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In this paper, I posit that from a research point of view, Data Science is a language. More precisely Data Science is doing Science using computer science as a language for datafied sciences; much as mathematics is the language of, e.g., physics. From this viewpoint, three (classes) of challenges for computer science are identified; complementing the challenges the closely related Big Data problem already poses to computer science. I discuss the challenges with references to, in my opinion, related, interesting directions in computer science research; note, I claim neither that these directions are the most appropriate to solve the challenges nor that the cited references represent the best work in their field, they are inspirational to me. So, what are these challenges? Firstly, if computer science is to be a language, what should that language look like? While our traditional specifications such as pseudocode are an excellent way to convey what has been done, they fail for more mathematics like reasoning about computations. Secondly, if computer science is to function as a foundation of other, datafied, sciences, its own foundations should be in order. While we have excellent foundations for supervised learning-e.g., by having loss functions to optimize and, more general, by PAC learning (Valiant in Commun ACM 27(11):1134-1142, 1984)-this is far less true for unsupervised learning. Kolmogorov complexity-or, more general, Algorithmic Information Theory-provides a solid base (Li and Vitanyi in An introduction to Kolmogorov complexity and its applications, Springer, Berlin, 1993). It provides an objective criterion to choose between competing hypotheses, but it lacks, e.g., an objective measure of the uncertainty of a discovery that datafied sciences need. Thirdly, datafied sciences come with new conceptual challenges. Data-driven scientists come up with data analysis questions that sometimes do and sometimes don't, fit our conceptual toolkit. Clearly, computer science does not suffer from a lack of interesting, deep, research problems. However, the challenges posed by data science point to a large reservoir of untapped problems. Interesting, stimulating problems, not in the least because they are posed by our colleagues in datafied sciences. It is an exciting time to be a computer scientist.

2nd International Congress on Human-Computer Interaction, Optimization and Robotic Applications, HORA 2020 -- 26 June 2020 through 27 June 2020 -- -- 162106 2-s2.0-85089705154 Recent progress in software and hardware has allowed different data measurements in a variety of fields to be captured. These measures are produced continuously at very fluctuating data rates. For example, network sensors, web logs and computer network traffic. Computer-intensive activities are the collection, query and removal of these data sets. Mining data sources include the recovery of knowledge systems incorporated into templates and trends on streams of non-stop information. Because of the importance of its applications and the increasing generation of data stream research, information. Information. Information. Analysis applications for data streams can range from critical scientific and astronomical applications to major business and financial applications. Algorithms, processes and structures Streaming challenges have been developed over the last three years. We present the newest in this increasingly important field in this review paper. © 2020 IEEE.

Objective This article reviews the available evidence and guidance on methods to identify reports of quasi-experimental (QE) studies to inform systematic reviews of health care, public health, international development, education, crime and justice, and social welfare. Study Design and Setting Research, guidance, and examples of search strategies were identified by searching a range of databases, key guidance documents, selected reviews, conference proceedings, and personal communication. Current practice and research evidence were summarized. Results Four thousand nine hundred twenty-four records were retrieved by database searches, and additional documents were obtained by other searches. QE studies are challenging to identify efficiently because they have no standardized nomenclature and may be indexed in various ways. Reliable search filters are not available. There is a lack of specific resources devoted to collecting QE studies and little evidence on where best to search. Conclusion Searches to identify QE studies should search a range of resources and, until indexing improves, use strategies that focus on the topic rather than the study design. Better definitions, better indexing in databases, prospective registers, and reporting guidance are required to improve the retrieval of QE studies and promote systematic reviews of what works based on the evidence from such studies.

Emergency situations associated with falls are a serious concern for an aging society. Yet following the recent development within ICT, a significant number of solutions have been proposed to track body movement and detect falls using various sensor technologies, thereby facilitating fall detection and in some cases prevention. A number of recent reviews on fall detection methods using ICT technologies have emerged in the literature and an increasingly popular approach considers combining information from several sensor sources to assess falls. The aim of this paper is to review in detail the subfield of fall detection techniques that explicitly considers the use of multisensor fusion based methods to assess and determine falls. The paper highlights key differences between the single sensor-based approach and a multifusion one. The paper also describes and categorizes the various systems used, provides information on the challenges of a multifusion approach, and finally discusses trends for future work.

