Textpresso for Neuroscience: Searching the Full Text of Thousands of Neuroscience Research Papers

Textpresso is a text-mining system for scientific literature. Its two major features are access to the full text of research papers and the development and use of categories of biological concepts as well as categories that describe or relate objects. A search engine enables the user to search for one or a combination of these categories and/or keywords within an entire literature. Here we describe Textpresso for Neuroscience, part of the core Neuroscience Information Framework (NIF). The Textpresso site currently consists of 67,500 full text papers and 131,300 abstracts. We show that using categories in literature can make a pure keyword query more refined and meaningful. We also show how semantic queries can be formulated with categories only. We explain the build and content of the database and describe the main features of the web pages and the advanced search options. We also give detailed illustrations of the web service developed to provide programmatic access to Textpresso. This web service is used by the NIF interface to access Textpresso. The standalone website of Textpresso for Neuroscience can be accessed at http://www.textpresso.org/neuroscience

From Frequency to Meaning: Vector Space Models of Semantics

Computers understand very little of the meaning of human language. This profoundly limits our ability to give instructions to computers, the ability of computers to explain their actions to us, and the ability of computers to analyse and process text. Vector space models (VSMs) of semantics are beginning to address these limits. This paper surveys the use of VSMs for semantic processing of text. We organize the literature on VSMs according to the structure of the matrix in a VSM. There are currently three broad classes of VSMs, based on term-document, word-context, and pair-pattern matrices, yielding three classes of applications. We survey a broad range of applications in these three categories and we take a detailed look at a specific open source project in each category. Our goal in this survey is to show the breadth of applications of VSMs for semantics, to provide a new perspective on VSMs for those who are already familiar with the area, and to provide pointers into the literature for those who are less familiar with the field

CHORUS Deliverable 4.3: Report from CHORUS workshops on national initiatives and metadata

Minutes of the following Workshops: • National Initiatives on Multimedia Content Description and Retrieval, Geneva, October 10th, 2007. • Metadata in Audio-Visual/Multimedia production and archiving, Munich, IRT, 21st – 22nd November 2007 Workshop in Geneva 10/10/2007 This highly successful workshop was organised in cooperation with the European Commission. The event brought together the technical, administrative and financial representatives of the various national initiatives, which have been established recently in some European countries to support research and technical development in the area of audio-visual content processing, indexing and searching for the next generation Internet using semantic technologies, and which may lead to an internet-based knowledge infrastructure. The objective of this workshop was to provide a platform for mutual information and exchange between these initiatives, the European Commission and the participants. Top speakers were present from each of the national initiatives. There was time for discussions with the audience and amongst the European National Initiatives. The challenges, communalities, difficulties, targeted/expected impact, success criteria, etc. were tackled. This workshop addressed how these national initiatives could work together and benefit from each other. Workshop in Munich 11/21-22/2007 Numerous EU and national research projects are working on the automatic or semi-automatic generation of descriptive and functional metadata derived from analysing audio-visual content. The owners of AV archives and production facilities are eagerly awaiting such methods which would help them to better exploit their assets.Hand in hand with the digitization of analogue archives and the archiving of digital AV material, metadatashould be generated on an as high semantic level as possible, preferably fully automatically. All users of metadata rely on a certain metadata model. All AV/multimedia search engines, developed or under current development, would have to respect some compatibility or compliance with the metadata models in use. The purpose of this workshop is to draw attention to the specific problem of metadata models in the context of (semi)-automatic multimedia search

Variational Deep Semantic Hashing for Text Documents

As the amount of textual data has been rapidly increasing over the past decade, efficient similarity search methods have become a crucial component of large-scale information retrieval systems. A popular strategy is to represent original data samples by compact binary codes through hashing. A spectrum of machine learning methods have been utilized, but they often lack expressiveness and flexibility in modeling to learn effective representations. The recent advances of deep learning in a wide range of applications has demonstrated its capability to learn robust and powerful feature representations for complex data. Especially, deep generative models naturally combine the expressiveness of probabilistic generative models with the high capacity of deep neural networks, which is very suitable for text modeling. However, little work has leveraged the recent progress in deep learning for text hashing. In this paper, we propose a series of novel deep document generative models for text hashing. The first proposed model is unsupervised while the second one is supervised by utilizing document labels/tags for hashing. The third model further considers document-specific factors that affect the generation of words. The probabilistic generative formulation of the proposed models provides a principled framework for model extension, uncertainty estimation, simulation, and interpretability. Based on variational inference and reparameterization, the proposed models can be interpreted as encoder-decoder deep neural networks and thus they are capable of learning complex nonlinear distributed representations of the original documents. We conduct a comprehensive set of experiments on four public testbeds. The experimental results have demonstrated the effectiveness of the proposed supervised learning models for text hashing.Comment: 11 pages, 4 figure

Interoperability and FAIRness through a novel combination of Web technologies

Data in the life sciences are extremely diverse and are stored in a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG for pathway data or UniProt for protein data) to those that are general-purpose (such as FigShare, Zenodo, Dataverse or EUDAT). These data have widely different levels of sensitivity and security considerations. For example, clinical observations about genetic mutations in patients are highly sensitive, while observations of species diversity are generally not. The lack of uniformity in data models from one repository to another, and in the richness and availability of metadata descriptions, makes integration and analysis of these data a manual, time-consuming task with no scalability. Here we explore a set of resource-oriented Web design patterns for data discovery, accessibility, transformation, and integration that can be implemented by any general- or special-purpose repository as a means to assist users in finding and reusing their data holdings. We show that by using off-the-shelf technologies, interoperability can be achieved atthe level of an individual spreadsheet cell. We note that the behaviours of this architecture compare favourably to the desiderata defined by the FAIR Data Principles, and can therefore represent an exemplar implementation of those principles. The proposed interoperability design patterns may be used to improve discovery and integration of both new and legacy data, maximizing the utility of all scholarly outputs