Learning a single-hidden layer feedforward neural network using a rank correlation-based strategy with application to high dimensional gene expression and proteomic spectra datasets in cancer detection
Publication date: Available online 15 June 2018 Source:Journal of Biomedical Informatics Author(s): Smaranda Belciug, Florin Gorunescu Methods based on microarrays (MA), mass spectrometry (MS), and machine learning (ML) algorithms have evolved rapidly in recent years, allowing for early detection of several types of cancer. A pitfall of these approaches, however, is the overfitting of data due to large number of attributes and small number of instances -- a phenomenon known as the 'curse of dimensionality'. A potentially fruitful idea to avoid this drawback is to develop algorithms that combine fast computation with a fil...
Source: Journal of Biomedical Informatics - June 15, 2018 Category: Information Technology Source Type: research

A study of Generalizability of Recurrent Neural Network-Based Predictive Models for Heart Failure Onset Risk using a Large and Heterogeneous EHR Data set
In this study, we evaluated an RNN model, RETAIN, over Cerner Health Facts® EMR data, for heart failure onset risk prediction. Our data set included over 150,000 heart failure patients and over 1,000,000 controls from nearly 400 hospitals. Convincingly, RETAIN achieved an AUC of 82% in comparison to an AUC of 79% for logistic regression, demonstrating the power of more expressive deep learning models for EHR predictive modeling. The prediction performance fluctuated across different patient groups and varied from hospital to hospital. Also, we trained RETAIN models on individual hospitals and found that the model can b...
Source: Journal of Biomedical Informatics - June 15, 2018 Category: Information Technology Source Type: research

A data-driven framework of typical treatment process extraction and evaluation
Conclusion The extracted typical treatment processes are intuitive and can provide managerial guidance for CP redesign and optimization. In addition, our work can assist clinicians in clearly understanding their routine treatment processes and recommend optimal treatment pathways for patients. Graphical abstract (Source: Journal of Biomedical Informatics)
Source: Journal of Biomedical Informatics - June 15, 2018 Category: Information Technology Source Type: research

Graph-based biomedical text summarization: An itemset mining and sentence clustering approach
Conclusion The carried out research suggests that the incorporation of domain-specific knowledge and frequent itemset mining equips the summarization system in a better way to address the informativeness measurement of the sentences. Moreover, clustering the graph nodes (sentences) can enable the summarizer to target different main subthemes of a source document efficiently. The evaluation results show that the proposed approach can significantly improve the performance of the summarization systems in the biomedical domain. Graphical abstract (Source: Journal of Biomedical Informatics)
Source: Journal of Biomedical Informatics - June 15, 2018 Category: Information Technology Source Type: research

Letter to the Editor( Response from author): MeSH qualifiers, publication types and relation occurrence frequency are also useful for a better sentence-level extraction of biomedical relations
Publication date: Available online 14 June 2018 Source:Journal of Biomedical Informatics Author(s): Yijia Zhang (Source: Journal of Biomedical Informatics)
Source: Journal of Biomedical Informatics - June 14, 2018 Category: Information Technology Source Type: research

From Lexical Regularities to Axiomatic Patterns for the Quality Assurance of Biomedical Terminologies and Ontologies
Publication date: Available online 14 June 2018 Source:Journal of Biomedical Informatics Author(s): Philip van Damme, Manuel Quesada-Martínez, Ronald Cornet, Jesualdo Tomás Fernández-Breis Ontologies and terminologies have been identified as key resources for the achievement of semantic interoperability in biomedical domains. The development of ontologies is performed as a joint work by domain experts and knowledge engineers. The maintenance and auditing of these resources is also the responsibility of such experts, and this is usually a time-consuming, mostly manual task. Manual auditing is impractic...
Source: Journal of Biomedical Informatics - June 14, 2018 Category: Information Technology Source Type: research

