-based diagnostic decision support framework called CliniqIR. It uses clinical text records, the Unified Medical Language System Metathesaurus, and 33 million PubMed abstracts to classify a broad spectrum of diagnoses independent of training data availability. CliniqIR is designed to be compatible with any IR framework. Therefore, we implemented it using both dense and sparse retrieval approaches. We compared CliniqIR's performance to that of pretrained clinical transformer models such as Clinical Bidirectional Encoder Representations from Transformers (ClinicalBERT) in supervised and zero-shot settings. Subsequently, we combined the strength of supervised fine-tuned ClinicalBERT and CliniqIR to build an ensemble framework that delivers state-of-the-art diagnostic predictions. On a complex diagnosis data set (DC3) without any training data, CliniqIR models returned the correct diagnosis within their top 3 predictions. On the Medical Information Mart for Intensive Care III data set, CliniqIR models surpassed ClinicalBERT in predicting diagnoses with <5 training samples by an average difference in mean reciprocal rank of 0.10. In a zero-shot setting where models received no disease-specific training, CliniqIR still outperformed the pretrained transformer models with a greater mean reciprocal rank of at least 0.10. Furthermore, in most conditions, our ensemble framework surpassed the performance of its individual components, demonstrating its enhanced ability to make precise diagnostic predictions. Our experiments highlight the importance of IR in leveraging unstructured knowledge resources to identify infrequently encountered diagnoses. In addition, our ensemble framework benefits from combining the complementary strengths of the supervised and retrieval-based models to diagnose a broad spectrum of diseases.

Enhancing Medical Image Retrieval with UMLS-Integrated CNN-Based Text Indexing.

In recent years, Convolutional Neural Network (CNN) models have demonstrated notable advancements in various domains such as image classification and Natural Language Processing (NLP). Despite their success in image classification tasks, their potential impact on medical image retrieval, particularly in text-based medical image retrieval (TBMIR) tasks, has not yet been fully realized. This could be attributed to the complexity of the ranking process, as there is ambiguity in treating TBMIR as an image retrieval task rather than a traditional information retrieval or NLP task. To address this gap, our paper proposes a novel approach to re-ranking medical images using a Deep Matching Model (DMM) and Medical-Dependent Features (MDF). These features incorporate categorical attributes such as medical terminologies and imaging modalities. Specifically, our DMM aims to generate effective representations for query and image metadata using a personalized CNN, facilitating matching between these representations. By using MDF, a semantic similarity matrix based on Unified Medical Language System (UMLS) meta-thesaurus, and a set of personalized filters taking into account some ranking features, our deep matching model can effectively consider the TBMIR task as an image retrieval task, as previously mentioned. To evaluate our approach, we performed experiments on the medical ImageCLEF datasets from 2009 to 2012. The experimental results show that the proposed model significantly enhances image retrieval performance compared to the baseline and state-of-the-art approaches.

АВТОМАТИЗИРОВАННАЯ СИСТЕМА ИЗВЛЕЧЕНИЯ КЛИНИЧЕСКИ РЕЛЕВАНТНЫХ ТЕРМИНОВ UMLS ИЗ ТЕКСТОВ АНГЛОЯЗЫЧНЫХ СТАТЕЙ НА ПРИМЕРЕ АКСИАЛЬНОГО СПОНДИЛОАРТРИТА

