We introduce a new dataset, MELINDA, for Multimodal biomEdicaL experImeNt methoD clAssification. The dataset is collected in a fully automated distant supervision manner, where the labels are obtained from an existing curated database, and the actual contents are extracted from papers associated with each of the records in the database. We benchmark various state-of-the-art NLP and computer vision models, including unimodal models which only take either caption texts or images as inputs, and multimodal models. Extensive experiments and analysis show that multimodal models, despite outperforming unimodal ones, still need improvements especially on a less-supervised way of grounding visual concepts with languages, and better transferability to low resource domains. We release our dataset and the benchmarks to facilitate future research in multimodal learning, especially to motivate targeted improvements for applications in scientific domains.

Evidence plays a crucial role in any biomedical research narrative, providing justification for some claims and refutation for others.We seek to build models of scientific argument using information extraction methods from fulltext papers.We present the capability of automatically extracting text fragments from primary research papers that describe the evidence presented in that paper's figures, which arguably provides the raw material of any scientific argument made within the paper.We apply richly contextualized deep representation learning pre-trained on biomedical domain corpus to the analysis of scientific discourse structures and the extraction of "evidence fragments" (i.e., the text in the results section describing data presented in a specified subfigure) from a set of biomedical experimental research articles.We first demonstrate our state-of-the-art scientific discourse tagger on two scientific discourse tagging datasets and its transferability to new datasets.We then show the benefit of leveraging scientific discourse tags for downstream tasks such as claim-extraction and evidence fragment detection.Our work demonstrates the potential of using evidence fragments derived from figure spans for improving the quality of scientific claims by cataloging, indexing and reusing evidence fragments as independent documents.

The availability of massive datasets in genetics, neuroimaging, mobile health, and other subfields of biology and medicine promises new insights but also poses significant challenges. To realize the potential of big data in biomedicine, the National Institutes of Health launched the Big Data to Knowledge (BD2K) initiative, funding several centers of excellence in biomedical data analysis and a Training Coordinating Center (TCC) tasked with facilitating online and inperson training of biomedical researchers in data science. A major initiative of the BD2K TCC is to automatically identify, describe, and organize data science training resources available on the Web and provide personalized training paths for users. In this paper, we describe the construction of ERuDIte, the Educational Resource Discovery Index for Data Science, and its release as linked data. ERuDIte contains over 11,000 training resources including courses, video tutorials, conference talks, and other materials. The metadata for these resources is described uniformly using Schema.org. We use machine learning techniques to tag each resource with concepts from the Data Science Education Ontology, which we developed to further describe resource content. Finally, we map references to people and organizations in learning resources to entities in DBpedia, DBLP, and ORCID, embedding our collection in the web of linked data. We hope that ERuDIte will provide a framework to foster open linked educational resources on the Web.

Published scientific figure is a valuable information resource, but often occur as composite images. The ImageCLEF meeting presented a shared evaluation in 2016 to use machine learning to split these composite figures into components automatically. We adapted an existing high-performance object detection method to analyze the substructure of published biomedical figures by developing a novel multi-branch output convolution neural network to predict irregular panel layouts and provide augmented training data to drive learning. Our system has an accuracy of 86.8% on the 2016 ImageCLEF Medical dataset and 83.1% on a new dataset derived from open access papers from the INTACT database of molecular interactions.

Our goal is to generate reading lists for students that help them optimally learn technical material.Existing retrieval algorithms return items directly relevant to a query but do not return results to help users read about the concepts supporting their query.This is because the dependency structure of concepts that must be understood before reading material pertaining to a given query is never considered.Here we formulate an information-theoretic view of concept dependency and present methods to construct a "concept graph" automatically from a text corpus.We perform the first human evaluation of concept dependency edges (to be published as open data), and the results verify the feasibility of automatic approaches for inferring concepts and their dependency relations.This result can support search capabilities that may be tuned to help users learn a subject rather than retrieve documents based on a single query.

BACKGROUND: We address the goal of curating observations from published experiments in a generalizable form; reasoning over these observations to generate interpretations and then querying this interpreted knowledge to supply the supporting evidence. We present web-application software as part of the 'BioScholar' project (R01-GM083871) that fully instantiates this process for a well-defined domain: using tract-tracing experiments to study the neural connectivity of the rat brain. RESULTS: The main contribution of this work is to provide the first instantiation of a knowledge representation for experimental observations called 'Knowledge Engineering from Experimental Design' (KEfED) based on experimental variables and their interdependencies. The software has three parts: (a) the KEfED model editor - a design editor for creating KEfED models by drawing a flow diagram of an experimental protocol; (b) the KEfED data interface - a spreadsheet-like tool that permits users to enter experimental data pertaining to a specific model; (c) a 'neural connection matrix' interface that presents neural connectivity as a table of ordinal connection strengths representing the interpretations of tract-tracing data. This tool also allows the user to view experimental evidence pertaining to a specific connection. BioScholar is built in Flex 3.5. It uses Persevere (a noSQL database) as a flexible data store and PowerLoom® (a mature First Order Logic reasoning system) to execute queries using spatial reasoning over the BAMS neuroanatomical ontology. CONCLUSIONS: We first introduce the KEfED approach as a general approach and describe its possible role as a way of introducing structured reasoning into models of argumentation within new models of scientific publication. We then describe the design and implementation of our example application: the BioScholar software. This is presented as a possible biocuration interface and supplementary reasoning toolkit for a larger, more specialized bioinformatics system: the Brain Architecture Management System (BAMS).