Medical Concept Normalization in Social Media Posts with Recurrent Neural Networks
Publication date: Available online 12 June 2018 Source:Journal of Biomedical Informatics Author(s): Elena Tutubalina, Zulfat Miftahutdinov, Sergey Nikolenko, Valentin Malykh Text mining of scientific libraries and social media has already proven itself as a reliable tool for drug repurposing and hypothesis generation. The task of mapping a disease mention to a concept in a controlled vocabulary, typically to the standard thesaurus in the Unified Medical Language System (UMLS), is known as medical concept normalization. This task is challenging due to the differences in the use of medical terminology between health care pr...
Source: Journal of Biomedical Informatics - June 12, 2018 Category: Information Technology Source Type: research

Greater Patient Health Information Control to Improve the Sustainability of Health Information Exchanges
Publication date: Available online 9 June 2018 Source:Journal of Biomedical Informatics Author(s): Mohamed Abdelhamid Health information exchanges (HIEs) are multisided platforms that facilitate the sharing of patient health information (PHI) between providers and payers across organizations within a region, community or hospital system. The benefits of HIEs to payers and providers include lower cost, faster services, and better health outcome. However, most HIEs have configured the patient healthcare consent process to give all providers who sign up with the exchange access to PHI for all consenting patients, leaving no ...
Source: Journal of Biomedical Informatics - June 9, 2018 Category: Information Technology Source Type: research

Modeling Asynchronous Event Sequences with RNNs
Publication date: Available online 5 June 2018 Source:Journal of Biomedical Informatics Author(s): Stephen Wu, Sijia Liu, Sunghwan Sohn, Sungrim Moon, Chung-il Wi, Young Juhn, Hongfang Liu Sequences of events have often been modeled with computational techniques, but typical preprocessing steps and problem settings do not explicitly address the ramifications of timestamped events. Clinical data, such as is found in electronic health records (EHRs), typically comes with timestamp information. In this work, we define event sequences and their properties: synchronicity, evenness, and co-cardinality; we then show how asynchro...
Source: Journal of Biomedical Informatics - June 6, 2018 Category: Information Technology Source Type: research

Benchmarking Deep Learning Models on Large Healthcare Datasets
Publication date: Available online 5 June 2018 Source:Journal of Biomedical Informatics Author(s): Sanjay Purushotham, Chuizheng Meng, Zhengping Che, Yan Liu Deep learning models (aka Deep Neural Networks) have revolutionized many fields including computer vision, natural language processing, speech recognition, and is being increasingly used in clinical healthcare applications. However, few works exist which have benchmarked the performance of the deep learning models with respect to the state-of-the-art machine learning models and prognostic scoring systems on publicly available healthcare datasets. In this paper, we pr...
Source: Journal of Biomedical Informatics - June 5, 2018 Category: Information Technology Source Type: research

Patient similarity for precision medicine: a systematic review
Publication date: Available online 1 June 2018 Source:Journal of Biomedical Informatics Author(s): E. Parimbelli, S. Marini, L. Sacchi, R. Bellazzi Evidence-based medicine is the most prevalent paradigm adopted by physicians. Clinical practice guidelines typically define a set of recommendations together with eligibility criteria that restrict their applicability to a specific group of patients. The ever-growing size and availability of health-related data is currently challenging the broad definitions of guideline-defined patient groups. Precision medicine leverages on genetic, phenotypic, or psychosocial characteristics...
Source: Journal of Biomedical Informatics - June 1, 2018 Category: Information Technology Source Type: research

Evaluation of Natural Language Processing (NLP) Systems to Annotate Drug Product Labeling with MedDRA Terminology
Conclusions The results demonstrate that it may be feasible to use NLP tools to extract and map AE terms to MedDRA PTs. However, the NLP tools we tested would need to be modified or reconfigured to lower the error rates to support their use in a regulatory setting. Tools specific for extracting AE terms from drug labels and mapping the terms to MedDRA PTs may need to be developed to support pharmacovigilance. Conducting research using additional NLP systems on a larger, diverse GSL would also be informative. Graphical abstract (Source: Journal of Biomedical Informatics)
Source: Journal of Biomedical Informatics - June 1, 2018 Category: Information Technology Source Type: research