Significance. Early detection of axial spondyloarthritis (axSpA) is a complex clinical task. Quality improvement of axSpA diagnostics in primary care settings is possible with the help of decision-making information systems based on the ontological approach application. The key stage of the decision-making system development consists of the elaboration of a set of clinical terms. This set should fully describe clinical area or sub-area under study. One of the essential requirements is compliance of the clinical terms used with the existing clinical nomenclatures. Currently, the largest set of clinical terms is the Unified Medical Language System (UMLS) metathesaurus. The majority of UMLS terms is presented in English only. The development of tools for the analysis of unstructured texts and recognition of clinically relevant UMLS entities make it possible to elaborate a set of terms describing axSpA diagnostic aspects. This will also help to compile a list of UMLS terminology nomenclatures for their priority adaptation and expert translation into Russian. The purpose of this study is to develop an automated system for recognizing clinically relevant UMLS terms in texts of the English-language articles. Material and methods. The research material has included English terms (11.2 million) aggregated from 76 nome6nclatures of the current UMLS (2022AB) version. In addition, the study has used texts of PubMed clinical abstracts in English. Queries to the UMLS graph model, semantic algorithms for unstructured texts and machine-learning methods have been applied for data collection and analysis. Results. The study has elaborated a set of high-accuracy regular expressions (F1-score=98%) for metadata elimination from the text corpus. Then the authors have identified patterns for searching clinically relevant terms in the aggregated set of UMLS concepts. Using a logistic regression algorithm, the authors have trained a binary classification model. Input data for the created classificatory are information about an UMLS term. Output data are a label indicating the presence or absence of clinical relevance. Conclusion. The binary classification model has been validated individually and double-tested on different data samples. Values of the accuracy, sensitivity and specificity of metrics equal to 91%, 90% and 91%, respectively, for the validation sample (a number of axSpA terms). In addition, this model has been tested on the sets of terms aggregated for any two diseases. Values of the accuracy metric equal to 91% and 90%, respectively. With the help of the developed machine-learning model, the study has estimated that UMLS contains 1.5 million unique terms applicable to describing a clinical picture. In addition, lists of priority UMLS data sources and thematic groups have been compiled. These clinically relevant UMLS terms should be adapted and translated into Russian as soon as possible.

Performance assessment of ontology matching systems for FAIR data

BackgroundOntology matching should contribute to the interoperability aspect of FAIR data (Findable, Accessible, Interoperable, and Reusable). Multiple data sources can use different ontologies for annotating their data and, thus, creating the need for dynamic ontology matching services. In this experimental study, we assessed the performance of ontology matching systems in the context of a real-life application from the rare disease domain. Additionally, we present a method for analyzing top-level classes to improve precision.ResultsWe included three ontologies (NCIt, SNOMED CT, ORDO) and three matching systems (AgreementMakerLight 2.0, FCA-Map, LogMap 2.0). We evaluated the performance of the matching systems against reference alignments from BioPortal and the Unified Medical Language System Metathesaurus (UMLS). Then, we analyzed the top-level ancestors of matched classes, to detect incorrect mappings without consulting a reference alignment. To detect such incorrect mappings, we manually matched semantically equivalent top-level classes of ontology pairs. AgreementMakerLight 2.0, FCA-Map, and LogMap 2.0 had F1-scores of 0.55, 0.46, 0.55 for BioPortal and 0.66, 0.53, 0.58 for the UMLS respectively. Using vote-based consensus alignments increased performance across the board. Evaluation with manually created top-level hierarchy mappings revealed that on average 90% of the mappings’ classes belonged to top-level classes that matched.ConclusionsOur findings show that the included ontology matching systems automatically produced mappings that were modestly accurate according to our evaluation. The hierarchical analysis of mappings seems promising when no reference alignments are available. All in all, the systems show potential to be implemented as part of an ontology matching service for querying FAIR data. Future research should focus on developing methods for the evaluation of mappings used in such mapping services, leading to their implementation in a FAIR data ecosystem.

Context-Enriched Learning Models for Aligning Biomedical Vocabularies at Scale in the UMLS Metathesaurus.