Recommendation algorithms have been researched extensively to help people deal with abundance of information. In recent years, the incorporation of multiple relevance criteria has attracted increased interest. Such multi-criteria recommendation approaches are researched as a paradigm for building intelligent systems that can be tailored to multiple interest indicators of end-users – such as combinations of implicit and explicit interest indicators in the form of ratings or ratings on multiple relevance dimensions. Nevertheless, evaluation of these recommendation techniques in the context of real-life applications still remains rather limited. Previous studies dealing with the evaluation of recommender systems have outlined that the performance of such algorithms is often dependent on the dataset – and indicate the importance of carrying out careful testing and parameterization. Especially when looking at large scale datasets, it becomes very difficult to deploy evaluation methods that may help in assessing the effect that different system components have to the overall design. In this paper, we study how layered evaluation can be applied for the case of a multi-criteria recommendation service that we plan to deploy for paper recommendation using the Mendeley dataset. The paper introduces layered evaluation and suggests two experiments that may help assess the components of the envisaged system separately. ispartof: pages:1189-1197 ispartof: Procedia Computer Science vol:18 pages:1189-1197 ispartof: 2013 International Conference on Computational Science location:SPAIN, Barcelona date:5 Jun - 7 Jun 2013 status: published

Traditional activity-centric process modeling languages treat data as simple black boxes acting as input or output for activities. Many alternate and emerging process modeling paradigms, such as case handling and artifact-centric process modeling, give data a more central role. This is achieved by introducing lifecycles and states for data objects, which is beneficial when modeling data-or knowledge-intensive processes. We assume that traditional activity-centric process modeling languages lack the capabilities to adequately capture the complexity of such processes. To verify this assumption we conducted an online interview among BPM experts. The results not only allow us to identify various profiles of persons modeling business processes, but also the problems that exist in contemporary modeling languages w.r.t. The modeling of business data. Overall, this preliminary empirical study confirms the necessity of data-awareness in process modeling notations in general.

Fungi are versatile organisms; they exist on earth in all extremes of conditions. Fungi are sources of important chemical entities which may be both beneficial and deleterious. Biotechnology has helped to harness this potential of Fungi in a positive direction. The advancements in Genomics and Proteomics have opened up new horizon in research. Improved advanced Molecular Biological Technologies have given a boost to our understanding of genes and helped us to exploit the full potential of Fungi. Bioinformatics and Statistical sciences are indispensable in this regard. Databases are available, providing fast, efficient, meaningful interpretation and analysis of vast amounts of data generated in scientific laboratories.

Through massive parallelism, distributed systems enable the multiplication of productivity. Unfortunately, increas- ing the scale of available machines to users will also mul- tiply debugging when failure occurs. Data mining allows the extraction of patterns within large amounts of data and therefore forms the foundation for a useful method of de- bugging, particularly within such distributed systems. This paper outlines a successful application of data mining in troubleshooting distributed systems, proposes a framework for further study, and speculates on other future work. We propose that data mining techniques can be applied to the problem of large scale troubleshooting. If both jobs and the resources that they consume are annotated with structured information relevant to success or failure, then classification algorithms can be used to find properties of each that correlate with success or failure. In the one- million jobs example above, an ideal troubleshooter would report to the user something like: Your jobs always fail on Linux 2.8 machines, always fail on cluster X between mid- night and 6 A.M, and fail with 50% probability on machines owned by user Y. Further, these discoveries may be used to automatically avoid making bad placement decisions that waste time and resources. We hasten to note that this form of data mining is not a panacea. It does not explain why failures happen, or make any attempt to diagnose problems in fine detail. It only proposes to the user properties correlated with suc- cess or failure. Other tools and techniques may be applied to extract causes. Rather, data mining allows the user of a large system to rapidly make generalizations to improve the throughput and reliability of a system without engag- ing in low level debugging. These generalizations may be used later at leisure to locate and repair problems. In addi- tion, the problem of distributed debugging, with its unique idiosyncracies and dynamics, lends itself as a compelling application for data mining research. Standard off-the-shelf methodologies might not be directly applicable for large, dynamic, and evolving system. It is desired to implement techniques that are capable of incremental self-revision and adaptation. The goal of our paper is to serve as a proof-of- concept and identify venues for compelling future research.