Comprehensive Methodology to Monitor Longitudinal Change Patterns during EHR Implementations: a Case Study at a Large Health Care Delivery Network
Conclusion Our results and methodology can guide the broader medical and informatics communities by informing what and how to continuously monitor EHR impact on quality, productivity, and safety. Graphical abstract (Source: Journal of Biomedical Informatics)
Source: Journal of Biomedical Informatics - May 29, 2018 Category: Information Technology Source Type: research

MeSH qualifiers and types of publications as well as the occurrence frequency of relations within publications can be useful for a better sentence-level extraction of biomedical relations from scientific literature
Publication date: Available online 29 May 2018 Source:Journal of Biomedical Informatics Author(s): Houcemeddine Turki, Mohamed Ali Hadj Taieb, Mohamed Ben Aouicha (Source: Journal of Biomedical Informatics)
Source: Journal of Biomedical Informatics - May 29, 2018 Category: Information Technology Source Type: research

Automated Depression Analysis Using Convolutional Neural Networks from Speech
Publication date: Available online 29 May 2018 Source:Journal of Biomedical Informatics Author(s): Lang He, Cui Cao To help clinicians to efficiently diagnose the severity of a person’s depression, the affective computing community and the artificial intelligence field have shown a growing interest in designing automated systems. The speech features have useful information for the diagnosis of depression. However, manually designing and domain knowledge are still important for the selection of the feature, which makes the process labor consuming and subjective. In recent years, deep-learned features based on neural ...
Source: Journal of Biomedical Informatics - May 29, 2018 Category: Information Technology Source Type: research

Complex overlapping concepts: An effective auditing methodology for families of similarly structured BioPortal ontologies
Publication date: Available online 28 May 2018 Source:Journal of Biomedical Informatics Author(s): Ling Zheng, Yan Chen, Gai Elhanan, Yehoshua Perl, James Geller, Christopher Ochs In previous research, we have demonstrated for a number of ontologies that structurally complex concepts (for different definitions of “complex”) in an ontology are more likely to exhibit errors than other concepts. Thus, such complex concepts often become fertile ground for quality assurance (QA) in ontologies. They should be audited first. One example of complex concepts is given by “overlapping concepts” (to be defined...
Source: Journal of Biomedical Informatics - May 28, 2018 Category: Information Technology Source Type: research

An overview on the emerging area of identification, characterization, and assessment of health apps
This article presents an overview of the recent literature in this field and categorizes - by discussing some specific examples - the various methodologies introduced so far for the identification, characterization, and assessment of health apps. Specifically, this article outlines the most significant web-based resources for app identification, relevant frameworks for descriptive characterization of apps’ features, and a number of methods for the assessment of quality along its various components (e.g., evidence base, trustworthiness, privacy, or user engagement). The development of methods to characterize the apps&...
Source: Journal of Biomedical Informatics - May 28, 2018 Category: Information Technology Source Type: research

Extracting similar terms from multiple EMR-based semantic embeddings to support chart reviews
Conclusions Clinical information can be more quickly retrieved and synthesized when using semantically similar term from multiple embeddings. Graphical abstract (Source: Journal of Biomedical Informatics)
Source: Journal of Biomedical Informatics - May 22, 2018 Category: Information Technology Source Type: research

