Knowledge-based Biomedical Data Science 2019

Knowledge-based biomedical data science (KBDS) involves the design and implementation of computer systems that act as if they knew about biomedicine. Such systems depend on formally represented knowledge in computer systems, often in the form of knowledge graphs. Here we survey the progress in the last year in systems that use formally represented knowledge to address data science problems in both clinical and biological domains, as well as on approaches for creating knowledge graphs. Major themes include the relationships between knowledge graphs and machine learning, the use of natural language processing, and the expansion of knowledge-based approaches to novel domains, such as Chinese Traditional Medicine and biodiversity.Comment: Manuscript 43 pages with 3 tables; Supplemental material 43 pages with 3 table

Construction of the Literature Graph in Semantic Scholar

We describe a deployed scalable system for organizing published scientific literature into a heterogeneous graph to facilitate algorithmic manipulation and discovery. The resulting literature graph consists of more than 280M nodes, representing papers, authors, entities and various interactions between them (e.g., authorships, citations, entity mentions). We reduce literature graph construction into familiar NLP tasks (e.g., entity extraction and linking), point out research challenges due to differences from standard formulations of these tasks, and report empirical results for each task. The methods described in this paper are used to enable semantic features in www.semanticscholar.orgComment: To appear in NAACL 2018 industry trac

Neural Networks forBuilding Semantic Models and Knowledge Graphs

1noL'abstract è presente nell'allegato / the abstract is in the attachmentopen677. INGEGNERIA INFORMATInoopenFutia, Giusepp

Keywords at Work: Investigating Keyword Extraction in Social Media Applications

This dissertation examines a long-standing problem in Natural Language Processing (NLP) -- keyword extraction -- from a new angle. We investigate how keyword extraction can be formulated on social media data, such as emails, product reviews, student discussions, and student statements of purpose. We design novel graph-based features for supervised and unsupervised keyword extraction from emails, and use the resulting system with success to uncover patterns in a new dataset -- student statements of purpose. Furthermore, the system is used with new features on the problem of usage expression extraction from product reviews, where we obtain interesting insights. The system while used on student discussions, uncover new and exciting patterns. While each of the above problems is conceptually distinct, they share two key common elements -- keywords and social data. Social data can be messy, hard-to-interpret, and not easily amenable to existing NLP resources. We show that our system is robust enough in the face of such challenges to discover useful and important patterns. We also show that the problem definition of keyword extraction itself can be expanded to accommodate new and challenging research questions and datasets.PHDComputer Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/145929/1/lahiri_1.pd

Recent Developments in Smart Healthcare

Medicine is undergoing a sector-wide transformation thanks to the advances in computing and networking technologies. Healthcare is changing from reactive and hospital-centered to preventive and personalized, from disease focused to well-being centered. In essence, the healthcare systems, as well as fundamental medicine research, are becoming smarter. We anticipate significant improvements in areas ranging from molecular genomics and proteomics to decision support for healthcare professionals through big data analytics, to support behavior changes through technology-enabled self-management, and social and motivational support. Furthermore, with smart technologies, healthcare delivery could also be made more efficient, higher quality, and lower cost. In this special issue, we received a total 45 submissions and accepted 19 outstanding papers that roughly span across several interesting topics on smart healthcare, including public health, health information technology (Health IT), and smart medicine

Towards Machine-Assisted Meta Studies of Astrophysical Data From the Scientific Literature