Information or data fusion of data from different sources are ubiquitous in many applications, from epidemiology, medical, biological, political, and intelligence to military applications. Data fusion involves integration of spectral, imaging, text, and many other sensor data. For example, in epidemiology, information is often obtained based on many studies conducted by different researchers at different regions with different protocols. In the medical field, the diagnosis of a disease is often based on imaging (MRI, X-Ray, CT), clinical examination, and lab results. In the biological field, information is obtained based on studies conducted on many different species. In military field, information is obtained based on data from radar sensors, text messages, chemical biological sensor, acoustic sensor, optical warning and many other sources. Many methodologies are used in the data integration process, from classical, Bayesian, to evidence based expert systems. The implementation of the data integration ranges from pure software design to a mixture of software and hardware. In this review we summarize the methodologies and implementations of data fusion process, and illustrate in more detail the methodologies involved in three examples. We propose a unified multi-stage and multi-path mapping approach to the data fusion process, and point out future prospects andmore » challenges.« less

Keeping up with the rapidly growing literature has become virtually impossible for most scientists. This can have dire consequences. First, we may waste research time and resources on reinventing the wheel simply because we can no longer maintain a reliable grasp on the published literature. Second, and perhaps more detrimental, judicious (or serendipitous) combination of knowledge from different scientific disciplines, which would require following disparate and distinct research literatures, is rapidly becoming impossible for even the most ardent readers of research publications. Text mining -- the automated extraction of information from (electronically) published sources -- could potentially fulfil an important role -- but only if we know how to harness its strengths and overcome its weaknesses. As we do not expect that the rate at which scientific results are published will decrease, text mining tools are now becoming essential in order to cope with, and derive maximum benefit from, this information explosion. In genomics, this is particularly pressing as more and more rare disease-causing variants are found and need to be understood. Not being conversant with this technology may put scientists and biomedical regulators at a severe disadvantage. In this review, we introduce the basic concepts underlying modern text mining and its applications in genomics and systems biology. We hope that this review will serve three purposes: (i) to provide a timely and useful overview of the current status of this field, including a survey of present challenges; (ii) to enable researchers to decide how and when to apply text mining tools in their own research; and (iii) to highlight how the research communities in genomics and systems biology can help to make text mining from biomedical abstracts and texts more straightforward.

After its discovery in the 1950 s, the autophagy research field has seen its annual number of publications climb from tens to thousands. The ever-growing number of autophagy publications is a wealth of information but presents a challenge to researchers, especially those new to the field, who are looking for a general overview of the field to, for example, determine current topics of the field or formulate new hypotheses. Here, we employed text mining tools to extract research trends in the autophagy field, including those of genes, terms, and topics. The publication trend of the field can be separated into three phases. The exponential rise in publication number began in the last phase and is most likely spurred by a series of highly cited research papers published in previous phases. The exponential increase in papers has resulted in a larger variety of research topics, with the majority involving those that are directly physiologically relevant, such as disease and modulating autophagy. Our findings provide researchers a summary of the history of the autophagy research field and perhaps hints of what is to come. Abbreviations: 5Y-IF: 5-year impact factor; AIS: article influence score; EM: electron microscopy; HGNC: HUGO gene nomenclature committee; LDA: latent Dirichlet allocation; MeSH: medical subject headings; ncRNA: non-coding RNA

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.