Leveraging Semantic Labels for Multi-level Abstraction in Medical Process Mining and Trace Comparison
Publication date: Available online 21 May 2018 Source:Journal of Biomedical Informatics Author(s): Giorgio Leonardi, Manuel Striani, Silvana Quaglini, Anna Cavallini, Stefania Montani Many medical information systems record data about the executed process instances in the form of an event log. In this paper, we present a framework, able to convert actions in the event log into higher level concepts, at different levels of abstraction, on the basis of domain knowledge. Abstracted traces are then provided as an input to trace comparison and semantic process discovery. Our abstraction mechanism is able to manage non trivial ...
Source: Journal of Biomedical Informatics - May 21, 2018 Category: Information Technology Source Type: research

Intradialytic blood pressure pattern recognition based on density peak clustering
In this study, we proposed a new approach to identify IBP patterns to classify ESRD patients. We used the dynamic time warping (DTW) algorithm to measure the similarity between two series of IBP data. Five blood pressure (BP) patterns were identified by applying the density peak clustering algorithm (DPCA) to the IBP data. To illustrate the association between BP patterns and prognosis, we constructed three random survival forest (RSF) models with different covariates. Model accuracy was improved 3.7∼6.3% by the inclusion of BP patterns. The results suggest that BP patterns have critical clinical and prognostic signifi...
Source: Journal of Biomedical Informatics - May 21, 2018 Category: Information Technology Source Type: research

Assessing data quality and the variability of source data verification auditing methods in clinical research settings
Conclusions A wide range of SDV auditing methods are reported in the published literature though no uniform SDV auditing method could be determined for “best practice” in clinical trials. Published audit methodology articles are warranted for the development of a standardised SDV auditing method to monitor data quality in clinical research settings. Graphical abstract (Source: Journal of Biomedical Informatics)
Source: Journal of Biomedical Informatics - May 19, 2018 Category: Information Technology Source Type: research

Simulation of Patient Flow in Multiple Healthcare Units using Process and Data Mining Techniques for Model Identification
Conclusion The proposed approach, methods, and solutions provide a conceptual, methodological, and programming framework for the implementation of a simulation of complex and diverse scenarios within a flow of patients for different purposes: decision making, training, management optimization, and others. Graphical abstract (Source: Journal of Biomedical Informatics)
Source: Journal of Biomedical Informatics - May 17, 2018 Category: Information Technology Source Type: research

New JBI policy emphasizes substantive, practical methodological innovations for biomedical privacy and security papers
Publication date: Available online 17 May 2018 Source:Journal of Biomedical Informatics Author(s): William A. Yasnoff, Edward H. Shortliffe (Source: Journal of Biomedical Informatics)
Source: Journal of Biomedical Informatics - May 17, 2018 Category: Information Technology Source Type: research

Detecting pathway biomarkers of diabetic progression with differential entropy
Publication date: Available online 12 May 2018 Source:Journal of Biomedical Informatics Author(s): Zhi-Ping Liu, Rui Gao Gene expression profiling techniques measure the transcriptional dynamics of thousands of genes in parallel manners. The available high-throughput transcriptomic datasets provide unprecedented opportunities of detecting biomarkers or signatures of complex diseases such as diabetes. In this work, we propose a computational method based on differential entropy to identify diabetic pathway biomarkers in rats from gene expression profiling data. We first collect the knowledgebase-documented pathways and map...
Source: Journal of Biomedical Informatics - May 12, 2018 Category: Information Technology Source Type: research

Predicting microRNA-disease associations using label propagation based on linear neighborhood similarity
In this study, we present a label propagation model with linear neighborhood similarity, called LPLNS, to predict unobserved miRNA-disease associations. Additionally, a preprocessing step is performed to derive new interaction likelihood profiles that will contribute to the prediction since new miRNAs and diseases lack known associations. Our results demonstrate that the LPLNS model based on the known disease-miRNA associations could achieve impressive performance with an AUC of 0.9034. Furthermore, we observed that the LPLNS model based on new interaction likelihood profiles could improve the performance to an AUC of 0.91...
Source: Journal of Biomedical Informatics - May 12, 2018 Category: Information Technology Source Type: research

