The MeSH-gram Neural Network Model: Extending Word Embedding Vectors with MeSH Concepts for UMLS Semantic Similarity and Relatedness in the Biomedical Domain

Eliciting semantic similarity between concepts in the biomedical domain remains a challenging task. Recent approaches founded on embedding vectors have gained in popularity as they risen to efficiently capture semantic relationships The underlying idea is that two words that have close meaning gather similar contexts. In this study, we propose a new neural network model named MeSH-gram which relies on a straighforward approach that extends the skip-gram neural network model by considering MeSH (Medical Subject Headings) descriptors instead words. Trained on publicly available corpus PubMed MEDLINE, MeSH-gram is evaluated on reference standards manually annotated for semantic similarity. MeSH-gram is first compared to skip-gram with vectors of size 300 and at several windows contexts. A deeper comparison is performed with tewenty existing models. All the obtained results of Spearman's rank correlations between human scores and computed similarities show that MeSH-gram outperforms the skip-gram model, and is comparable to the best methods but that need more computation and external resources.Comment: 6 pages, 2 table

Computerization of workflows, guidelines and care pathways: a review of implementation challenges for process-oriented health information systems

There is a need to integrate the various theoretical frameworks and formalisms for modeling clinical guidelines, workflows, and pathways, in order to move beyond providing support for individual clinical decisions and toward the provision of process-oriented, patient-centered, health information systems (HIS). In this review, we analyze the challenges in developing process-oriented HIS that formally model guidelines, workflows, and care pathways. A qualitative meta-synthesis was performed on studies published in English between 1995 and 2010 that addressed the modeling process and reported the exposition of a new methodology, model, system implementation, or system architecture. Thematic analysis, principal component analysis (PCA) and data visualisation techniques were used to identify and cluster the underlying implementation ‘challenge’ themes. One hundred and eight relevant studies were selected for review. Twenty-five underlying ‘challenge’ themes were identified. These were clustered into 10 distinct groups, from which a conceptual model of the implementation process was developed. We found that the development of systems supporting individual clinical decisions is evolving toward the implementation of adaptable care pathways on the semantic web, incorporating formal, clinical, and organizational ontologies, and the use of workflow management systems. These architectures now need to be implemented and evaluated on a wider scale within clinical settings

Semantic Inference on Clinical Documents: Combining Machine Learning Algorithms With an Inference Engine for Effective Clinical Diagnosis and Treatment

Clinical practice calls for reliable diagnosis and optimized treatment. However, human errors in health care remain a severe issue even in industrialized countries. The application of clinical decision support systems (CDSS) casts light on this problem. However, given the great improvement in CDSS over the past several years, challenges to their wide-scale application are still present, including: 1) decision making of CDSS is complicated by the complexity of the data regarding human physiology and pathology, which could render the whole process more time-consuming by loading big data related to patients; and 2) information incompatibility among different health information systems (HIS) makes CDSS an information island, i.e., additional input work on patient information might be required, which would further increase the burden on clinicians. One popular strategy is the integration of CDSS in HIS to directly read electronic health records (EHRs) for analysis. However, gathering data from EHRs could constitute another problem, because EHR document standards are not unified. In addition, HIS could use different default clinical terminologies to define input data, which could cause additional misinterpretation. Several proposals have been published thus far to allow CDSS access to EHRs via the redefinition of data terminologies according to the standards used by the recipients of the data flow, but they mostly aim at specific versions of CDSS guidelines. This paper views these problems in a different way. Compared with conventional approaches, we suggest more fundamental changes; specifically, uniform and updatable clinical terminology and document syntax should be used by EHRs, HIS, and their integrated CDSS. Facilitated data exchange will increase the overall data loading efficacy, enabling CDSS to read more information for analysis at a given time. Furthermore, a proposed CDSS should be based on self-learning, which dynamically updates a knowledge model according to the data-stream-based upcoming data set. The experiment results show that our system increases the accuracy of the diagnosis and treatment strategy designs

Doctor of Philosophy

dissertationDomain adaptation of natural language processing systems is challenging because it requires human expertise. While manual e ort is e ective in creating a high quality knowledge base, it is expensive and time consuming. Clinical text adds another layer of complexity to the task due to privacy and con dentiality restrictions that hinder the ability to share training corpora among di erent research groups. Semantic ambiguity is a major barrier for e ective and accurate concept recognition by natural language processing systems. In my research I propose an automated domain adaptation method that utilizes sublanguage semantic schema for all-word word sense disambiguation of clinical narrative. According to the sublanguage theory developed by Zellig Harris, domain-speci c language is characterized by a relatively small set of semantic classes that combine into a small number of sentence types. Previous research relied on manual analysis to create language models that could be used for more e ective natural language processing. Building on previous semantic type disambiguation research, I propose a method of resolving semantic ambiguity utilizing automatically acquired semantic type disambiguation rules applied on clinical text ambiguously mapped to a standard set of concepts. This research aims to provide an automatic method to acquire Sublanguage Semantic Schema (S3) and apply this model to disambiguate terms that map to more than one concept with di erent semantic types. The research is conducted using unmodi ed MetaMap version 2009, a concept recognition system provided by the National Library of Medicine, applied on a large set of clinical text. The project includes creating and comparing models, which are based on unambiguous concept mappings found in seventeen clinical note types. The e ectiveness of the nal application was validated through a manual review of a subset of processed clinical notes using recall, precision and F-score metrics