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OBJECTIVES: The International Society for Bipolar Disorders Big Data Task Force assembled leading researchers in the field of bipolar disorder (BD), machine learning, and big data with extensive experience to evaluate the rationale of machine learning and big data analytics strategies for BD.METHOD: A task force was convened to examine and integrate findings from the scientific literature related to machine learning and big data based studies to clarify terminology and to describe challenges and potential applications in the field of BD. We also systematically searched PubMed, Embase, and Web of Science for articles published up to January 2019 that used machine learning in BD.RESULTS: The results suggested that big data analytics has the potential to provide risk calculators to aid in treatment decisions and predict clinical prognosis, including suicidality, for individual patients. This approach can advance diagnosis by enabling discovery of more relevant data-driven phenotypes, as well as by predicting transition to the disorder in high-risk unaffected subjects. We also discuss the most frequent challenges that big data analytics applications can face, such as heterogeneity, lack of external validation and replication of some studies, cost and non-stationary distribution of the data, and lack of appropriate funding.CONCLUSION: Machine learning-based studies, including atheoretical data-driven big data approaches, provide an opportunity to more accurately detect those who are at risk, parse-relevant phenotypes as well as inform treatment selection and prognosis. However, several methodological challenges need to be addressed in order to translate research findings to clinical settings.

Gaining knowledge and actionable insights from complex, high-dimensional and heterogeneous biomedical data remains a key challenge in transforming health care. Various types of data have been emerging in modern biomedical research, including electronic health records, imaging, -omics, sensor data and text, which are complex, heterogeneous, poorly annotated and generally unstructured. Traditional data mining and statistical learning approaches typically need to first perform feature engineering to obtain effective and more robust features from those data, and then build prediction or clustering models on top of them. There are lots of challenges on both steps in a scenario of complicated data and lacking of sufficient domain knowledge. The latest advances in deep learning technologies provide new effective paradigms to obtain end-to-end learning models from complex data. In this article, we review the recent literature on applying deep learning technologies to advance the health care domain. Based on the analyzed work, we suggest that deep learning approaches could be the vehicle for translating big biomedical data into improved human health. However, we also note limitations and needs for improved methods development and applications, especially in terms of ease-of-understanding for domain experts and citizen scientists. We discuss such challenges and suggest developing holistic and meaningful interpretable architectures to bridge deep learning models and human interpretability.

Motivation: Discovering useful associations between biomedical concepts has been one of the main goals in biomedical text-mining, and understanding their biomedical contexts is crucial in the discovery process. Hence, we need a text-mining system that helps users explore various types of (possibly hidden) associations in an easy and comprehensible manner. Results: This article describes FACTA+, a real-time text-mining system for finding and visualizing indirect associations between biomedical concepts from MEDLINE abstracts. The system can be used as a text search engine like PubMed with additional features to help users discover and visualize indirect associations between important biomedical concepts such as genes, diseases and chemical compounds. FACTA+ inherits all functionality from its predecessor, FACTA, and extends it by incorporating three new features: (i) detecting biomolecular events in text using a machine learning model, (ii) discovering hidden associations using co-occurrence statistics between concepts, and (iii) visualizing associations to improve the interpretability of the output. To the best of our knowledge, FACTA+ is the first real-time web application that offers the functionality of finding concepts involving biomolecular events and visualizing indirect associations of concepts with both their categories and importance. Availability: FACTA+ is available as a web application at http://refine1-nactem.mc.man.ac.uk/facta/, and its visualizer is available at http://refine1-nactem.mc.man.ac.uk/facta-visualizer/. Contact: tsuruoka@jaist.ac.jp

Motivation: In neuroscience, as in many other scientific domains, the primary form of knowledge dissemination is through published articles. One challenge for modern neuroinformatics is finding methods to make the knowledge from the tremendous backlog of publications accessible for search, analysis and the integration of such data into computational models. A key example of this is metascale brain connectivity, where results are not reported in a normalized repository. Instead, these experimental results are published in natural language, scattered among individual scientific publications. This lack of normalization and centralization hinders the large-scale integration of brain connectivity results. In this article, we present text-mining models to extract and aggregate brain connectivity results from 13.2 million PubMed abstracts and 630 216 full-text publications related to neuroscience. The brain regions are identified with three different named entity recognizers (NERs) and then normalized against two atlases: the Allen Brain Atlas (ABA) and the atlas from the Brain Architecture Management System (BAMS). We then use three different extractors to assess inter-region connectivity. Results: NERs and connectivity extractors are evaluated against a manually annotated corpus. The complete in litero extraction models are also evaluated against in vivo connectivity data from ABA with an estimated precision of 78%. The resulting database contains over 4 million brain region mentions and over 100 000 (ABA) and 122 000 (BAMS) potential brain region connections. This database drastically accelerates connectivity literature review, by providing a centralized repository of connectivity data to neuroscientists. Availability and implementation: The resulting models are publicly available at github.com/BlueBrain/bluima. Contact: renaud.richardet@epfl.ch Supplementary information: Supplementary data are available at Bioinformatics online.