Exploiting Semantic Patterns over Biomedical Knowledge Graphs for Predicting Treatment and Causative Relations
Conclusions We employed semantic graph patterns connecting pairs of candidate entities in a knowledge graph as features to predict treatment/causative relations between them. We provide what we believe is the first evidence in direct prediction of biomedical relations based on graph features. Our work complements lexical pattern based approaches in that the graph patterns can be used as additional features for weakly supervised relation prediction. Graphical abstract (Source: Journal of Biomedical Informatics)
Source: Journal of Biomedical Informatics - May 12, 2018 Category: Information Technology Source Type: research

Usability Evaluation of a Medication Reconciliation Tool: Embedding Safety Probes to Assess Users ’ Detection of Medication Discrepancies
Conclusion This is one of the first studies to evaluate the usability of a collaborative medication reconciliation tool and assess HCPs’ and patients’ detection of medication discrepancies. Results demonstrate that embedded safety probes can enhance standard usability methods by measuring additional, clinically-focused usability outcomes. The novel safety probes we used may serve as an initial, standard set for future medication reconciliation research. More prevalent use of safety probes could strengthen usability research for a variety of health information technologies. Graphical abstract (Source: Journal of...
Source: Journal of Biomedical Informatics - May 9, 2018 Category: Information Technology Source Type: research

An effective neural model extracting document level chemical-induced disease relations from biomedical literature
Publication date: Available online 8 May 2018 Source:Journal of Biomedical Informatics Author(s): Wei Zheng, Hongfei Lin, Zhiheng Li, Xiaoxia Liu, Zhengguang Li, Bo Xu, Yijia Zhang, Zhihao Yang, Jian Wang Since identifying relations between chemicals and diseases (CDR) are important for biomedical research and healthcare, the challenge proposed by BioCreative V requires automatically mining causal relationships between chemicals and diseases which may span sentence boundaries. Although most systems explore feature engineering and knowledge bases to recognize document level CDR relations, feature learning automatically is ...
Source: Journal of Biomedical Informatics - May 8, 2018 Category: Information Technology Source Type: research

Classification of Forensic Autopsy Reports through Conceptual Graph-based Document Representation Model
This study employs text categorization techniques for the classification of open narrative forensic autopsy reports. One of the key steps in text classification is document representation. In document representation, a clinical report is transformed into a format that is suitable for classification. The traditional document representation technique for text categorization is the bag-of-words (BoW) technique. In this study, the traditional BoW technique is ineffective in classifying forensic autopsy reports because it merely extracts frequent but discriminative features from clinical reports. Moreover, this technique fails ...
Source: Journal of Biomedical Informatics - May 5, 2018 Category: Information Technology Source Type: research

PerKApp: a General Purpose Persuasion Architecture For Healthy Lifestyles
Publication date: Available online 2 May 2018 Source:Journal of Biomedical Informatics Author(s): Rosa Maimone, Marco Guerini, Mauro Dragoni, Tania Bailoni, Claudio Eccher Automatically monitoring and supporting healthy lifestyle is a recent research trend, fostered by the availability of low-cost monitoring devices, and it can significantly contribute to the prevention of chronic diseases deriving from incorrect diet and lack of physical activity. In this paper, we present a general purpose architecture for persuasion scenarios and behavioral change. The architecture is designed to be easily portable across languages and...
Source: Journal of Biomedical Informatics - May 3, 2018 Category: Information Technology Source Type: research

Automatic address validation and health record review to identify homeless Social Security Disability applicants
Conclusion We were able to identify many more homeless patients through a combination of automatic address validation and natural language processing of unstructured electronic health records. Graphical abstract (Source: Journal of Biomedical Informatics)
Source: Journal of Biomedical Informatics - April 27, 2018 Category: Information Technology Source Type: research