Background The Appalachian population is distinct, not just culturally and geographically but also in its health care needs, facing the most health care disparities in the United States. To meet these unique demands, Appalachian medical centers need an arsenal of analytics and data science tools with the foundation of a centralized data warehouse to transform health care data into actionable clinical interventions. However, this is an especially challenging task given the fragmented state of medical data within Appalachia and the need for integration of other types of data such as environmental, social, and economic with medical data. Objective This paper aims to present the structure and process of the development of an integrated platform at a midlevel Appalachian academic medical center along with its initial uses. Methods The Appalachian Informatics Platform was developed by the Appalachian Clinical and Translational Science Institute’s Division of Clinical Informatics and consists of 4 major components: a centralized clinical data warehouse, modeling (statistical and machine learning), visualization, and model evaluation. Data from different clinical systems, billing systems, and state- or national-level data sets were integrated into a centralized data warehouse. The platform supports research efforts by enabling curation and analysis of data using the different components, as appropriate. Results The Appalachian Informatics Platform is functional and has supported several research efforts since its implementation for a variety of purposes, such as increasing knowledge of the pathophysiology of diseases, risk identification, risk prediction, and health care resource utilization research and estimation of the economic impact of diseases. Conclusions The platform provides an inexpensive yet seamless way to translate clinical and translational research ideas into clinical applications for regions similar to Appalachia that have limited resources and a largely rural population.

Motivation Most currently available text mining tools share two characteristics that make them less than optimal for use by biomedical researchers: they require extensive specialist skills in natural language processing and they were built on the assumption that they should optimize global performance metrics on representative datasets. This is a problem because most end-users are not natural language processing specialists and because biomedical researchers often care less about global metrics like F-measure or representative datasets than they do about more granular metrics such as precision and recall on their own specialized datasets. Thus, there are fundamental mismatches between the assumptions of much text mining work and the preferences of potential end-users. Results This article introduces the concept of Agile text mining, and presents the PubAnnotation ecosystem as an example implementation. The system approaches the problems from two perspectives: it allows the reformulation of text mining by biomedical researchers from the task of assembling a complete system to the task of retrieving warehoused annotations, and it makes it possible to do very targeted customization of the pre-existing system to address specific end-user requirements. Two use cases are presented: assisted curation of the GlycoEpitope database, and assessing coverage in the literature of pre-eclampsia-associated genes. Availability and implementation The three tools that make up the ecosystem, PubAnnotation, PubDictionaries and TextAE are publicly available as web services, and also as open source projects. The dictionaries and the annotation datasets associated with the use cases are all publicly available through PubDictionaries and PubAnnotation, respectively.

Background Social media are considered promising and viable sources of data for gaining insights into various disease conditions and patients’ attitudes, behaviors, and medications. They can be used to recognize communication and behavioral themes of problematic use of prescription drugs. However, mining and analyzing social media data have challenges and limitations related to topic deduction and data quality. As a result, we need a structured approach to analyze social media content related to drug abuse in a manner that can mitigate the challenges and limitations surrounding the use of such data. Objective This study aimed to develop and evaluate a framework for mining and analyzing social media content related to drug abuse. The framework is designed to mitigate challenges and limitations related to topic deduction and data quality in social media data analytics for drug abuse. Methods The proposed framework started with defining different terms related to the keywords, categories, and characteristics of the topic of interest. We then used the Crimson Hexagon platform to collect data based on a search query informed by a drug abuse ontology developed using the identified terms. We subsequently preprocessed the data and examined the quality using an evaluation matrix. Finally, a suitable data analysis approach could be used to analyze the collected data. Results The framework was evaluated using the opioid epidemic as a drug abuse case analysis. We demonstrated the applicability of the proposed framework to identify public concerns toward the opioid epidemic and the most discussed topics on social media related to opioids. The results from the case analysis showed that the framework could improve the discovery and identification of topics in social media domains characterized by a plethora of highly diverse terms and lack of a commonly available dictionary or language by the community, such as in the case of opioid and drug abuse. Conclusions The proposed framework addressed the challenges related to topic detection and data quality. We demonstrated the applicability of the proposed framework to identify the common concerns toward the opioid epidemic and the most discussed topics on social media related to opioids.

Computer science is essentially an applied or engineering science, creating tools. In Data Mining, those tools are supposed to help humans understand large amounts of data. In this position paper, I argue that for all the progress that has been made in Data Mining, in particular Pattern Mining, we are lacking insight into three key aspects: 1) How pattern mining algorithms perform quantitatively, 2) How to choose parameter settings, and 3) How to relate found patterns to the processes that generated the data. I illustrate the issue by surveying existing work in light of these concerns and pointing to the (relatively few) papers that have attempted to fill in the gaps. I argue further that progress regarding those questions is held back by a lack of data with varying, controlled properties, and that this lack is unlikely to be remedied by the ever increasing collection of real-life data. Instead, I am convinced that we will need to make a science of digital data generation, and use it to develop guidance to data practitioners.