In the Life Sciences ‘omics’ data is increasingly generated by different high-throughput technologies. Often only the integration of these data allows uncovering biological insights that can be experimentally validated or mechanistically modelled, i.e. sophisticated computational approaches are required to extract the complex non-linear trends present in omics data. Classification techniques allow training a model based on variables (e.g. SNPs in genetic association studies) to separate different classes (e.g. healthy subjects versus patients). Random Forest (RF) is a versatile classification algorithm suited for the analysis of these large data sets. In the Life Sciences, RF is popular because RF classification models have a high-prediction accuracy and provide information on importance of variables for classification. For omics data, variables or conditional relations between variables are typically important for a subset of samples of the same class. For example: within a class of cancer patients certain SNP combinations may be important for a subset of patients that have a specific subtype of cancer, but not important for a different subset of patients. These conditional relationships can in principle be uncovered from the data with RF as these are implicitly taken into account by the algorithm during the creation of the classification model. This review details some of the to the best of our knowledge rarely or never used RF properties that allow maximizing the biological insights that can be extracted from complex omics data sets using RF.

The real-world data analysis and processing using data mining techniques often are facing observations that contain missing values. The main challenge of mining datasets is the existence of missing values. The missing values in a dataset should be imputed using the imputation method to improve the data mining methods’ accuracy and performance. There are existing techniques that use k-nearest neighbors algorithm for imputing the missing values but determining the appropriate k value can be a challenging task. There are other existing imputation techniques that are based on hard clustering algorithms. When records are not well-separated, as in the case of missing data, hard clustering provides a poor description tool in many cases. In general, the imputation depending on similar records is more accurate than the imputation depending on the entire dataset's records. Improving the similarity among records can result in improving the imputation performance. This paper proposes two numerical missing data imputation methods. A hybrid missing data imputation method is initially proposed, called KI, that incorporates k-nearest neighbors and iterative imputation algorithms. The best set of nearest neighbors for each missing record is discovered through the records similarity by using the k-nearest neighbors algorithm (kNN). To improve the similarity, a suitable k value is estimated automatically for the kNN. The iterative imputation method is then used to impute the missing values of the incomplete records by using the global correlation structure among the selected records. An enhanced hybrid missing data imputation method is then proposed, called FCKI, which is an extension of KI. It integrates fuzzy c-means, k-nearest neighbors, and iterative imputation algorithms to impute the missing data in a dataset. The fuzzy c-means algorithm is selected because the records can belong to multiple clusters at the same time. This can lead to further improvement for similarity. FCKI searches a cluster, instead of the whole dataset, to find the best k-nearest neighbors. It applies two levels of similarity to achieve a higher imputation accuracy. The performance of the proposed imputation techniques is assessed by using fifteen datasets with variant missing ratios for three types of missing data; MCAR, MAR, MNAR. These different missing data types are generated in this work. The datasets with different sizes are used in this paper to validate the model. Therefore, proposed imputation techniques are compared with other missing data imputation methods by means of three measures; the root mean square error (RMSE), the normalized root mean square error (NRMSE), and the mean absolute error (MAE). The results show that the proposed methods achieve better imputation accuracy and require significantly less time than other missing data imputation methods.

Objectives This paper aims to provide a theoretical clarification of the health informatics field by conducting a quantitative review analysis of the health informatics literature. And this paper aims to map scientific networks; to uncover the explicit and hidden patterns, knowledge structures, and sub-structures in scientific networks; to track the flow and burst of scientific topics; and to discover what effects they have on the scientific growth of health informatics. Methods This study was a quantitative literature review of the health informatics field, employing text mining and bibliometric research methods. This paper reviews 30,115 articles with health informatics as their topic, which are indexed in the Web of Science Core Collection Database from 1974 to 2018. This study analyzed and mapped four networks: author co-citation network, co-occurring author keywords and keywords plus, co-occurring subject categories, and country co-citation network. We used CiteSpace 5.3 and VOSviewer to analyze data, and we used Gephi 0.9.2 and VOSviewer to visualize the networks. Results This study found that the three major themes of the literature from 1974 to 2018 were the utilization of computer science in healthcare, the impact of health informatics on patient safety and the quality of healthcare, and decision support systems. The study found that, since 2016, health informatics has entered a new era to provide predictive, preventative, personalized, and participatory healthcare systems. Conclusions This study found that the future strands of research may be patient-generated health data, deep learning algorithms, quantified self and self-tracking tools, and Internet of Things based decision support systems.

