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Objective: We report the development of the patient-centered myAURA application and suite of methods designed to aid epilepsy patients, caregivers, and researchers in making decisions about care and self-management. Materials and Methods: myAURA rests on the federation of an unprecedented collection of heterogeneous data resources relevant to epilepsy, such as biomedical databases, social media, and electronic health records. A generalizable, open-source methodology was developed to compute a multi-layer knowledge graph linking all this heterogeneous data via the terms of a human-centered biomedical dictionary. Results: The power of the approach is first exemplified in the study of the drug-drug interaction phenomenon. Furthermore, we employ a novel network sparsification methodology using the metric backbone of weighted graphs, which reveals the most important edges for inference, recommendation, and visualization, such as pharmacology factors patients discuss on social media. The network sparsification approach also allows us to extract focused digital cohorts from social media whose discourse is more relevant to epilepsy or other biomedical problems. Finally, we present our patient-centered design and pilot-testing of myAURA, including its user interface, based on focus groups and other stakeholder input. Discussion: The ability to search and explore myAURA's heterogeneous data sources via a sparsified multi-layer knowledge graph, as well as the combination of those layers in a single map, are useful features for integrating relevant information for epilepsy. Conclusion: Our stakeholder-driven, scalable approach to integrate traditional and non-traditional data sources, enables biomedical discovery and data-powered patient self-management in epilepsy, and is generalizable to other chronic conditions.

Coordinated collaboration is essential to realize the added value of and infrastructure requirements for global image data sharing in the life sciences. In this White Paper, we take a first step at presenting some of the most common use cases as well as critical/emerging use cases of (including the use of artificial intelligence for) biological and medical image data, which would benefit tremendously from better frameworks for sharing (including technical, resourcing, legal, and ethical aspects). In the second half of this paper, we paint an ideal world scenario for how global image data sharing could work and benefit all life sciences and beyond. As this is still a long way off, we conclude by suggesting several concrete measures directed toward our institutions, existing imaging communities and data initiatives, and national funders, as well as publishers. Our vision is that within the next ten years, most researchers in the world will be able to make their datasets openly available and use quality image data of interest to them for their research and benefit. This paper is published in parallel with a companion White Paper entitled Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data, which addresses challenges and opportunities related to producing well-documented and high-quality image data that is ready to be shared. The driving goal is to address remaining challenges and democratize access to everyday practices and tools for a spectrum of biomedical researchers, regardless of their expertise, access to resources, and geographical location., Comment: This manuscript (arXiv:2401.13023) is published with a closely related companion entitled, Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data, which can be found at the following link, arXiv:2401.13022

Large tree structures are ubiquitous and real-world relational datasets often have information associated with nodes (e.g., labels or other attributes) and edges (e.g., weights or distances) that need to be communicated to the viewers. Yet, scalable, easy to read tree layouts are difficult to achieve. We consider tree layouts to be readable if they meet some basic requirements: node labels should not overlap, edges should not cross, edge lengths should be preserved, and the output should be compact. There are many algorithms for drawing trees, although very few take node labels or edge lengths into account, and none optimizes all requirements above. With this in mind, we propose a new scalable method for readable tree layouts. The algorithm guarantees that the layout has no edge crossings and no label overlaps, and optimizes one of the remaining aspects: desired edge lengths and compactness. We evaluate the performance of the new algorithm by comparison with related earlier approaches using several real-world datasets, ranging from a few thousand nodes to hundreds of thousands of nodes. Tree layout algorithms can be used to visualize large general graphs, by extracting a hierarchy of progressively larger trees. We illustrate this functionality by presenting several map-like visualizations generated by the new tree layout algorithm.