Label-indicator morpheme growth on LSTM for Chinese healthcare question department classification
Conclusions The proposed method is effective for the departments classification of patients questions and serves as a useful system for the automatic understanding of patient questions. Graphical abstract (Source: Journal of Biomedical Informatics)
Source: Journal of Biomedical Informatics - April 27, 2018 Category: Information Technology Source Type: research

Identifying and Characterizing Highly Similar Notes in Big Clinical Note Datasets
Conclusions We showed that among the EHR from our institution and from the publicly-available MIMIC-III dataset, there were a significant number of near-to-exact duplicated notes. Graphical abstract (Source: Journal of Biomedical Informatics)
Source: Journal of Biomedical Informatics - April 19, 2018 Category: Information Technology Source Type: research

Accurate Filtering of Privacy-Sensitive Information in Raw Genomic Data
We present the first filter that can be indistinctly applied to reads of any length, i.e., making it usable with any recent or future sequencing technologies. The filter is accurate, in the sense that it detects all known sensitive nucleotides except those located in highly variable regions (less than 10 nucleotides remain undetected per genome instead of 100,000 in previous works). It has far less false positives than previously known methods (10% instead of 60%) and can detect sensitive nucleotides despite sequencing errors (86% detected instead of 56% with 2% of mutations). Finally, practical experiments demonstrate hig...
Source: Journal of Biomedical Informatics - April 14, 2018 Category: Information Technology Source Type: research

Co-occurrence of medical conditions: Exposing patterns through probabilistic topic modeling of snomed codes
This study aims to identify and characterize patterns of co-occurring medical conditions in patients employing a probabilistic framework. Specifically, we apply topic modeling in a non-traditional way to find associations across SNOMED-CT codes assigned and recorded in the EHRs of >13,000 patients diagnosed with kidney disease. Unlike most prior work on topic modeling, we apply the method to codes rather than to natural language. Moreover, we quantitatively evaluate the topics, assessing their tightness and distinctiveness, and also assess the medical validity of our results. Our experiments show that each topic is ...
Source: Journal of Biomedical Informatics - April 13, 2018 Category: Information Technology Source Type: research

Big data handling mechanisms in the healthcare applications: A comprehensive and systematic literature review
Publication date: Available online 12 April 2018 Source:Journal of Biomedical Informatics Author(s): Asma Pashazadeh, Nima Jafari Navimipour Healthcare provides many services such as diagnosing, treatment, prevention of diseases, illnesses, injuries, and other physical and mental disorders. Large-scale distributed data processing applications in healthcare as a basic concept operates on large amounts of data. Therefore, big data application functions are the main part of healthcare operations, but there was not any comprehensive and systematic survey about studying and evaluating the important techniques in this field. Th...
Source: Journal of Biomedical Informatics - April 13, 2018 Category: Information Technology Source Type: research

The Vision of Personally Managed Health Data: Barriers, Approaches and Roadmap for the Future
Publication date: Available online 11 April 2018 Source:Journal of Biomedical Informatics Author(s): Haridimos Kondylakis, Lefteris Koumakis, Manolis Tsiknakis, Stephan Kiefer (Source: Journal of Biomedical Informatics)
Source: Journal of Biomedical Informatics - April 12, 2018 Category: Information Technology Source Type: research

Research Electronic Data Capture (REDCap ®) used as an audit tool with a built-in database
Publication date: Available online 9 April 2018 Source:Journal of Biomedical Informatics Author(s): Signe H. Kragelund, Mona Kjærsgaard, Søren Jensen-Fangel, Rita A. Leth, Nina Ank The aim of this study was to develop an audit tool with a built-in database using Research Electronic Data Capture (REDCap®) as part of an antimicrobial stewardship program at a regional hospital in the Central Denmark Region, and to analyse the need, if any, to involve more than one expert in the evaluation of cases of antimicrobial treatment, and the level of agreement among the experts. Patients treated with systemic antimic...
Source: Journal of Biomedical Informatics - April 9, 2018 Category: Information Technology Source Type: research