In the field of cancer genomics, the broad availability of genetic information offered by next-generation sequencing technologies and rapid growth in biomedical publication has led to the advent of the big-data era. Integration of artificial intelligence (AI) approaches such as machine learning, deep learning, and natural language processing (NLP) to tackle the challenges of scalability and high dimensionality of data and to transform big data into clinically actionable knowledge is expanding and becoming the foundation of precision medicine. In this paper, we review the current status and future directions of AI application in cancer genomics within the context of workflows to integrate genomic analysis for precision cancer care. The existing solutions of AI and their limitations in cancer genetic testing and diagnostics such as variant calling and interpretation are critically analyzed. Publicly available tools or algorithms for key NLP technologies in the literature mining for evidence-based clinical recommendations are reviewed and compared. In addition, the present paper highlights the challenges to AI adoption in digital healthcare with regard to data requirements, algorithmic transparency, reproducibility, and real-world assessment, and discusses the importance of preparing patients and physicians for modern digitized healthcare. We believe that AI will remain the main driver to healthcare transformation toward precision medicine, yet the unprecedented challenges posed should be addressed to ensure safety and beneficial impact to healthcare.

Overfitting is one of the critical problems in developing models by machine learning. With machine learning becoming an essential technology in computational biology, we must include training about overfitting in all courses that introduce this technology to students and practitioners. We here propose a hands-on training for overfitting that is suitable for introductory level courses and can be carried out on its own or embedded within any data science course. We use workflow-based design of machine learning pipelines, experimentation-based teaching, and hands-on approach that focuses on concepts rather than underlying mathematics. We here detail the data analysis workflows we use in training and motivate them from the viewpoint of teaching goals. Our proposed approach relies on Orange, an open-source data science toolbox that combines data visualization and machine learning, and that is tailored for education in machine learning and explorative data analysis., Author summary Every teacher strives for an a-ha moment, a sudden revelation by the student who gained a fundamental insight she will always remember. In the past years, authors of this paper have been tailoring their courses in machine learning to include material that could lead students to such discoveries. We aim to expose machine learning to practitioners–not only computer scientists but also molecular biologists and students of biomedicine, that is, the end-users of bioinformatics’ computational approaches. In this article, we lay out a course that aims to teach about overfitting, one of the key concepts in machine learning that needs to be understood, mastered, and avoided in data science applications. We propose a hands-on approach that uses an open-source workflow-based data science toolbox that combines data visualization and machine learning. In the proposed training about overfitting, we first deceive the students, then expose the problem, and finally challenge them to find the solution. In the paper, we present three lessons in overfitting and associated data analysis workflows and motivate the use of introduced computation methods by relating them to concepts conveyed by instructors.

Data scientists aim to provide techniques and tools to the clinicians to manage the new coronavirus disease. Nowadays, new emerging tools based on Artificial Intelligence (AI), Image Processing (IP) and Machine Learning (ML) are contributing to the improvement of healthcare and treatments of different diseases. This paper reviews the most recent research efforts and approaches related to these new data driven techniques and tools in combination with the exploitation of the already available COVID-19 datasets. The tools can assist clinicians and nurses in efficient decision making with complex and heavily heterogeneous data, even in hectic and overburdened Intensive Care Units (ICU) scenarios. The datasets and techniques underlying these tools can help finding a more correct diagnosis. The paper also describes how these innovative AI+IP+ML-based methods (e.g., conventional X-ray imaging, clinical laboratory data, respiratory monitoring and automatic adjustments, etc.) can assist in the process of easing both the care of infected patients in ICUs and Emergency Rooms and the discovery of new treatments (drugs).