Objective: Ubiquitous internet access is reshaping the way we live, but it is accompanied by unprecedented challenges in preventing chronic diseases that are usually planted by long exposure to unhealthy lifestyles. This paper proposes leveraging online shopping behaviors as a proxy for personal lifestyle choices to improve chronic disease prevention literacy, targeted for times when e-commerce user experience has been assimilated into most people's everyday lives. Methods: Longitudinal query logs and purchase records from 15 million online shoppers were accessed, constructing a broad spectrum of lifestyle features covering various product categories and buyer personas. Using the lifestyle-related information preceding online shoppers' first purchases of specific prescription drugs, we could determine associations between their past lifestyle choices and whether they suffered from a particular chronic disease. Results: Novel lifestyle risk factors were discovered in two exemplars--depression and type 2 diabetes, most of which showed reasonable consistency with existing healthcare knowledge. Further, such empirical findings could be adopted to locate online shoppers at higher risk of these chronic diseases with decent accuracy [i.e., (area under the receiver operating characteristic curve) AUC=0.68 for depression and AUC=0.70 for type 2 diabetes], closely matching the performance of screening surveys benchmarked against medical diagnosis. Conclusions: Mining online shopping behaviors can point medical experts to a series of lifestyle issues associated with chronic diseases that are less explored to date. Hopefully, unobtrusive chronic disease surveillance via e-commerce sites can grant consenting individuals a privilege to be connected more readily with the medical profession and sophistication., Comment: 58 pages with appendices, 5 figures, 17 tables

Responding to the U.S. opioid crisis requires a holistic approach supported by evidence from linking and analyzing multiple data sources. This paper discusses how 20 available resources can be combined to answer pressing public health questions related to the crisis. It presents a network view based on U.S. geographical units and other standard concepts, crosswalked to communicate the coverage and interlinkage of these resources. These opioid-related datasets can be grouped by four themes: (1) drug prescriptions, (2) opioid related harms, (3) opioid treatment workforce, jobs, and training, and (4) drug policy. An interactive network visualization was created and is freely available online; it lets users explore key metadata, relevant scholarly works, and data interlinkages in support of informed decision making through data analysis., Comment: Draft for Preventive Medicine Report Journal

Effective adoption of online platforms for teaching, learning, and skill development is essential to both academic institutions and workplaces. Adoption of online learning has been abruptly accelerated by COVID19 pandemic, drawing attention to research on pedagogy and practice for effective online instruction. Online learning requires a multitude of skills and resources spanning from learning management platforms to interactive assessment tools, combined with multimedia content, presenting challenges to instructors and organizations. This study focuses on ways that learning sciences and visual learning analytics can be used to design, and to improve, online workforce training in advanced manufacturing. Scholars and industry experts, educational researchers, and specialists in data analysis and visualization collaborated to study the performance of a cohort of 900 professionals enrolled in an online training course focused on additive manufacturing. The course was offered through MITxPro, MIT Open Learning is a professional learning organization which hosts in a dedicated instance of the edX platform. This study combines learning objective analysis and visual learning analytics to examine the relationships among learning trajectories, engagement, and performance. The results demonstrate how visual learning analytics was used for targeted course modification, and interpretation of learner engagement and performance, such as by more direct mapping of assessments to learning objectives, and to expected and actual time needed to complete each segment of the course. The study also emphasizes broader strategies for course designers and instructors to align course assignments, learning objectives, and assessment measures with learner needs and interests, and argues for a synchronized data infrastructure to facilitate effective just in time learning and continuous improvement of online courses., Comment: 36 pages, 5 figures

The National Institutes of Health's (NIH) Human Biomolecular Atlas Program (HuBMAP) aims to create a comprehensive high-resolution atlas of all the cells in the healthy human body. Multiple laboratories across the United States are collecting tissue specimens from different organs of donors who vary in sex, age, and body size. Integrating and harmonizing the data derived from these samples and 'mapping' them into a common three-dimensional (3D) space is a major challenge. The key to making this possible is a 'Common Coordinate Framework' (CCF), which provides a semantically annotated, 3D reference system for the entire body. The CCF enables contributors to HuBMAP to 'register' specimens and datasets within a common spatial reference system, and it supports a standardized way to query and 'explore' data in a spatially and semantically explicit manner. [...] This paper describes the construction and usage of a CCF for the human body and its reference implementation in HuBMAP. The CCF consists of (1) a CCF Clinical Ontology, which provides metadata about the specimen and donor (the 'who'); (2) a CCF Semantic Ontology, which describes 'what' part of the body a sample came from and details anatomical structures, cell types, and biomarkers (ASCT+B); and (3) a CCF Spatial Ontology, which indicates 'where' a tissue sample is located in a 3D coordinate system. An initial version of all three CCF ontologies has been implemented for the first HuBMAP Portal release. It was successfully used by Tissue Mapping Centers to semantically annotate and spatially register 48 kidney and spleen tissue blocks. The blocks can be queried and explored in their clinical, semantic, and spatial context via the CCF user interface in the HuBMAP Portal., Comment: 24 pages with SI, 6 figures, 5 tables