OBJECTIVE: As biomedical technology becomes increasingly sophisticated, researchers can probe ever more subtle effects with the added requirement that the investigation of small effects often requires the acquisition of large amounts of data. In biomedicine, these data are often acquired at, and later shared between, multiple sites. There are both technological and sociological hurdles to be overcome for data to be passed between researchers and later made accessible to the larger scientific community. The goal of the Biomedical Informatics Research Network (BIRN) is to address the challenges inherent in biomedical data sharing. MATERIALS AND METHODS: BIRN tools are grouped into 'capabilities' and are available in the areas of data management, data security, information integration, and knowledge engineering. BIRN has a user-driven focus and employs a layered architectural approach that promotes reuse of infrastructure. BIRN tools are designed to be modular and therefore can work with pre-existing tools. BIRN users can choose the capabilities most useful for their application, while not having to ensure that their project conforms to a monolithic architecture. RESULTS: BIRN has implemented a new software-based data-sharing infrastructure that has been put to use in many different domains within biomedicine. BIRN is actively involved in outreach to the broader biomedical community to form working partnerships. CONCLUSION: BIRN's mission is to provide capabilities and services related to data sharing to the biomedical research community. It does this by forming partnerships and solving specific, user-driven problems whose solutions are then available for use by other groups.

This paper presents a technical description of the methods used to generate an interactive, two-dimensional visualization of 60,568 grants funded by the National Institutes of Health in 2007. The visualization is made intelligible by providing interactive features for assessing the data in a web-based visual browser, see http://www.nihmaps.org. The key features include deep zooming, selection, full-text querying, overlays, color-coding schemes, and multi-level labeling. Major insights, broader applicability, and future directions are discussed.

Curating information from the literature for storage in databases is a crucial task in biological research, and many groups assign a particular person or team to that process. We are developing a general-purpose approach to representing the design of a biomedical experiment and provide a manageable template for that experiment's data: "Knowledge Engineering from Experimental Design" (KEfED). The KEfED model allows us to impose a formal and well-grounded structure on the data contained in scientific articles, based on relationships between the dependent and independent variables that make up a scientific experiment. We use this structure to add value to the data contained in the articles by performing directed information retrieval, adding basic forms of reasoning using additional information such as anatomical atlases and taxonomies from external ontologies. We use a graphical interface for constructing KEfED models and a first-order logic reasoning system that performs inference over such models.

BACKGROUND: Anatomical studies of neural circuitry describing the basic wiring diagram of the brain produce intrinsically spatial, highly complex data of great value to the neuroscience community. Published neuroanatomical atlases provide a spatial framework for these studies. We have built an informatics framework based on these atlases for the representation of neuroanatomical knowledge. This framework not only captures current methods of anatomical data acquisition and analysis, it allows these studies to be collated, compared and synthesized within a single system. RESULTS: We have developed an atlas-viewing application ('NeuARt II') in the Java language with unique functional properties. These include the ability to use copyrighted atlases as templates within which users may view, save and retrieve data-maps and annotate them with volumetric delineations. NeuARt II also permits users to view multiple levels on multiple atlases at once. Each data-map in this system is simply a stack of vector images with one image per atlas level, so any set of accurate drawings made onto a supported atlas (in vector graphics format) could be uploaded into NeuARt II. Presently the database is populated with a corpus of high-quality neuroanatomical data from the laboratory of Dr Larry Swanson (consisting 64 highly-detailed maps of PHAL tract-tracing experiments, made up of 1039 separate drawings that were published in 27 primary research publications over 17 years). Herein we take selective examples from these data to demonstrate the features of NeuArt II. Our informatics tool permits users to browse, query and compare these maps. The NeuARt II tool operates within a bioinformatics knowledge management platform (called 'NeuroScholar') either as a standalone or a plug-in application. CONCLUSION: Anatomical localization is fundamental to neuroscientific work and atlases provide an easily-understood framework that is widely used by neuroanatomists and non-neuroanatomists alike. NeuARt II, the neuroinformatics tool presented here, provides an accurate and powerful way of representing neuroanatomical data in the context of commonly-used brain atlases for visualization, comparison and analysis. Furthermore, it provides a framework that supports the delivery and manipulation of mapped data either as a standalone system or as a component in a larger knowledge management system.