The Unified Medical Language System (UMLS) Metathesaurus construction process mainly relies on lexical algorithms and manual expert curation for integrating over 200 biomedical vocabularies. A lexical-based learning model (LexLM) was developed to predict synonymy among Metathesaurus terms and largely outperforms a rule-based approach (RBA) that approximates the current construction process. However, the LexLM has the potential for being improved further because it only uses lexical information from the source vocabularies, while the RBA also takes advantage of contextual information. We investigate the role of multiple types of contextual information available to the UMLS editors, namely source synonymy (SS), source semantic group (SG), and source hierarchical relations (HR), for the UMLS vocabulary alignment (UVA) problem. In this paper, we develop multiple variants of context-enriched learning models (ConLMs) by adding to the LexLM the types of contextual information listed above. We represent these context types in context-enriched knowledge graphs (ConKGs) with four variants ConSS, ConSG, ConHR, and ConAll. We train these ConKG embeddings using seven KG embedding techniques. We create the ConLMs by concatenating the ConKG embedding vectors with the word embedding vectors from the LexLM. We evaluate the performance of the ConLMs using the UVA generalization test datasets with hundreds of millions of pairs. Our extensive experiments show a significant performance improvement from the ConLMs over the LexLM, namely +5.0% in precision (93.75%), +0.69% in recall (93.23%), +2.88% in F1 (93.49%) for the best ConLM. Our experiments also show that the ConAll variant including the three context types takes more time, but does not always perform better than other variants with a single context type. Finally, our experiments show that the pairs of terms with high lexical similarity benefit most from adding contextual information, namely +6.56% in precision (94.97%), +2.13% in recall (93.23%), +4.35% in F1 (94.09%) for the best ConLM. The pairs with lower degrees of lexical similarity also show performance improvement with +0.85% in F1 (96%) for low similarity and +1.31% in F1 (96.34%) for no similarity. These results demonstrate the importance of using contextual information in the UVA problem.

High Throughput Neurological Phenotyping with MetaMap

The phenotyping of neurological patients involves the conversion of signs and symptoms into machine readable codes selected from an appropriate ontology. The phenotyping of neurological patients is manual and laborious. MetaMap is used for high throughput mapping of the medical literature to concepts in the Unified Medical Language System Metathesaurus (UMLS). MetaMap was evaluated as a tool for the high throughput phenotyping of neurological patients. Based on 15 patient histories from electronic health records, 30 patient histories from neurology textbooks, and 20 clinical summaries from the Online Mendelian Inheritance in Man repository, MetaMap showed a recall of 61-89%, a precision of 84-93%, and an accuracy of 56-84% for the identification of phenotype concepts. The most common cause of false negatives (failure to recognize a phenotype concept) was an inability of MetaMap to find concepts that were represented as a description or a definition of the concept. The most common cause of false positives (incorrect identification of a concept in the text) was a failure to recognize that a concept was negated. MetaMap shows potential for high throughput phenotyping of neurological patients if the problems of false negatives and false positives can be solved.

Evaluating Biomedical Word Embeddings for Vocabulary Alignment at Scale in the UMLS Metathesaurus Using Siamese Networks.

Recent work uses a Siamese Network, initialized with BioWordVec embeddings (distributed word embeddings), for predicting synonymy among biomedical terms to automate a part of the UMLS (Unified Medical Language System) Metathesaurus construction process. We evaluate the use of contextualized word embeddings extracted from nine different biomedical BERT-based models for synonymy prediction in the UMLS by replacing BioWordVec embeddings with embeddings extracted from each biomedical BERT model using different feature extraction methods. Surprisingly, we find that Siamese Networks initialized with BioWordVec embeddings still outperform the Siamese Networks initialized with embedding extracted from biomedical BERT model.

Customizable Natural Language Processing Biomarker Extraction Tool.

Natural language processing (NLP) in pathology reports to extract biomarker information is an ongoing area of research. MetaMap is a natural language processing tool developed and funded by the National Library of Medicine to map biomedical text to the Unified Medical Language System Metathesaurus by applying specific tags to clinically relevant terms. Although results are useful without additional postprocessing, these tags lack important contextual information. Our novel method takes terminology-driven semantic tags and incorporates those into a semantic frame that is task-specific to add necessary context to MetaMap. We use important contextual information to capture biomarker results to support Community Health System's use of Precision Medicine treatments for patients with cancer. For each biomarker, the name, type, numeric quantifiers, non-numeric qualifiers, and the time frame are extracted. These fields then associate biomarkers with their context in the pathology report such as test type, probe intensity, copy-number changes, and even failed results. A selection of 6,713 relevant reports contained the following standard-of-care biomarkers for metastatic breast cancer: breast cancer gene 1 and 2, estrogen receptor, progesterone receptor, human epidermal growth factor receptor 2, and programmed death-ligand 1. The method was tested on pathology reports from the internal pathology laboratory at Henry Ford Health System. A certified tumor registrar reviewed 400 tests, which showed > 95% accuracy for all extracted biomarker types. Using this new method, it is possible to extract high-quality, contextual biomarker information, and this represents a significant advance in biomarker extraction.