How does your education impact your professional career? Ideally, the courses you take help you identify, get hired for, and perform the job you always wanted. However, not all courses provide skills that transfer to existing and future jobs; skill terms used in course descriptions might be different from those listed in job advertisements; and there might exist a considerable skill gap between what is taught in courses and what is needed for a job. In this study, we propose a novel method to integrate extensive course description and job advertisement data by leveraging heterogeneous data integration and community detection. The innovative heterogeneous graph approach along with identified skill communities enables cross-domain information recommendation, e.g., given an educational profile, job recommendations can be provided together with suggestions on education opportunities for re- and upskilling in support of lifelong learning., Comment: 6 pages, 1 figure, 2 tables

Understanding the emergence, co-evolution, and convergence of science and technology (S&T) areas offers competitive intelligence for researchers, managers, policy makers, and others. The resulting data-driven decision support helps set proper research and development (R&D) priorities; develop future S&T investment strategies; monitor key authors, organizations, or countries; perform effective research program assessment; and implement cutting-edge education/training efforts. This paper presents new funding, publication, and scholarly network metrics and visualizations that were validated via expert surveys. The metrics and visualizations exemplify the emergence and convergence of three areas of strategic interest: artificial intelligence (AI), robotics, and internet of things (IoT) over the last 20 years (1998-2017). For 32,716 publications and 4,497 NSF awards, we identify their conceptual space (using the UCSD map of science), geospatial network, and co-evolution landscape. The findings demonstrate how the transition of knowledge (through cross-discipline publications and citations) and the emergence of new concepts (through term bursting) create a tangible potential for interdisciplinary research and new disciplines., Comment: 10 figures

The days that precede Valentine's Day are characterized by extensive gift shopping activities all across the globe. In China, where much shopping takes place online, there has been an explosive growth in e-commerce sales during Valentine's Day over the recent years. This exploratory study investigates the extent to which each product category and each shopper group can exhibit romantic love within China's e-market throughout the 2 weeks leading up to 2019 Valentine's Day. Massive data from Alibaba, the biggest e-commerce retailer worldwide, are utilized to formulate an innovative romance index (RI) to quantitatively measure e-romantic values for products and shoppers. On this basis, millions of shoppers, along with their millions of products purchased around Valentine's Day, are analyzed as a case study to demonstrate their love consumption and romantic gift-giving. The results of the analysis are then illustrated to help understand Chinese e-romance based on the perspectives of different product categories and shopper groups. This empirical information visualization also contributes to improving the segmentation, targeting, and positioning of China's e-market for Valentine's Day., Comment: 14 pages, 3 figures, 3 tables

Several ongoing international efforts are developing methods of localizing single cells within organs or mapping the entire human body at the single cell level, including the Chan Zuckerberg Initiative's Human Cell Atlas (HCA), and the Knut and Allice Wallenberg Foundation's Human Protein Atlas (HPA), and the National Institutes of Health's Human BioMolecular Atlas Program (HuBMAP). Their goals are to understand cell specialization, interactions, spatial organization in their natural context, and ultimately the function of every cell within the body. In the same way that the Human Genome Project had to assemble sequence data from different people to construct a complete sequence, multiple centers around the world are collecting tissue specimens from a diverse population that varies in age, race, sex, and body size. A challenge will be combining these heterogeneous tissue samples into a 3D reference map that will enable multiscale, multidimensional Google Maps-like exploration of the human body. Key to making alignment of tissue samples work is identifying and using a coordinate system called a Common Coordinate Framework (CCF), which defines the positions, or "addresses", in a reference body, from whole organs down to functional tissue units and individual cells. In this perspective, we examine the concept of a CCF based on the vasculature and describe why it would be an attractive choice for mapping the human body., Comment: 8 pages, 2 figures

