Unsupervised word embeddings capture latent knowledge from materials science literature.

The overwhelming majority of scientific knowledge is published as text, which is difficult to analyse by either traditional statistical analysis or modern machine learning methods. By contrast, the main source of machine-interpretable data for the materials research community has come from structured property databases1,2, which encompass only a small fraction of the knowledge present in the research literature. Beyond property values, publications contain valuable knowledge regarding the connections and relationships between data items as interpreted by the authors. To improve the identification and use of this knowledge, several studies have focused on the retrieval of information from scientific literature using supervised natural language processing3-10, which requires large hand-labelled datasets for training. Here we show that materials science knowledge present in the published literature can be efficiently encoded as information-dense word embeddings11-13 (vector representations of words) without human labelling or supervision. Without any explicit insertion of chemical knowledge, these embeddings capture complex materials science concepts such as the underlying structure of the periodic table and structure-property relationships in materials. Furthermore, we demonstrate that an unsupervised method can recommend materials for functional applications several years before their discovery. This suggests that latent knowledge regarding future discoveries is to a large extent embedded in past publications. Our findings highlight the possibility of extracting knowledge and relationships from the massive body of scientific literature in a collective manner, and point towards a generalized approach to the mining of scientific literature

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

The role of handbooks in knowledge creation and diffusion: A case of science and technology studies

Genre is considered to be an important element in scholarly communication and in the practice of scientific disciplines. However, scientometric studies have typically focused on a single genre, the journal article. The goal of this study is to understand the role that handbooks play in knowledge creation and diffusion and their relationship with the genre of journal articles, particularly in highly interdisciplinary and emergent social science and humanities disciplines. To shed light on these questions we focused on handbooks and journal articles published over the last four decades belonging to the research area of Science and Technology Studies (STS), broadly defined. To get a detailed picture we used the full-text of five handbooks (500,000 words) and a well-defined set of 11,700 STS articles. We confirmed the methodological split of STS into qualitative and quantitative (scientometric) approaches. Even when the two traditions explore similar topics (e.g., science and gender) they approach them from different starting points. The change in cognitive foci in both handbooks and articles partially reflects the changing trends in STS research, often driven by technology. Using text similarity measures we found that, in the case of STS, handbooks play no special role in either focusing the research efforts or marking their decline. In general, they do not represent the summaries of research directions that have emerged since the previous edition of the handbook.Comment: Accepted for publication in Journal of Informetric

Natural Language Query in the Biochemistry and Molecular Biology Domains Based on Cognition Search™

Motivation: With the tremendous growth in scientific literature, it is necessary to improve upon the standard pattern matching style of the available search engines. Semantic NLP may be the solution to this problem. Cognition Search (CSIR) is a natural language technology. It is best used by asking a simple question that might be answered in textual data being queried, such as MEDLINE. CSIR has a large English dictionary and semantic database. Cognition’s semantic map enables the search process to be based on meaning rather than statistical word pattern matching and, therefore, returns more complete and relevant results. The Cognition Search engine uses downward reasoning and synonymy which also improves recall. It improves precision through phrase parsing and word sense disambiguation.
Result: Here we have carried out several projects to "teach" the CSIR lexicon medical, biochemical and molecular biological language and acronyms from curated web-based free sources. Vocabulary from the Alliance for Cell Signaling (AfCS), the Human Genome Nomenclature Consortium (HGNC), the United Medical Language System (UMLS) Meta-thesaurus, and The International Union of Pure and Applied Chemistry (IUPAC) was introduced into the CSIR dictionary and curated. The resulting system was used to interpret MEDLINE abstracts. Meaning-based search of MEDLINE abstracts yields high precision (estimated at >90%), and high recall (estimated at >90%), where synonym information has been encoded. The present implementation can be found at http://MEDLINE.cognition.com. 
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Induction of Word and Phrase Alignments for Automatic Document Summarization

Current research in automatic single document summarization is dominated by two effective, yet naive approaches: summarization by sentence extraction, and headline generation via bag-of-words models. While successful in some tasks, neither of these models is able to adequately capture the large set of linguistic devices utilized by humans when they produce summaries. One possible explanation for the widespread use of these models is that good techniques have been developed to extract appropriate training data for them from existing document/abstract and document/headline corpora. We believe that future progress in automatic summarization will be driven both by the development of more sophisticated, linguistically informed models, as well as a more effective leveraging of document/abstract corpora. In order to open the doors to simultaneously achieving both of these goals, we have developed techniques for automatically producing word-to-word and phrase-to-phrase alignments between documents and their human-written abstracts. These alignments make explicit the correspondences that exist in such document/abstract pairs, and create a potentially rich data source from which complex summarization algorithms may learn. This paper describes experiments we have carried out to analyze the ability of humans to perform such alignments, and based on these analyses, we describe experiments for creating them automatically. Our model for the alignment task is based on an extension of the standard hidden Markov model, and learns to create alignments in a completely unsupervised fashion. We describe our model in detail and present experimental results that show that our model is able to learn to reliably identify word- and phrase-level alignments in a corpus of pairs

PubServer: literature searches by homology.

PubServer, available at http://pubserver.burnham.org/, is a tool to automatically collect, filter and analyze publications associated with groups of homologous proteins. Protein entries in databases such as Entrez Protein database at NCBI contain information about publications associated with a given protein. The scope of these publications varies a lot: they include studies focused on biochemical functions of individual proteins, but also reports from genome sequencing projects that introduce tens of thousands of proteins. Collecting and analyzing publications related to sets of homologous proteins help in functional annotation of novel protein families and in improving annotations of well-studied protein families or individual genes. However, performing such collection and analysis manually is a tedious and time-consuming process. PubServer automatically collects identifiers of homologous proteins using PSI-Blast, retrieves literature references from corresponding database entries and filters out publications unlikely to contain useful information about individual proteins. It also prepares simple vocabulary statistics from titles, abstracts and MeSH terms to identify the most frequently occurring keywords, which may help to quickly identify common themes in these publications. The filtering criteria applied to collected publications are user-adjustable. The results of the server are presented as an interactive page that allows re-filtering and different presentations of the output

POS Tagging and its Applications for Mathematics

Content analysis of scientific publications is a nontrivial task, but a useful and important one for scientific information services. In the Gutenberg era it was a domain of human experts; in the digital age many machine-based methods, e.g., graph analysis tools and machine-learning techniques, have been developed for it. Natural Language Processing (NLP) is a powerful machine-learning approach to semiautomatic speech and language processing, which is also applicable to mathematics. The well established methods of NLP have to be adjusted for the special needs of mathematics, in particular for handling mathematical formulae. We demonstrate a mathematics-aware part of speech tagger and give a short overview about our adaptation of NLP methods for mathematical publications. We show the use of the tools developed for key phrase extraction and classification in the database zbMATH