Complex Analyses on Clinical Information Systems Using Restricted Natural Language Querying to Resolve Time-Event Dependencies
Conclusion An evaluation of results of the research studies based on the comparison between CliniDAL and SQL solutions reveals high usability and efficiency of CliniDAL’s solution. Graphical abstract (Source: Journal of Biomedical Informatics)
Source: Journal of Biomedical Informatics - April 9, 2018 Category: Information Technology Source Type: research

The Ranking of Scientists: Computational Calculation of Z-score
Publication date: Available online 6 April 2018 Source:Journal of Biomedical Informatics Author(s): Enver Zerem, Suad Kunosić (Source: Journal of Biomedical Informatics)
Source: Journal of Biomedical Informatics - April 7, 2018 Category: Information Technology Source Type: research

ProFUSO: Business process and ontology-based framework to develop ubiquitous computing support systems for chronic patients ’ management
Publication date: Available online 5 April 2018 Source:Journal of Biomedical Informatics Author(s): Angel Jimenez-Molina, Jorge Gaete-Villegas, Javier Fuentes New advances in telemedicine, ubiquitous computing, and artificial intelligence have supported the emergence of more advanced applications and support systems for chronic patients. This trend addresses the important problem of chronic illnesses, highlighted by multiple international organizations as a core issue in future healthcare. Despite the myriad of exciting new developments, each application and system is designed and implemented for specific purposes and lac...
Source: Journal of Biomedical Informatics - April 6, 2018 Category: Information Technology Source Type: research

Bimodal Fuzzy Analytic Hierarchy Process (BFAHP) For Coronary Heart Disease Risk Assessment
Publication date: Available online 4 April 2018 Source:Journal of Biomedical Informatics Author(s): Farnaz Sabahi Rooted deeply in medical multiple criteria decision-making (MCDM), risk assessment is very important especially when applied to the risk of being affected by deadly diseases such as coronary heart disease (CHD). CHD risk assessment is a stochastic, uncertain, and highly dynamic process influenced by various known and unknown variables. In recent years, there has been a great interest in fuzzy analytic hierarchy process (FAHP), a popular methodology for dealing with uncertainty in MCDM. This paper proposes a ne...
Source: Journal of Biomedical Informatics - April 4, 2018 Category: Information Technology Source Type: research

Using insurance claims to predict and improve hospitalizations and biologics use in members with inflammatory bowel diseases
Conclusion The success of our approach provides a roadmap for how claims data can complement traditional medical decision making with personalized, data-driven predictive medicine. Graphical abstract (Source: Journal of Biomedical Informatics)
Source: Journal of Biomedical Informatics - April 3, 2018 Category: Information Technology Source Type: research

A Hybrid Model Based on Neural Networks for Biomedical Relation Extraction
Publication date: Available online 27 March 2018 Source:Journal of Biomedical Informatics Author(s): Yijia Zhang, Hongfei Lin, Zhihao Yang, Jian Wang, Shaowu Zhang, Yuanyuan, Sun, Liang Yang Biomedical relation extraction can automatically extract high-quality biomedical relations from biomedical texts, which is a vital step for the mining of biomedical knowledge hidden in the literature. Recurrent neural networks (RNNs) and convolutional neural networks (CNNs) are two major neural network models for biomedical relation extraction. Neural network-based methods for biomedical relation extraction typically focus on the sent...
Source: Journal of Biomedical Informatics - March 27, 2018 Category: Information Technology Source Type: research