Effective treatment strategies exist for substance use disorder (SUD), however severe hurdles remain in ensuring adequacy of the SUD treatment (SUDT) workforce as well as improving SUDT affordability, access and stigma. Although evidence shows recent increases in SUD medication access from expanding Medicaid availability under the Affordable Care Act, it is yet unknown whether these policies also led to a growth in the changes in the nature of hiring in SUDT related workforce, partly due to poor data availability. Our study uses novel data to shed light on recent trends in a fast-evolving and policy-relevant labor market, and contributes to understanding the current SUDT related workforce and the effect of Medicaid expansion on hiring attempts in this sector. We examine attempts over 2010-2018 at hiring in the SUDT and related behavioral health sector as background for estimating the causal effect of the 2014-and-beyond state Medicaid expansion on these outcomes through "difference-in-difference" econometric models. We use Burning Glass Technologies (BGT) data covering virtually all U.S. job postings by employers. Nationally, we find little growth in the sector's hiring attempts in 2010-2018 relative to the rest of the economy or to health care as a whole. However, this masks diverging trends in subsectors, which saw reduction in hospital based hiring attempts, increases towards outpatient facilities, and changes in occupational hiring demand shifting from medical personnel towards counselors and social workers. Although Medicaid expansion did not lead to any statistically significant or meaningful change in overall hiring attempts, there was a shift in the hiring landscape., Comment: 7 figures, 20 pages

Human subject studies that map-like visualizations are as good or better than standard node-link representations of graphs, in terms of task performance, memorization and recall of the underlying data, and engagement [SSKB14, SSKB15]. With this in mind, we propose the Zoomable Multi-Level Tree (ZMLT) algorithm for multi-level tree-based, map-like visualization of large graphs. We propose seven desirable properties that such visualization should maintain and an algorithm that accomplishes them. (1) The abstract trees represent the underlying graph appropriately at different level of details; (2) The embedded trees represent the underlying graph appropriately at different levels of details; (3) At every level of detail we show real vertices and real paths from the underlying graph; (4) If any node or edge appears in a given level, then they also appear in all deeper levels; (5) All nodes at the current level and higher levels are labeled and there are no label overlaps; (6) There are no edge crossings on any level; (7) The drawing area is proportional to the total area of the labels. This algorithm is implemented and we have a functional prototype for the interactive interface in a web browser.

Transformative technologies are enabling the construction of three dimensional (3D) maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, consortia, and the biomedical research community at large towards the shared vision of a comprehensive, accessible 3D molecular and cellular atlas of the human body, in health and various disease settings., Comment: 20 pages, 3 figures

We show how faceted search using a combination of traditional classification systems and mixed-membership topic models can go beyond keyword search to inform resource discovery, hypothesis formulation, and argument extraction for interdisciplinary research. Our test domain is the history and philosophy of scientific work on animal mind and cognition. The methods can be generalized to other research areas and ultimately support a system for semi-automatic identification of argument structures. We provide a case study for the application of the methods to the problem of identifying and extracting arguments about anthropomorphism during a critical period in the development of comparative psychology. We show how a combination of classification systems and mixed-membership models trained over large digital libraries can inform resource discovery in this domain. Through a novel approach of "drill-down" topic modeling---simultaneously reducing both the size of the corpus and the unit of analysis---we are able to reduce a large collection of fulltext volumes to a much smaller set of pages within six focal volumes containing arguments of interest to historians and philosophers of comparative psychology. The volumes identified in this way did not appear among the first ten results of the keyword search in the HathiTrust digital library and the pages bear the kind of "close reading" needed to generate original interpretations that is the heart of scholarly work in the humanities. Zooming back out, we provide a way to place the books onto a map of science originally constructed from very different data and for different purposes. The multilevel approach advances understanding of the intellectual and societal contexts in which writings are interpreted., Comment: revised, 29 pages, 3 figures

