Identifying relationships between concepts is a key aspect of scientific knowledge synthesis. Finding these links often requires a researcher to laboriously search through scien- tific papers and databases, as the size of these resources grows ever larger. In this paper we describe how distributional semantics can be used to unify structured knowledge graphs with unstructured text to predict new relationships between medical concepts, using a probabilistic generative model. Our approach is also designed to ameliorate data sparsity and scarcity issues in the medical domain, which make language modelling more challenging. Specifically, we integrate the medical relational database (SemMedDB) with text from electronic health records (EHRs) to perform knowledge graph completion. We further demonstrate the ability of our model to predict relationships between tokens not appearing in the relational database.
Neural language models @cite_4 are an approach to learning embeddings which use a word's representation to its surrounding context. This relies on the fact that words with similar meanings have similar contexts (the distributional hypothesis of language @cite_9 ), which forces their representations to be similar. Intriguingly, it was observed @cite_10 @cite_19 that the geometry of the resulting space preserved between terms. An example is a consistent offset vector existing between Berlin' and Germany', and Dublin' and Ireland', seemingly representing the relationship capital city of country . This property has been exploited to perform knowledge-base completion, for example @cite_19 @cite_11 @cite_16 , however these approaches have restricted their attention to edge-discovery a knowledge graph. To such a graph we therefore developed a model @cite_8 which can combine structured and unstructured data sources while explicitly modelling the types of relationships present in the structured data.
@cite_4 @cite_8 @cite_9 @cite_19 @cite_16 @cite_10 @cite_11
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In a document network such as a citation network of scientific documents, web-logs, etc., the content produced by authors exhibits their interest in certain topics. In addition some authors influence other authors' interests. In this work, we propose to model the influence of cited authors along with the interests of citing authors. Moreover, we hypothesize that apart from the citations present in documents, the context surrounding the citation mention provides extra topical information about the cited authors. However, associating terms in the context to the cited authors remains an open problem. We propose novel document generation schemes that incorporate the context while simultaneously modeling the interests of citing authors and influence of the cited authors. Our experiments show significant improvements over baseline models for various evaluation criteria such as link prediction between document and cited author, and quantitatively explaining unseen text. A citing sentence is one that appears in a scientific article and cites previous work. Citing sentences have been studied and used in many applications. For example, they have been used in scientific paper summarization, automatic survey generation, paraphrase identification, and citation function classification. Citing sentences that cite multiple papers are common in scientific writing. This observation should be taken into consideration when using citing sentences in applications. For instance, when a citing sentence is used in a summary of a scientific paper, only the fragments of the sentence that are relevant to the summarized paper should be included in the summary. In this paper, we present and compare three different approaches for identifying the fragments of a citing sentence that are related to a given target reference. Our methods are: word classification, sequence labeling, and segment classification. Our experiments show that segment classification achieves the best results. Abstract Documents in computer-readable form can be used to provide information about other documents, i.e. those they cite. To do this efficiently requires procedures for computer recognition of citing statements. This is not easy, especially for multi-sentence citing statements. Computer recognition procedures have been developed which are accurate to the following extent: 73 of the words in statements selected by computer procedures as being citing statements are words which are correctly attributable to the corresponding documents. The retrieval effectiveness of computer-recognized citing statements was tested in the following way. First, for eight retrieval requests in inorganiic chemistry, average recall by search of Chemical Abstracts Service indexing and Chemical Abstracts abstract text words was found to be 50 . Words from citing statements referring to the papers to be retrieved were then added to the index terms and abstract words as additional access points, and searching was repeated. Average recall increased to 70 . Only words from citing statements published within a year of the cited papers were used. The retrieval effect of citing statement words alone (published within a year) without index or abstract terms was the following: average recall was 40 . When just the words of the titles of the cited papers were added to those citing statement words, average recall increased to 50 . Purpose – The purpose of this paper is to suggest an alternative to the widely used Times Cited criterion for analysing citation networks. The approach involves taking account of the natures of the papers that cite a given paper, so as to differentiate between papers that attract the same number of citations.Design methodology approach – ArticleRank is an algorithm that has been derived from Google's PageRank algorithm to measure the influence of journal articles. ArticleRank is applied to two datasets – a citation network based on an early paper on webometrics, and a self‐citation network based on the 19 most cited papers in the Journal of Documentation – using citation data taken from the Web of Knowledge database.Findings – ArticleRank values provide a different ranking of a set of papers from that provided by the corresponding Times Cited values, and overcomes the inability of the latter to differentiate between papers with the same numbers of citations. The difference in rankings between Times Cited ... Citation relationship between scientific publications has been successfully used for scholarly bibliometrics, information retrieval and data mining tasks, and citation-based recommendation algorithms are well documented. While previous studies investigated citation relations from various viewpoints, most