Using the Unified Medical Language System to Expand the Operative Stress Score – First Use Case

The Unified Medical Language System (UMLS) maps relationships between and within >100 biomedical vocabularies, including Current Procedural Terminology (CPT) codes, creating a powerful knowledge resource which can accelerate clinical research. We used synonymy and concepts relating hierarchical structure of CPT codes within the UMLS, (1) guiding surgical experts in expanding the Operative Stress Score (OSS) from 565 originally rated CPT codes to additional, 1,853 related procedures; (2) establishing validity of the association between the added OSS ratings and 30-day outcomes in VASQIP (2015-2018). The UMLS Metathesaurus and Semantic Network was converted into an interactive graph database (https://github.com/dbmi-pitt/UMLS-Graph) delineating ontology relatedness. From this UMLS-graph, the CPT hierarchy was queried obtaining all paths from each code to the hierarchical apex. Of 1,853 added ratings, 43% and 76% were siblings and cousins of original OSS CPT codes. Of 857,577 VASQIP cases (mean age, 64±11years; 91% male; 75% white), 786,122 (92%) and 71,455 (8%) were rated in the original and added OSS. Compared to original, added OSS cases included more females (14% versus 9%) and frail patients (25% versus 19%) undergoing high stress procedures (11% versus 8%; all P <.001). Postoperative mortality consistently increased with OSS. Very low stress procedures had <0.5% (original, 0.4% [95%CI, 0.4%-0.5%] versus added, 0.9% [95%CI, 0.6%-1.2%]) and very high 3.8% (original, 3.5% [95%CI, 3.0%-4.0%] versus added, 5.8% [95%CI, 4.6-7.3%]) mortality rates. The synonymy and concepts relating biomedical data within the UMLS can be abstracted and efficiently used to expand the utility of existing clinical research tools.

PhenClust, a standalone tool for identifying trends within sets of biological phenotypes using semantic similarity and the Unified Medical Language System metathesaurus.

ObjectivesWe sought to cluster biological phenotypes using semantic similarity and create an easy-to-install, stable, and reproducible tool.Materials and MethodsWe generated Phenotype Clustering (PhenClust)—a novel application of semantic similarity for interpreting biological phenotype associations—using the Unified Medical Language System (UMLS) metathesaurus, demonstrated the tool’s application, and developed Docker containers with stable installations of two UMLS versions.ResultsPhenClust identified disease clusters for drug network-associated phenotypes and a meta-analysis of drug target candidates. The Dockerized containers eliminated the requirement that the user install the UMLS metathesaurus.DiscussionClustering phenotypes summarized all phenotypes associated with a drug network and two drug candidates. Docker containers can support dissemination and reproducibility of tools that are otherwise limited due to insufficient software support.ConclusionPhenClust can improve interpretation of high-throughput biological analyses where many phenotypes are associated with a query and the Dockerized PhenClust achieved our objective of decreasing installation complexity.

Improving early diagnosis of rare diseases using Natural Language Processing in unstructured medical records: an illustration from Dravet syndrome