Notions of community quality underlie network clustering. While studies surrounding network clustering are increasingly common, a precise understanding of the realtionship between different cluster quality metrics is unknown. In this paper, we examine the relationship between stand-alone cluster quality metrics and information recovery metrics through a rigorous analysis of four widely-used network clustering algorithms -- Louvain, Infomap, label propagation, and smart local moving. We consider the stand-alone quality metrics of modularity, conductance, and coverage, and we consider the information recovery metrics of adjusted Rand score, normalized mutual information, and a variant of normalized mutual information used in previous work. Our study includes both synthetic graphs and empirical data sets of sizes varying from 1,000 to 1,000,000 nodes. We find significant differences among the results of the different cluster quality metrics. For example, clustering algorithms can return a value of 0.4 out of 1 on modularity but score 0 out of 1 on information recovery. We find conductance, though imperfect, to be the stand-alone quality metric that best indicates performance on information recovery metrics. Our study shows that the variant of normalized mutual information used in previous work cannot be assumed to differ only slightly from traditional normalized mutual information. Smart local moving is the best performing algorithm in our study, but discrepancies between cluster evaluation metrics prevent us from declaring it absolutely superior. Louvain performed better than Infomap in nearly all the tests in our study, contradicting the results of previous work in which Infomap was superior to Louvain. We find that although label propagation performs poorly when clusters are less clearly defined, it scales efficiently and accurately to large graphs with well-defined clusters.

Public agencies like the U.S. National Science Foundation (NSF) and the National Institutes of Health (NIH) award tens of billions of dollars in annual science funding. How can this money be distributed as efficiently as possible to best promote scientific innovation and productivity? The present system relies primarily on peer review of project proposals. In 2010 alone, NSF convened more than 15,000 scientists to review 55,542 proposals. Although considered the scientific gold standard, peer review requires significant overhead costs, and may be subject to biases, inconsistencies, and oversights. We investigate a class of funding models in which all participants receive an equal portion of yearly funding, but are then required to anonymously donate a fraction of their funding to peers. The funding thus flows from one participant to the next, each acting as if he or she were a funding agency themselves. Here we show through a simulation conducted over large-scale citation data (37M articles, 770M citations) that such a distributed system for science may yield funding patterns similar to existing NIH and NSF distributions, but may do so at much lower overhead while exhibiting a range of other desirable features. Self-correcting mechanisms in scientific peer evaluation can yield an efficient and fair distribution of funding. The proposed model can be applied in many situations in which top-down or bottom-up allocation of public resources is either impractical or undesirable, e.g. public investments, distribution chains, and shared resource management., Comment: main paper: 7 pages, excl. references + supplemental materials (9), 4 figures

The study of science at the individual micro-level frequently requires the disambiguation of author names. The creation of author's publication oeuvres involves matching the list of unique author names to names used in publication databases. Despite recent progress in the development of unique author identifiers, e.g., ORCID, VIVO, or DAI, author disambiguation remains a key problem when it comes to large-scale bibliometric analysis using data from multiple databases. This study introduces and validates a new methodology called seed+expand for semi-automatic bibliographic data collection for a given set of individual authors. Specifically, we identify the oeuvre of a set of Dutch full professors during the period 1980-2011. In particular, we combine author records from the National Research Information System (NARCIS) with publication records from the Web of Science. Starting with an initial list of 8,378 names, we identify "seed publications" for each author using five different approaches. Subsequently, we "expand" the set of publication in three different approaches. The different approaches are compared and resulting oeuvres are evaluated on precision and recall using a "gold standard" dataset of authors for which verified publications in the period 2001-2010 are available., Comment: Paper accepted for the ISSI 2013, small changes in the text due to referee comments, one figure added (Fig 3)