of them share the same assumption that, if paper1 cites paper2 (or author1 cites author2), they are connected, regardless of citation importance, sentiment, reason, topic, or motivation. However, this assumption is oversimplified. In this study, we employ an innovative "context-rich heterogeneous network" approach, which paves a new way for citation recommendation task. In the network, we characterize 1) the importance of citation relationships between citing and cited papers, and 2) the topical citation motivation. Unlike earlier studies, the citation information, in this paper, is characterized by citation textual contexts extracted from the full-text citing paper. We also propose algorithm to cope with the situation when large portion of full-text missing information exists in the bibliographic repository. Evaluation results show that, context-rich heterogeneous network can significantly enhance the citation recommendation performance. Mapping of science and technology can be done at different levels of aggregation, using a variety of methods. In this paper, we propose a method in which title words are used as indicators for the content of a research topic, and cited references are used as the context in which words get their meaning. Research topics are represented by sets of papers that are similar in terms of these word-reference combinations. In this way we use words without neglecting differences and changes in their meanings. The method has several advantages, such as high coverage of publications. As an illustration we apply the method to produce knowledge maps of information science. In recent years scholars have built maps of science by connecting the academic fields that cite each other, are cited together, or that cite a similar literature. But since scholars cannot always publish in the fields they cite, or that cite them, these science maps are only rough proxies for the potential of a scholar, organization, or country, to enter a new academic field. Here we use a large dataset of scholarly publications disambiguated at the individual level to create a map of science-or research space-where links connect pairs of fields based on the probability that an individual has published in both of them. We find that the research space is a significantly more accurate predictor of the fields that individuals and organizations will enter in the future than citation based science maps. At the country level, however, the research space and citations based science maps are equally accurate. These findings show that data on career trajectories-the set of fields that individuals have previously published in-provide more accurate predictors of future research output for more focalized units-such as individuals or organizations-than citation based science maps. Scholars are increasingly citing electronic “web references” which are not preserved in libraries or full text archives. WebCite is a new standard for citing web references. To “webcite” a document involves archiving the cited Web page through www.webcitation.org and citing the WebCite permalink instead of (or in addition to) the unstable live Web page. This journal has amended its “instructions for authors” accordingly, asking authors to archive cited Web pages before submitting a manuscript. Almost 200 other journals are already using the system. We discuss the rationale for WebCite, its technology, and how scholars, editors, and publishers can benefit from the service. Citing scholars initiate an archiving process of all cited Web references, ideally before they submit a manuscript. Authors of online documents and websites which are expected to be cited by others can ensure that their work is permanently available by creating an archived copy using WebCite and providing the citation information including the WebCite link on their Web document(s). Editors should ask their authors to cache all cited Web addresses (Uniform Resource Locators, or URLs) “prospectively” before submitting their manuscripts to their journal. Editors and publishers should also instruct their copyeditors to cache cited Web material if the author has not done so already. Finally, WebCite can process publisher submitted “citing articles” (submitted for example as eXtensible Markup Language [XML] documents) to automatically archive all cited Web pages shortly before or on publication. Finally, WebCite can act as a focussed crawler, caching retrospectively references of already published articles. Copyright issues are addressed by honouring respective Internet standards (robot exclusion files, no-cache and no-archive tags). Long-term preservation is ensured by agreements with libraries and digital preservation organizations. The resulting WebCite Index may also have applications for research assessment exercises, being able to measure the impact of Web services and published Web documents through access and Web citation metrics. @PARASPLIT [J Med Internet Res 2005;7(5):e60] A new form of document coupling called co-citation is defined as the frequency with which two documents are cited together. The co-citation frequency of two scientific papers can be determined by comparing lists of citing documents in the Science Citation Index and counting identical entries. Networks of co-cited papers can be generated for specific scientific specialties, and an example is drawn from the literature of particle physics. Co-citation patterns are found to differ significantly from bibliographic coupling patterns, but to agree generally with patterns of direct citation. Clusters of co-cited papers provide a new way to study the specialty structure of science. They may provide a new approach to indexing and to the creation of SDI profiles. In this work, we address the problem of joint modeling of text and citations in the topic modeling framework. We present two different models called the Pairwise-Link-LDA and the Link-PLSA-LDA models. The Pairwise-Link-LDA model combines the ideas of LDA [4] and Mixed Membership Block Stochastic Models [1] and allows modeling arbitrary link structure. However, the model is computationally expensive, since it involves modeling the presence or absence of a citation (link) between every pair of documents. The second model solves this problem by assuming that the link structure is a bipartite graph. As the name indicates, Link-PLSA-LDA model combines the LDA and PLSA models into a single graphical model. Our experiments on a subset of Citeseer data show that both these models are able to predict unseen data better than the baseline model of Erosheva and Lafferty [8], by capturing the notion of topical similarity between the contents of the cited and citing documents. Our experiments on two