BackgroundThe growing use of Electronic Health Records (EHRs) is promoting the application of data mining in health-care. A promising use of big data in this field is to develop models to support early diagnosis and to establish natural history. Dravet Syndrome (DS) is a rare developmental and epileptic encephalopathy that commonly initiates in the first year of life with febrile seizures (FS). Age at diagnosis is often delayed after 2 years, as it is difficult to differentiate DS at onset from FS. We aimed to explore if some clinical terms (concepts) are significantly more used in the electronic narrative medical reports of individuals with DS before the age of 2 years compared to those of individuals with FS. These concepts would allow an earlier detection of patients with DS resulting in an earlier orientation toward expert centers that can provide early diagnosis and care.MethodsData were collected from the Necker Enfants Malades Hospital using a document-based data warehouse, Dr Warehouse, which employs Natural Language Processing, a computer technology consisting in processing written information. Using Unified Medical Language System Meta-thesaurus, phenotype concepts can be recognized in medical reports. We selected individuals with DS (DS Cohort) and individuals with FS (FS Cohort) with confirmed diagnosis after the age of 4 years. A phenome-wide analysis was performed evaluating the statistical associations between the phenotypes of DS and FS, based on concepts found in the reports produced before 2 years and using a series of logistic regressions.ResultsWe found significative higher representation of concepts related to seizures’ phenotypes distinguishing DS from FS in the first phases, namely the major recurrence of complex febrile convulsions (long-lasting and/or with focal signs) and other seizure-types. Some typical early onset non-seizure concepts also emerged, in relation to neurodevelopment and gait disorders.ConclusionsNarrative medical reports of individuals younger than 2 years with FS contain specific concepts linked to DS diagnosis, which can be automatically detected by software exploiting NLP. This approach could represent an innovative and sustainable methodology to decrease time of diagnosis of DS and could be transposed to other rare diseases.

Clinical Term Normalization Using Learned Edit Patterns and Subconcept Matching: System Development and Evaluation.

BackgroundClinical terms mentioned in clinical text are often not in their standardized forms as listed in clinical terminologies because of linguistic and stylistic variations. However, many automated downstream applications require clinical terms mapped to their corresponding concepts in clinical terminologies, thus necessitating the task of clinical term normalization.ObjectiveIn this paper, a system for clinical term normalization is presented that utilizes edit patterns to convert clinical terms into their normalized forms.MethodsThe edit patterns are automatically learned from the Unified Medical Language System (UMLS) Metathesaurus as well as from the given training data. The edit patterns are generalized sequences of edits that are derived from edit distance computations. The edit patterns are both character based as well as word based and are learned separately for different semantic types. In addition to these edit patterns, the system also normalizes clinical terms through the subconcepts mentioned within them.ResultsThe system was evaluated as part of the 2019 n2c2 Track 3 shared task of clinical term normalization. It obtained 80.79% accuracy on the standard test data. This paper includes ablation studies to evaluate the contributions of different components of the system. A challenging part of the task was disambiguation when a clinical term could be normalized to multiple concepts.ConclusionsThe learned edit patterns led the system to perform well on the normalization task. Given that the system is based on patterns, it is human interpretable and is also capable of giving insights about common variations of clinical terms mentioned in clinical text that are different from their standardized forms.

The impact of learning Unified Medical Language System knowledge embeddings in relation extraction from biomedical texts

We explored how knowledge embeddings (KEs) learned from the Unified Medical Language System (UMLS) Metathesaurus impact the quality of relation extraction on 2 diverse sets of biomedical texts. Two forms of KEs were learned for concepts and relation types from the UMLS Metathesaurus, namely lexicalized knowledge embeddings (LKEs) and unlexicalized KEs. A knowledge embedding encoder (KEE) enabled learning either LKEs or unlexicalized KEs as well as neural models capable of producing LKEs for mentions of biomedical concepts in texts and relation types that are not encoded in the UMLS Metathesaurus. This allowed us to design the relation extraction with knowledge embeddings (REKE) system, which incorporates either LKEs or unlexicalized KEs produced for relation types of interest and their arguments. The incorporation of either LKEs or unlexicalized KE in REKE advances the state of the art in relation extraction on 2 relation extraction datasets: the 2010 i2b2/VA dataset and the 2013 Drug-Drug Interaction Extraction Challenge corpus. Moreover, the impact of LKEs is superior, achieving F1 scores of 78.2 and 82.0, respectively. REKE not only highlights the importance of incorporating knowledge encoded in the UMLS Metathesaurus in a novel way, through 2 possible forms of KEs, but it also showcases the subtleties of incorporating KEs in relation extraction systems. Incorporating LKEs informed by the UMLS Metathesaurus in a relation extraction system operating on biomedical texts shows significant promise. We present the REKE system, which establishes new state-of-the-art results for relation extraction on 2 datasets when using LKEs.