Wisdom of artificial crowds feature selection in untargeted metabolomics: An application to the development of a blood-based diagnostic test for thrombotic myocardial infarction
Conclusions Strong evidence was observed that a statistical classifier utilizing WoAC feature selection can discriminate between human subjects presenting with thrombotic MI, non-thrombotic MI, and stable Coronary Artery Disease given abundances of selected plasma metabolites. Utilizing the abundances of twenty selected metabolites, a leave-one-out cross-validation estimated misclassification rate of 2.6% was observed. However, the WoAC feature selection strategy did not perform better than the Lasso over the current study. Graphical abstract (Source: Journal of Biomedical Informatics)
Source: Journal of Biomedical Informatics - March 23, 2018 Category: Information Technology Source Type: research

miR2Pathway: A Novel Analytical Method to Discover MicroRNA-mediated Dysregulated Pathways Involved in Hepatocellular Carcinoma
Publication date: Available online 22 March 2018 Source:Journal of Biomedical Informatics Author(s): Chaoxing Li, Valentin Dinu MicroRNAs (miRNAs) are small, non-coding RNAs involved in the regulation of gene expression at a post-transcriptional level. Recent studies have shown miRNAs as key regulators of a variety of biological processes, such as proliferation, differentiation, apoptosis, metabolism, etc. Aberrantly expressed miRNAs influence individual gene expression level, but rewired miRNA-mRNA connections can influence the activity of biological pathways. Here, we define rewired miRNA-mRNA connections as the differe...
Source: Journal of Biomedical Informatics - March 22, 2018 Category: Information Technology Source Type: research

Disease genes prediction by HMM based PU-learning using gene expression profiles
In this study, a novel method is introduced to predict disease candidate genes through gene expression profiles by learning hidden Markov models. In order to evaluate the proposed method, it is applied on a mixed part of 398 disease genes from three disease types and 12001 unlabeled genes. Compared to the other methods in literature, the experimental results indicate a significant improvement in favor of the proposed method. Graphical abstract (Source: Journal of Biomedical Informatics)
Source: Journal of Biomedical Informatics - March 20, 2018 Category: Information Technology Source Type: research

Incorporating Repeating Temporal Association Rules in Na ïve Bayes Classifiers for Coronary Heart Disease Diagnosis
Publication date: Available online 16 March 2018 Source:Journal of Biomedical Informatics Author(s): Kalia Orphanou, Arianna Dagliati, Lucia Sacchi, Athena Stassopoulou, Elpida Keravnou, Riccardo Bellazzi In this paper, we develop a Naïve Bayes classification model integrated with temporal association rules (TARs). A temporal pattern mining algorithm is used to detect TARs by identifying the most frequent temporal relationships among the derived basic temporal abstractions (TA). We develop and compare three classifiers that use as features the most frequent TARs as follows: i) representing the most frequent TARs dete...
Source: Journal of Biomedical Informatics - March 17, 2018 Category: Information Technology Source Type: research

Automatic assessment of functional health decline in older adults based on smart home data
Publication date: Available online 15 March 2018 Source:Journal of Biomedical Informatics Author(s): Ane Alberdi Aramendi, Alyssa Weakley, Asier Aztiria Goenaga, Maureen Schmitter-Edgecombe, Diane J. Cook In the context of an aging population, tools to help elderly to live independently must be developed. The goal of this paper is to evaluate the possibility of using unobtrusively collected activity-aware smart home behavioral data to automatically detect one of the most common consequences of aging: functional health decline. After gathering the longitudinal smart home data of 29 older adults for an average of > 2...
Source: Journal of Biomedical Informatics - March 16, 2018 Category: Information Technology Source Type: research

Local Spatial Obesity Analysis and Estimation Using Online Social Network Sensors
Publication date: Available online 15 March 2018 Source:Journal of Biomedical Informatics Author(s): Qindong Sun, Nan Wang, Shancang Li, Hongyi Zhou Recently, the online social networks (OSNs) have received considerable attentions as a revolutionary platform to offer users massive social interaction among users that enables users to be more involved in their own healthcare. The OSNs have also promoted increasing interests in the generation of analytical, data models in health informatics. This paper aims at developing an obesity identification, analysis, and estimation model, in which each individual user is regarded as a...
Source: Journal of Biomedical Informatics - March 16, 2018 Category: Information Technology Source Type: research