The ability to collect, store and analyze massive amounts of molecular and clinical data is fundamentally transforming the scientific method and its application in translational medicine. Collecting observations has always been a prerequisite for discovery, and great leaps in scientific understanding are accompanied by an expansion of this ability. Particle physics, astronomy and climate science, for example, have all greatly benefited from the development of new technologies enabling the collection of larger and more diverse data. Unlike medicine, however, each of these fields also has a mature theoretical framework on which new data can be evaluated and incorporated—to say it another way, there are no ‘first principals’ from which a healthy human could be analytically derived. The worry, and it is a valid concern, is that, without a strong theoretical underpinning, the inundation of data will cause medical research to devolve into a haphazard enterprise without discipline or rigor. The Age of Big Data harbors tremendous opportunity for biomedical advances, but will also be treacherous and demanding on future scientists.

Causal discovery is an increasingly important method for data analysis in the field of medical research. In this paper, we consider two challenges in causal discovery that occur very often when working with medical data: a mixture of discrete and continuous variables and a substantial amount of missing values. To the best of our knowledge, there are no methods that can handle both challenges at the same time. In this paper, we develop a new method that can handle these challenges based on the assumption that data are missing at random and that continuous variables obey a non-paranormal distribution. We demonstrate the validity of our approach for causal discovery on simulated data as well as on two real-world data sets from a monetary incentive delay task and a reversal learning task. Our results help in the understanding of the etiology of attention-deficit/hyperactivity disorder (ADHD). Electronic supplementary material The online version of this article (doi:10.1007/s41060-016-0034-x) contains supplementary material, which is available to authorized users.

Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case ofHomo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic datasets. Instead, novel, qualitatively different computational methods and paradigms are needed. We will witness the rapid extension ofcomputational pan-genomics, a new sub-area of research in computational biology. In this paper, we generalize existing definitions and understand apan-genomeas any collection of genomic sequences to be analyzed jointly or to be used as a reference. We examine already available approaches to construct and use pan-genomes, discuss the potential benefits of future technologies and methodologies, and review open challenges from the vantage point of the above-mentioned biological disciplines. As a prominent example for a computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations as graphs. We outline how this and other challenges from different application domains translate into common computational problems, point out relevant bioinformatics techniques and identify open problems in computer science. With this review, we aim to increase awareness that a joint approach to computational pan-genomics can help address many of the problems currently faced in various domains.

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.

SummaryBackground EHR systems have high potential to improve healthcare delivery and management. Although structured EHR data generates information in machine-readable formats, their use for decision support still poses technical challenges for researchers due to the need to preprocess and convert data into a matrix format. During our research, we observed that clinical informatics literature does not provide guidance for researchers on how to build this matrix while avoiding potential pitfalls.Objectives This article aims to provide researchers a roadmap of the main technical challenges of preprocessing structured EHR data and possible strategies to overcome them.Methods Along standard data processing stages – extracting database entries, defining features, processing data, assessing feature values and integrating data elements, within an EDPAI framework –, we identified the main challenges faced by researchers and reflect on how to address those challenges based on lessons learned from our research experience and on best practices from related literature. We highlight the main potential sources of error, present strategies to approach those challenges and discuss implications of these strategies.Results Following the EDPAI framework, researchers face five key challenges: (1) gathering and integrating data, (2) identifying and handling different feature types, (3) combining features to handle redundancy and granularity, (4) addressing data missingness, and (5) handling multiple feature values. Strategies to address these challenges include: crosschecking identifiers for robust data retrieval and integration; applying clinical knowledge in identifying feature types, in addressing redundancy and granularity, and in accommodating multiple feature values; and investigating missing patterns adequately.Conclusions This article contributes to literature by providing a roadmap to inform structured EHR data preprocessing. It may advise researchers on potential pitfalls and implications of methodological decisions in handling structured data, so as to avoid biases and help realize the benefits of the secondary use of EHR data.Citation: Ferrão JC, Oliveira MD, Janela F, Martins HMG. Preprocessing structured clinical data for predictive modeling and decision support – a roadmap to tackle the challenges.