Semantic Deep Learning: Prior Knowledge and a Type of Four-Term Embedding Analogy to Acquire Treatments for Well-Known Diseases.

BackgroundHow to treat a disease remains to be the most common type of clinical question. Obtaining evidence-based answers from biomedical literature is difficult. Analogical reasoning with embeddings from deep learning (embedding analogies) may extract such biomedical facts, although the state-of-the-art focuses on pair-based proportional (pairwise) analogies such as man:woman::king:queen (“queen = −man +king +woman”).ObjectiveThis study aimed to systematically extract disease treatment statements with a Semantic Deep Learning (SemDeep) approach underpinned by prior knowledge and another type of 4-term analogy (other than pairwise).MethodsAs preliminaries, we investigated Continuous Bag-of-Words (CBOW) embedding analogies in a common-English corpus with five lines of text and observed a type of 4-term analogy (not pairwise) applying the 3CosAdd formula and relating the semantic fields person and death: “dagger = −Romeo +die +died” (search query: −Romeo +die +died). Our SemDeep approach worked with pre-existing items of knowledge (what is known) to make inferences sanctioned by a 4-term analogy (search query −x +z1 +z2) from CBOW and Skip-gram embeddings created with a PubMed systematic reviews subset (PMSB dataset). Stage1: Knowledge acquisition. Obtaining a set of terms, candidate y, from embeddings using vector arithmetic. Some n-gram pairs from the cosine and validated with evidence (prior knowledge) are the input for the 3cosAdd, seeking a type of 4-term analogy relating the semantic fields disease and treatment. Stage 2: Knowledge organization. Identification of candidates sanctioned by the analogy belonging to the semantic field treatment and mapping these candidates to unified medical language system Metathesaurus concepts with MetaMap. A concept pair is a brief disease treatment statement (biomedical fact). Stage 3: Knowledge validation. An evidence-based evaluation followed by human validation of biomedical facts potentially useful for clinicians.ResultsWe obtained 5352 n-gram pairs from 446 search queries by applying the 3CosAdd. The microaveraging performance of MetaMap for candidate y belonging to the semantic field treatment was F-measure=80.00% (precision=77.00%, recall=83.25%). We developed an empirical heuristic with some predictive power for clinical winners, that is, search queries bringing candidate y with evidence of a therapeutic intent for target disease x. The search queries -asthma +inhaled_corticosteroids +inhaled_corticosteroid and -epilepsy +valproate +antiepileptic_drug were clinical winners, finding eight evidence-based beneficial treatments.ConclusionsExtracting treatments with therapeutic intent by analogical reasoning from embeddings (423K n-grams from the PMSB dataset) is an ambitious goal. Our SemDeep approach is knowledge-based, underpinned by embedding analogies that exploit prior knowledge. Biomedical facts from embedding analogies (4-term type, not pairwise) are potentially useful for clinicians. The heuristic offers a practical way to discover beneficial treatments for well-known diseases. Learning from deep learning models does not require a massive amount of data. Embedding analogies are not limited to pairwise analogies; hence, analogical reasoning with embeddings is underexploited.

Ontological and Non-Ontological Resources for Associating Medical Dictionary for Regulatory Activities Terms to SNOMED Clinical Terms With Semantic Properties.