We develop a new model for automatic extraction of reported measurements from the astrophysical literature, utilising modern Natural Language Processing techniques. We begin with a rules-based model for keyword-search-based extraction, and then proceed to develop artificial neural network models for full entity and relation extraction from free text. This process also requires the creation of hand-annotated datasets selected from the available astrophysical literature for training and validation purposes. We use a set of cosmological parameters to examine the model's ability to identify information relating to a specific parameter and to illustrate its capabilities, using the Hubble constant as a primary case study due to the well-document history of that parameter. Our results correctly highlight the current tension present in measurements of the Hubble constant and recover the 3.5σ discrepancy – demonstrating that the models are useful for meta-studies of astrophysical measurements from a large number of publications. From the other cosmological parameter results we can clearly observe the historical trends in the reported values of these quantities over the past two decades, and see the impacts of landmark publications on our understanding of cosmology. The outputs of these models, when applied to the article abstracts present in the arXiv repository, constitute a database of over 231,000 astrophysical numerical measurements, relating to over 61,000 different symbolic parameter representations – here a measurement refers to the combination of a numerical value and an identifier (i.e. a name or symbol) to give it physical meaning. We present an online interface (Numerical Atlas) to allow users to query and explore this database, based on parameter names and symbolic representations, and download the resulting datasets for their own research uses

Site-Specific Rules Extraction in Precision Agriculture

El incremento sostenible en la producción alimentaria para satisfacer las necesidades de una población mundial en aumento es un verdadero reto cuando tenemos en cuenta el impacto constante de plagas y enfermedades en los cultivos. Debido a las importantes pérdidas económicas que se producen, el uso de tratamientos químicos es demasiado alto; causando contaminación del medio ambiente y resistencia a distintos tratamientos. En este contexto, la comunidad agrícola divisa la aplicación de tratamientos más específicos para cada lugar, así como la validación automática con la conformidad legal. Sin embargo, la especificación de estos tratamientos se encuentra en regulaciones expresadas en lenguaje natural. Por este motivo, traducir regulaciones a una representación procesable por máquinas está tomando cada vez más importancia en la agricultura de precisión.Actualmente, los requisitos para traducir las regulaciones en reglas formales están lejos de ser cumplidos; y con el rápido desarrollo de la ciencia agrícola, la verificación manual de la conformidad legal se torna inabordable.En esta tesis, el objetivo es construir y evaluar un sistema de extracción de reglas para destilar de manera efectiva la información relevante de las regulaciones y transformar las reglas de lenguaje natural a un formato estructurado que pueda ser procesado por máquinas. Para ello, hemos separado la extracción de reglas en dos pasos. El primero es construir una ontología del dominio; un modelo para describir los desórdenes que producen las enfermedades en los cultivos y sus tratamientos. El segundo paso es extraer información para poblar la ontología. Puesto que usamos técnicas de aprendizaje automático, implementamos la metodología MATTER para realizar el proceso de anotación de regulaciones. Una vez creado el corpus, construimos un clasificador de categorías de reglas que discierne entre obligaciones y prohibiciones; y un sistema para la extracción de restricciones en reglas, que reconoce información relevante para retener el isomorfismo con la regulación original. Para estos componentes, empleamos, entre otra técnicas de aprendizaje profundo, redes neuronales convolucionales y “Long Short- Term Memory”. Además, utilizamos como baselines algoritmos más tradicionales como “support-vector machines” y “random forests”.Como resultado, presentamos la ontología PCT-O, que ha sido alineada con otras ontologías como NCBI, PubChem, ChEBI y Wikipedia. El modelo puede ser utilizado para la identificación de desórdenes, el análisis de conflictos entre tratamientos y la comparación entre legislaciones de distintos países. Con respecto a los sistemas de extracción, evaluamos empíricamente el comportamiento con distintas métricas, pero la métrica F1 es utilizada para seleccionar los mejores sistemas. En el caso del clasificador de categorías de reglas, el mejor sistema obtiene un macro F1 de 92,77% y un F1 binario de 85,71%. Este sistema usa una red “bidirectional long short-term memory” con “word embeddings” como entrada. En relación al extractor de restricciones de reglas, el mejor sistema obtiene un micro F1 de 88,3%. Este extractor utiliza como entrada una combinación de “character embeddings” junto a “word embeddings” y una red neuronal “bidirectional long short-term memory”.<br /