Motivation Pedigree analysis is a longstanding and powerful approach to gain insight into the underlying genetic factors in human health, but identifying, recruiting and genotyping families can be difficult, time consuming and costly. Development of high throughput methods to identify families and foster downstream analyses are necessary. Results This paper describes simple methods that allowed us to identify 173 368 family pedigrees with high probability using basic demographic data available in most electronic health records (EHRs). We further developed and validate a novel statistical method that uses EHR data to identify families more likely to have a major genetic component to their diseases risk. Lastly, we showed that incorporating EHR-linked family data into genetic association testing may provide added power for genetic mapping without additional recruitment or genotyping. The totality of these results suggests that EHR-linked families can enable classical genetic analyses in a high-throughput manner. Availability and implementation Pseudocode is provided as supplementary information Supplementary information Supplementary data are available at Bioinformatics online.

Motivation: Metabolic and signaling pathways are an increasingly important part of organizing knowledge in systems biology. They serve to integrate collective interpretations of facts scattered throughout literature. Biologists construct a pathway by reading a large number of articles and interpreting them as a consistent network, but most of the models constructed currently lack direct links to those articles. Biologists who want to check the original articles have to spend substantial amounts of time to collect relevant articles and identify the sections relevant to the pathway. Furthermore, with the scientific literature expanding by several thousand papers per week, keeping a model relevant requires a continuous curation effort. In this article, we present a system designed to integrate a pathway visualizer, text mining systems and annotation tools into a seamless environment. This will enable biologists to freely move between parts of a pathway and relevant sections of articles, as well as identify relevant papers from large text bases. The system, PathText, is developed by Systems Biology Institute, Okinawa Institute of Science and Technology, National Centre for Text Mining (University of Manchester) and the University of Tokyo, and is being used by groups of biologists from these locations. Contact: brian@monrovian.com.

Background: The language encompassing health conditions can also influence behaviors that affect health outcomes. Few published quantitative studies have been conducted that evaluate HIV-related terminology changes over time. To expand this research, this study included an analysis of a dataset of abstracts presented at the International AIDS Conference (IAC) from 1989 to 2014. These abstracts reflect the global response to HIV over 25 years. Two powerful methodologies were used to evaluate the dataset: text mining to convert the unstructured information into structured data for analysis and data visualization to represent the data visually to assess trends. Objective: The purpose of this project was to evaluate the evolving use of HIV-related language in abstracts presented at the IAC from 1989 to 2014. Methods: Over 80,000 abstracts were obtained from the International AIDS Society and imported into a Microsoft SQL Server database for data processing and text mining analyses. A text mining module within the KNIME Analytics Platform, an open source software, was then used to mine the partially processed data to create a terminology corpus of key HIV terms. Subject matter experts grouped the terms into categories. Tableau, a data visualization software, was used to visualize the frequency metrics associated with the terms as line graphs and word clouds. The visualized dashboards were reviewed to discern changes in terminology use across IAC years. Results: The major findings identify trends in HIV-related terminology over 25 years. The term “AIDS epidemic” was dominantly used from 1989 to 1991 and then declined in use. In contrast, use of the term “HIV epidemic” increased through 2014. Beginning in the mid-1990s, the term “treatment experienced” appeared with increasing frequency in the abstracts. Use of terms identifying individuals as “carriers or victims” of HIV rarely appeared after 2008. Use of the terms “HIV positive” and “HIV infected” peaked in the early-1990s and then declined in use. The terms “men who have sex with men” and “MSM” were rarely used until 1994; subsequently, use of these terms increased through 2014. The term “sex worker” steadily increased in frequency throughout conference years, whereas the term “prostitute” decreased over time. Conclusions: The results of this study highlight changes in HIV terminology use over 25 years, including the addition, disappearance, and changing use of terms that reflect advances in HIV research and medical practice and destigmatization of the disease. Coupled with findings from related quantitative research, HIV-related terminology recommendations based on results of this study are included. Adoption of these recommendations will further efforts to use less stigmatizing language and facilitate effective communication between health professionals and people affected by HIV. [JMIR Public Health Surveill 2018;4(2):e50]

Precision medicine will revolutionize the way we treat and prevent disease. A major barrier to the implementation of precision medicine that clinicians and translational scientists face is understanding the underlying mechanisms of disease. We are starting to address this challenge through automatic approaches for information extraction, representation and analysis. Recent advances in text and data mining have been applied to a broad spectrum of key biomedical questions in genomics, pharmacogenomics and other fields. We present an overview of the fundamental methods for text and data mining, as well as recent advances and emerging applications toward precision medicine.