Software is a complex entity, and its development needs careful planning and a high amount of time and cost. To assess quality of program, software measures are very helpful. Amongst the existing measures, coupling is an important design measure, which computes the degree of interdependence among the entities of a software system. Higher coupling leads to cognitive complexity and thus a higher probability occurrence of faults. Well in time prediction of fault-prone modules assists in saving time and cost of testing. This paper aims to capture important aspects of coupling and then assess the effectiveness of these aspects in determining fault-prone entities in the software system. We propose two coupling metrics, i.e., Vovel-in and Vovel-out, that capture the level of coupling and the volume of information flow. We empirically evaluate the effectiveness of the Vovel metrics in determining the fault-prone classes using five projects, i.e., Eclipse JDT, Equinox framework, Apache Lucene, Mylyn, and Eclipse PDE UI. Model building is done using univariate logistic regression and later Spearman correlation coefficient is computed with the existing coupling metrics to assess the coverage of unique information. Finally, the least correlated metrics are used for building multivariate logistic regression with and without the use of Vovel metrics, to assess the effectiveness of Vovel metrics. The results show the proposed metrics significantly improve the predicting of fault prone classes. Moreover, the proposed metrics cover a significant amount of unique information which is not covered by the existing well-known coupling metrics, i.e., CBO, RFC, Fan-in, and Fan-out. This paper, empirically evaluates the impact of coupling metrics, and more specifically the importance of level and volume of coupling in software fault prediction. The results advocate the prudent addition of proposed metrics due to their unique information coverage and significant predictive ability.

Healthcare is considered as one of the most promising application areas for artificial intelligence and analytics (AIA) just after the emergence of the latter. AI combined to analytics technologies is increasingly changing medical practice and healthcare in an impressive way using efficient algorithms from various branches of information technology (IT). Indeed, numerous works are published every year in several universities and innovation centers worldwide, but there are concerns about progress in their effective success. There are growing examples of AIA being implemented in healthcare with promising results. This review paper summarizes the past 5 years of healthcare applications of AIA, across different techniques and medical specialties, and discusses the current issues and challenges, related to this revolutionary technology. A total of 24,782 articles were identified. The aim of this paper is to provide the research community with the necessary background to push this field even further and propose a framework that will help integrate diverse AIA technologies around patient needs in various healthcare contexts, especially for chronic care patients, who present the most complex comorbidities and care needs.

Maximizing product use is a central goal of many businesses, which makes retention and monetization two central analytics metrics in games. Player retention may refer to various duration variables quantifying product use: total playtime or session playtime are popular research targets, and active playtime is well-suited for subscription games. Such research often has the goal of increasing player retention or conversely decreasing player churn. Survival analysis is a framework of powerful tools well suited for retention type data. This paper contributes new methods to game analytics on how playtime can be analyzed using survival analysis without covariates. Survival and hazard estimates provide both a visual and an analytic interpretation of the playtime phenomena as a funnel type nonparametric estimate. Metrics based on the survival curve can be used to aggregate this playtime information into a single statistic. Comparison of survival curves between cohorts provides a scientific AB-test. All these methods work on censored data and enable computation of confidence intervals. This is especially important in time and sample limited data which occurs during game development. Throughout this paper, we illustrate the application of these methods to real world game development problems on the Hipster Sheep mobile game.

In the last decade manufacturing experienced a shift towards digitalization. Cost decrease of sensors, wireless connectivity, and the opportunity to store big amounts of data pushed a process towards a next generation of IT industry. Manufacturing now has the opportunity to gather large quantities of data, coming from different areas, such as product and process design, assembly, material planning, quality control, scheduling, maintenance, fault detection and cover all the product life cycle phases. The extraction of value from data is a new challenge that companies are now experiencing. Therefore, the need for analytical information system is growing, in order to explore datasets and discover useful and often hidden information. Data analytics became a keyword in this context, but sometimes it is not clear how different methods or tools are defined and could be effectively used to analyze data in manufacturing. The paper aims to present and clarify the meaning of terms that are currently and frequently used in the context of analytics. The paper also provides an overview of the data analysis techniques that could be used to extract knowledge from data along the manufacturing process.

Improvement of data generating, processing, storing and networking technologies has made storing, capturing and sharing of data easier and cheaper than before and has enabled organizations to handle huge volume of data at high velocity and variety, named as big data. Big data offers many opportunities when the associated difficulties are addressed properly. Business Intelligence (BI) basically focuses on transforming raw data into usable, valuable and actionable information for decision-making. It can be classified as a kind of data-driven decision support system. Although big data related papers have increased for last fifteen years, there are not sufficient papers that directly overviews big data impact on BI. As data is growing exponentially, storage, process and analytics tools and technologies become more important for BI solutions. With the advent of big data, BI’s concept, architecture and capabilities are meant to be changed. Unlike a decades before, BI now is to be extract value from huge data ocean by using big data tools as well as classical ones. So, an interclusion has emerged between big data and BI. This paper overviews the current state of the art of BI and big data, and discuss how big data era affects BI solutions in general context.