Background: Formal definitions allow selecting terms (e.g., identifying all terms related to “Infectious disease” using the query “has causative agent organism”) and terminological reasoning (e.g., “hepatitis B” is a “hepatitis” and is an “infectious disease”). However, the standard international terminology Medical Dictionary for Regulatory Activities (MedDRA) used for coding adverse drug reactions in pharmacovigilance databases does not beneficiate from such formal definitions. Our objective was to evaluate the potential of reuse of ontological and non-ontological resources for generating such definitions for MedDRA. Methods: We developed several methods that collectively allow a semiautomatic semantic enrichment of MedDRA: 1) using MedDRA-to-SNOMED Clinical Terms (SNOMED CT) mappings (available in the Unified Medical Language System metathesaurus or other mapping resources, e.g., the MedDRA preferred term “hepatitis B” is associated to the SNOMED CT concept “type B viral hepatitis”) to extract term definitions (e.g., “hepatitis B” is associated with the following properties: has finding site liver structure, has associated morphology inflammation morphology, and has causative agent hepatitis B virus); 2) using MedDRA labels and lexical/syntactic methods for automatic decomposition of complex MedDRA terms (e.g., the MedDRA systems organ class “blood and lymphatic system disorders” is decomposed in blood system disorders and lymphatic system disorders) or automatic suggestions of properties (e.g., the string “cyclic” in preferred term “cyclic neutropenia” leads to the property has clinical course cyclic). Results: The Unified Medical Language System metathesaurus was the main ontological resource reusable for generating formal definitions for MedDRA terms. The non-ontological resources (another mapping resource provided by Nadkarni and Darer in 2010 and MedDRA labels) allowed defining few additional preferred terms. While the Ci4SeR tool helped the curator to define 1,935 terms by suggesting potential supplemental relations based on the parents’ and siblings’ semantic definition, defining manually all MedDRA terms remains expensive in time. Discussion: Several ontological and non-ontological resources are available for associating MedDRA terms to SNOMED CT concepts with semantic properties, but providing manual definitions is still necessary. The ontology of adverse events is a possible alternative but does not cover all MedDRA terms either. Perspectives are to implement more efficient techniques to find more logical relations between SNOMED CT and MedDRA in an automated way.

Construction of Disease Similarity Networks Using Concept Embedding and Ontology.

Discovering disease similarities are beneficial for the diagnosis and treatment of mental diseases. In this research, we proposed a data driven method, that is, integrating a variety of publicly available data resources including Unified Medical Language System (UMLS) Metathesaurus, Systematized Nomenclature of Medicine -- Clinical Terms (SNOMED CT) and cui2vec concept embedding to construct a mental disease similarity network. The resulting mental disease similarity network offered a new view for navigating and investigating disease relations; it also revealed popular mental disease in the literature in terms of the number of connections and similarities with other diseases. It shows that depressive disorder is directly connected with nine other popular diseases and connects 52 other diseases in the network. The top three popular mental diseases are depressive disorder, dysthymia (now known as persistent depressive disorder), and neurosis. Future research will focus on studying the clusters generated from the similarity network.

UMLS mapping and Word embeddings for ICD code assignment using the MIMIC-III intensive care database.

Diagnosis codes are used as a billing mechanism in the Electronic Health Record and have the capability to benefit decision support systems, which aim to assist coders by suggesting a relevant subset of potential codes to choose from. Due to the large set of possible labels and length of patient records, automatic ICD code assignment is considered to be a challenging task within the field of multi-label classification. This paper introduces a baseline for automatic ICD code assignment using Support Vector Machines (SVM) and FastText with Unified Medical Language System (UMLS) metathesaurus mappings into word embedding models. Training data is obtained from the Medical Information Mart for Intensive Care (MIMIC-III) database and extended with 'is-a' relationships from ICD-9 hierarchy. FastText is evaluated with different label count estimations, of which an approach based on label cardinality yields a F1-Score of 62.2%. FastText achieves high recall results and mentionable performance improvements over previous models. Reported values are obtained through 10-fold cross-validation.

Ontological representation-oriented term normalization and standardization of the Research Domain Criteria.

The Research Domain Criteria, launched by the National Institute of Mental Health, is a new dimensional and interdisciplinary research framework for mental disorders. The Research Domain Criteria matrix is its core part. Since an ontology has the strengths of supporting semantic inferencing and automatic data processing, we would like to transform the Research Domain Criteria matrix into an ontological structure. In terms of data normalization, which is the essential part of an ontology representation, the Research Domain Criteria elements (mainly in the Units of Analysis) have some limitations. In this article, we propose a series of solutions to improve data normalization of the Research Domain Criteria elements in the Units of Analysis, including leveraging standard terminologies (i.e. the Unified Medical Language System Metathesaurus), context-combining queries, and domain expertise. The evaluation results show the positive (Yes) percentage is more than 80 percent, indicating our work is favorably received by the mental health professionals, and we have formed a good data foundation for the Research Domain Criteria ontological representation in the future work.