Motivation: Deep sequencing of clinical samples is now an established tool for the detection of infectious pathogens, with direct medical applications. The large amount of data generated produces an opportunity to detect species even at very low levels, provided that computational tools can effectively profile the relevant metagenomic communities. Data interpretation is complicated by the fact that short sequencing reads can match multiple organisms and by the lack of completeness of existing databases, in particular for viral pathogens. Here we present metaMix, a Bayesian mixture model framework for resolving complex metagenomic mixtures. We show that the use of parallel Monte Carlo Markov chains for the exploration of the species space enables the identification of the set of species most likely to contribute to the mixture. Results: We demonstrate the greater accuracy of metaMix compared with relevant methods, particularly for profiling complex communities consisting of several related species. We designed metaMix specifically for the analysis of deep transcriptome sequencing datasets, with a focus on viral pathogen detection; however, the principles are generally applicable to all types of metagenomic mixtures. Availability and implementation: metaMix is implemented as a user friendly R package, freely available on CRAN: http://cran.r-project.org/web/packages/metaMix Contact: sofia.morfopoulou.10@ucl.ac.uk Supplementary information: Supplementary data are available at Bionformatics online.

The use of crowdsourcing to solve important but complex problems in biomedical and clinical sciences is growing and encompasses a wide variety of approaches. The crowd is diverse and includes online marketplace workers, health information seekers, science enthusiasts and domain experts. In this article, we review and highlight recent studies that use crowdsourcing to advance biomedicine. We classify these studies into two broad categories: (i) mining big data generated from a crowd (e.g. search logs) and (ii) active crowdsourcing via specific technical platforms, e.g. labor markets, wikis, scientific games and community challenges. Through describing each study in detail, we demonstrate the applicability of different methods in a variety of domains in biomedical research, including genomics, biocuration and clinical research. Furthermore, we discuss and highlight the strengths and limitations of different crowdsourcing platforms. Finally, we identify important emerging trends, opportunities and remaining challenges for future crowdsourcing research in biomedicine.

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.

Background: An ongoing challenge for smart homes research for aging-in-place is how to make sense of the large amounts of data from in-home sensors to facilitate real-time monitoring and develop reliable alerts. Objective: The objective of our study was to explore the usefulness of a routine-based approach for making sense of smart home data for the elderly. Methods: Maximum variation sampling was used to select three cases for an in-depth mixed methods exploration of the daily routines of three elderly participants in a smart home trial using 180 days of power use and motion sensor data and longitudinal interview data. Results: Sensor data accurately matched self-reported routines. By comparing daily movement data with personal routines, it was possible to identify changes in routine that signaled illness, recovery from bereavement, and gradual deterioration of sleep quality and daily movement. Interview and sensor data also identified changes in routine with variations in temperature and daylight hours. Conclusions: The findings demonstrated that a routine-based approach makes interpreting sensor data easy, intuitive, and transparent. They highlighted the importance of understanding and accounting for individual differences in preferences for routinization and the influence of the cyclical nature of daily routines, social or cultural rhythms, and seasonal changes in temperature and daylight hours when interpreting information based on sensor data. This research has demonstrated the usefulness of a routine-based approach for making sense of smart home data, which has furthered the understanding of the challenges that need to be addressed in order to make real-time monitoring and effective alerts a reality. [JMIR Mhealth Uhealth 2017;5(6):e52]