Purpose Data mining is widely considered necessary in many business applications for effective decision-making. The importance of business data mining is reflected by the existence of numerous surveys in the literature focusing on the investigation of related works using data mining techniques for solving specific business problems. The purpose of this paper is to answer the following question: What are the widely used data mining techniques in business applications? Design/methodology/approach The aim of this paper is to examine related surveys in the literature and thus to identify the frequently applied data mining techniques. To ensure the recent relevance and quality of the conclusions, the criterion for selecting related studies are that the works be published in reputed journals within the past 10 years. Findings There are 33 different data mining techniques employed in eight different application areas. Most of them are supervised learning techniques and the application area where such techniques are most often seen is bankruptcy prediction, followed by the areas of customer relationship management, fraud detection, intrusion detection and recommender systems. Furthermore, the widely used ten data mining techniques for business applications are the decision tree (including C4.5 decision tree and classification and regression tree), genetic algorithm, k-nearest neighbor, multilayer perceptron neural network, naïve Bayes and support vector machine as the supervised learning techniques and association rule, expectation maximization and k-means as the unsupervised learning techniques. Originality/value The originality of this paper is to survey the recent 10 years of related survey and review articles about data mining in business applications to identify the most popular techniques.

The popularity of Python is growing, especially in the field of data science. Consequently, there is an increasing number of free libraries available for usage. The aim of this review paper is to describe and compare the characteristics of different data mining and big data analysis libraries in Python. There is currently no paper dealing with the subject and describing pros and cons of all these libraries. Here we consider more than 20 libraries and separate them into six groups: core libraries, data preparation, data visualization, machine learning, deep learning and big data. Beside functionalities of a certain library, important factors for comparison are the number of contributors developing and maintaining the library and the size of the community. Bigger communities mean larger chances for easily finding solution to a certain problem. We currently recommend: pandas for data preparation ; Matplotlib, seaborn or Plotly for data visualization ; scikit-learn for machine learning ; TensorFlow, Keras and PyTorch for deep learning ; and Hadoop Streaming and PySpark for big data.

Summary Objective: To summarize recent research and present a selection of the best papers published in 2015 in the field of clinical Natural Language Processing (NLP). Method: A systematic review of the literature was performed by the two section editors of the IMIA Yearbook NLP section by searching bibliographic databases with a focus on NLP efforts applied to clinical texts or aimed at a clinical outcome. Section editors first selected a shortlist of candidate best papers that were then peer-reviewed by independent external reviewers. Results: The clinical NLP best paper selection shows that clinical NLP is making use of a variety of texts of clinical interest to contribute to the analysis of clinical information and the building of a body of clinical knowledge. The full review process highlighted five papers analyzing patient-authored texts or seeking to connect and aggregate multiple sources of information. They provide a contribution to the development of methods, resources, applications, and sometimes a combination of these aspects. Conclusions: The field of clinical NLP continues to thrive through the contributions of both NLP researchers and healthcare professionals interested in applying NLP techniques to impact clinical practice. Foundational progress in the field makes it possible to leverage a larger variety of texts of clinical interest for healthcare purposes.

Purpose– Among the growing number of data mining (DM) techniques, outlier detection has gained importance in many applications and also attracted much attention in recent times. In the past, outlier detection researched papers appeared in a safety care that can view as searching for the needles in the haystack. However, outliers are not always erroneous. Therefore, the purpose of this paper is to investigate the role of outliers in healthcare services in general and patient safety care, in particular.Design/methodology/approach– It is a combined DM (clustering and the nearest neighbor) technique for outliers’ detection, which provides a clear understanding and meaningful insights to visualize the data behaviors for healthcare safety. The outcomes or the knowledge implicit is vitally essential to a proper clinical decision-making process. The method is important to the semantic, and the novel tactic of patients’ events and situations prove that play a significant role in the process of patient care safety and medications.Findings– The outcomes of the paper is discussing a novel and integrated methodology, which can be inferring for different biological data analysis. It is discussed as integrated DM techniques to optimize its performance in the field of health and medical science. It is an integrated method of outliers detection that can be extending for searching valuable information and knowledge implicit based on selected patient factors. Based on these facts, outliers are detected as clusters and point events, and novel ideas proposed to empower clinical services in consideration of customers’ satisfactions. It is also essential to be a baseline for further healthcare strategic development and research works.Research limitations/implications– This paper mainly focussed on outliers detections. Outlier isolation that are essential to investigate the reason how it happened and communications how to mitigate it did not touch. Therefore, the research can be extended more about the hierarchy of patient problems.Originality/value– DM is a dynamic and successful gateway for discovering useful knowledge for enhancing healthcare performances and patient safety. Clinical data based outlier detection is a basic task to achieve healthcare strategy. Therefore, in this paper, the authors focussed on combined DM techniques for a deep analysis of clinical data, which provide an optimal level of clinical decision-making processes. Proper clinical decisions can obtain in terms of attributes selections that important to know the influential factors or parameters of healthcare services. Therefore, using integrated clustering and nearest neighbors techniques give more acceptable searched such complex data outliers, which could be fundamental to further analysis of healthcare and patient safety situational analysis.

The rapid development of social media technologies enables travellers to share travel experiences and opinions online by posting reviews, which then serve as information source for other travellers. However, the explosive growth of reviews and the proliferation of uninformative, biased or even false information make it very challenging for travellers to find credible information. To help travellers seek credible information, most current work apply mainly qualitative approaches to investigate the credibility of reviews or reviewers. This paper adopts an Impact Index to quantify the credibility of reviewers by simultaneously evaluating the expertise and trustworthiness of reviewers based on the number of reviews posted by them and the number of helpful votes received by those reviews. Furthermore, the Impact Index is enhanced into the Exposure-Impact Index by considering in addition reviewers' breadth of expertise in the form of the number of destinations on which reviewers posted reviews. To examine the effectiveness and applicability of Impact Index and Exposure-Impact Index, this paper evaluates them on several data sets collected from two rather different online travel communities: TripAdvisor, the world's largest travel community, and Qunar, one of the most popular travel communities in China. Experimental results show that both Impact Index and Exposure-Impact Index lead to more consistent results with human judgments than the state-of-the-art method in measuring the credibility of reviewers from diverse communities, manifesting their effectiveness and applicability.

open access article Banking as a data-intensive subject has been progressing continuously under the promoting influences of the era of big data. Exploring the advanced big data analytic tools like Data Mining (DM) techniques is key for the banking sector, which aims to reveal valuable information from the overwhelming volume of data and achieve better strategic management and customer satisfaction. In order to provide sound direction for the future research and development, a comprehensive and most up to date review of the current research status of DM in banking will be extremely beneficial. Since existing reviews only cover the applications until 2013, this paper aims to fill this research gap and presents the significant progressions and most recent DM implementations in banking post 2013. By collecting and analyzing the trends of research focus, data resources, technological aids, and data analytical tools, this paper contributes to bringing valuable insights with regard to the future developments of both DM and the banking sector along with a comprehensive one stop reference table. Moreover, we identify the key obstacles and present a summary for all interested parties that are facing the challenges of big data.

Summary Background: Natural Language Processing (NLP) methods are increasingly being utilized to mine knowledge from unstructured health-related texts. Recent advances in noisy text processing techniques are enabling researchers and medical domain experts to go beyond the information encapsulated in published texts (e.g., clinical trials and systematic reviews) and structured questionnaires, and obtain perspectives from other unstructured sources such as Electronic Health Records (EHRs) and social media posts. Objectives: To review the recently published literature discussing the application of NLP techniques for mining health-related information from EHRs and social media posts. Methods: Literature review included the research published over the last five years based on searches of PubMed, conference proceedings, and the ACM Digital Library, as well as on relevant publications referenced in papers. We particularly focused on the techniques employed on EHRs and social media data. Results: A set of 62 studies involving EHRs and 87 studies involving social media matched our criteria and were included in this paper. We present the purposes of these studies, outline the key NLP contributions, and discuss the general trends observed in the field, the current state of research, and important outstanding problems. Conclusions: Over the recent years, there has been a continuing transition from lexical and rule-based systems to learning-based approaches, because of the growth of annotated data sets and advances in data science. For EHRs, publicly available annotated data is still scarce and this acts as an obstacle to research progress. On the contrary, research on social media mining has seen a rapid growth, particularly because the large amount of unlabeled data available via this resource compensates for the uncertainty inherent to the data. Effective mechanisms to filter out noise and for mapping social media expressions to standard medical concepts are crucial and latent research problems. Shared tasks and other competitive challenges have been driving factors behind the implementation of open systems, and they are likely to play an imperative role in the development of future systems.