Drug-drug interactions (DDIs) constitute an important concern in drug development and postmarketing pharmacovigilance. They are considered the cause of many adverse drug effects exposing patients to higher risks and increasing public health system costs. Methods to follow-up and discover possible DDIs causing harm to the population are a primary aim of drug safety researchers. Here, we review different methodologies and recent advances using data mining to detect DDIs with impact on patients. We focus on data mining of different pharmacovigilance sources, such as the US Food and Drug Administration Adverse Event Reporting System and electronic health records from medical institutions, as well as on the diverse data mining studies that use narrative text available in the scientific biomedical literature and social media. We pay attention to the strengths but also further explain challenges related to these methods. Data mining has important applications in the analysis of DDIs showing the impact of the interactions as a cause of adverse effects, extracting interactions to create knowledge data sets and gold standards and in the discovery of novel and dangerous DDIs.

The dual role of the Protein Data Bank as a repository of all macromolecular structures and as the major source of structural metadata for further analysis is discussed and suggestions are made on how to identify models that contain errors and could potentially degrade the quality of meta analyses., Whereas the vast majority of the more than 85 000 crystal structures of macromolecules currently deposited in the Protein Data Bank are of high quality, some suffer from a variety of imperfections. Although this fact has been pointed out in the past, it is still worth periodic updates so that the metadata obtained by global analysis of the available crystal structures, as well as the utilization of the individual structures for tasks such as drug design, should be based on only the most reliable data. Here, selected abnormal deposited structures have been analysed based on the Bayesian reasoning that the correctness of a model must be judged against both the primary evidence as well as prior knowledge. These structures, as well as information gained from the corresponding publications (if available), have emphasized some of the most prevalent types of common problems. The errors are often perfect illustrations of the nature of human cognition, which is frequently influenced by preconceptions that may lead to fanciful results in the absence of proper validation. Common errors can be traced to negligence and a lack of rigorous verification of the models against electron density, creation of non-parsimonious models, generation of improbable numbers, application of incorrect symmetry, illogical presentation of the results, or violation of the rules of chemistry and physics. Paying more attention to such problems, not only in the final validation stages but during the structure-determination process as well, is necessary not only in order to maintain the highest possible quality of the structural repositories and databases but most of all to provide a solid basis for subsequent studies, including large-scale data-mining projects. For many scientists PDB deposition is a rather infrequent event, so the need for proper training and supervision is emphasized, as well as the need for constant alertness of reason and critical judgment as absolutely necessary safeguarding measures against such problems. Ways of identifying more problematic structures are suggested so that their users may be properly alerted to their possible shortcomings.

openaire: EC/H2020/662725/EU//IBSEN Background: Mental and behavioral disorders are the main cause of disability worldwide. However, their diagnosis is challenging due to a lack of reliable biomarkers; current detection is based on structured clinical interviews which can be biased by the patient’s recall ability, affective state, changing in temporal frames, etc. While digital platforms have been introduced as a possible solution to this complex problem, there is little evidence on the extent of usability and usefulness of these platforms. Therefore, more studies where digital data is collected in larger scales are needed to collect scientific evidence on the capacities of these platforms. Most of the existing platforms for digital psychiatry studies are designed as monolithic systems for a certain type of study; publications from these studies focus on their results, rather than the design features of the data collection platform. Inevitably, more tools and platforms will emerge in the near future to fulfill the need for digital data collection for psychiatry. Currently little knowledge is available from existing digital platforms for future data collection platforms to build upon. Objective: The objective of this work was to identify the most important features for designing a digital platform for data collection for mental health studies, and to demonstrate a prototype platform that we built based on these design features. Methods: We worked closely in a multidisciplinary collaboration with psychiatrists, software developers, and data scientists and identified the key features which could guarantee short-term and long-term stability and usefulness of the platform from the designing stage to data collection and analysis of collected data. Results: The key design features that we identified were flexibility of access control, flexibility of data sources, and first-order privacy protection. We also designed the prototype platform Non-Intrusive Individual Monitoring Architecture (Niima), where we implemented these key design features. We described why each of these features are important for digital data collection for psychiatry, gave examples of projects where Niima was used or is going to be used in the future, and demonstrated how incorporating these design principles opens new possibilities for studies. Conclusions: The new methods of digital psychiatry are still immature and need further research. The design features we suggested are a first step to design platforms which can adapt to the upcoming requirements of digital psychiatry.