different data sets on the link prediction task show that the Link-PLSA-LDA model performs the best on the citation prediction task, while also remaining highly scalable. In addition, we also present some interesting visualizations generated by each of the models. The old Asian legend about the blind men and the elephant comes to mind when looking at how different authors of scientific papers describe a piece of related prior work. It turns out that different citations to the same paper often focus on different aspects of that paper and that neither provides a full description of its full set of contributions. In this article, we will describe our investigation of this phenomenon. We studied citation summaries in the context of research papers in the biomedical domain. A citation summary is the set of citing sentences for a given article and can be used as a surrogate for the actual article in a variety of scenarios. It contains information that was deemed by peers to be important. Our study shows that citation summaries overlap to some extent with the abstracts of the papers and that they also differ from them in that they focus on different aspects of these papers than do the abstracts. In addition to this, co-cited articles (which are pairs of articles cited by another article) tend to be similar. We show results based on a lexical similarity metric called cohesion to justify our claims. © 2008 Wiley Periodicals, Inc. Historically, papers have been physically bound to the journal in which they were published; but in the digital age papers are available individually, no longer tied to their respective journals. Hence, papers now can be read and cited based on their own merits, independently of the journal's physical availability, reputation, or impact factor (IF). We compare the strength of the relationship between journals' IFs and the actual citations received by their respective papers from 1902 to 2009. Throughout most of the 20th century, papers' citation rates were increasingly linked to their respective journals' IFs. However, since 1990, the advent of the digital age, the relation between IFs and paper citations has been weakening. This began first in physics, a field that was quick to make the transition into the electronic domain. Furthermore, since 1990 the overall proportion of highly cited papers coming from highly cited journals has been decreasing and, of these highly cited papers, the proportion not coming from highly cited journals has been increasing. Should this pattern continue, it might bring an end to the use of the IF as a way to evaluate the quality of journals, papers, and researchers. © 2012 Wiley Periodicals, Inc. When we write or prepare to write a research paper, we always have appropriate references in mind. However, there are most likely references we have missed and should have been read and cited. As such a good citation recommendation system would not only improve our paper but, overall, the efficiency and quality of literature search. Usually, a citation's context contains explicit words explaining the citation. Using this, we propose a method that "translates" research papers into references. By considering the citations and their contexts from existing papers as parallel data written in two different "languages", we adopt the translation model to create a relationship between these two "vocabularies". Experiments on both CiteSeer and CiteULike dataset show that our approach outperforms other baseline methods and increase the precision, recall and f-measure by at least 5 to 10 , respectively. In addition, our approach runs much faster in the both training and recommending stage, which proves the effectiveness and the scalability of our work. An overwhelming number of news articles are available every day via the internet. Unfortunately, it is impossible for us to peruse more than a handful; furthermore it is difficult to ascertain an article’s social context, i.e., is it popular, what sorts of people are reading it, etc. In this paper, we develop a system to address this problem in the restricted domain of political news by harnessing implicit and explicit contextual information from the blogosphere. Specifically, we track thousands of blogs and the news articles they cite, collapsing news articles that have highly overlapping content. We then tag each article with the number of blogs citing it, the political orientation of those blogs, and the level of emotional charge expressed in the blog posts that link to the news article. We summarize and present the results to the user via a novel visualization which displays this contextual information; the user can then find the most popular articles, the articles most cited by liberals, the articles most emotionally discussed in the political blogosphere, etc. Patent prior art search is a type of search in the patent domain where documents are searched for that describe the work previously carried out related to a patent application. The goal of this search is to check whether the idea in the patent application is novel. Vocabulary mismatch is one of the main problems of patent retrieval which results in low retrievability of similar documents for a given patent application. In this paper we show how the term distribution of the cited documents in an initially retrieved ranked list can be used to address the vocabulary mismatch. We propose a method for query modeling estimation which utilizes the citation links in a pseudo relevance feedback set. We first build a topic dependent citation graph, starting from the initially retrieved set of feedback documents and utilizing citation links of feedback documents to expand the set. We identify the important documents in the topic dependent citation graph using a citation analysis measure. We then use the term distribution of the documents in the citation graph to estimate a query model by identifying the distinguishing terms and their respective weights. We then use these terms to expand our original query. We use CLEF-IP 2011 collection to evaluate the effectiveness of our query modeling approach for prior art search. We also study the influence of different parameters on the performance of the proposed method. The experimental results demonstrate that the proposed approach significantly improves the recall over a state-of-the-art baseline which uses the link-based structure of the citation graph but not the term distribution of the cited documents. Classification, which involves finding rules that partition a given da.ta set into disjoint groups, is one class of data mining problems. Approaches proposed so far for mining classification rules for large databases are mainly decision tree based symbolic learning methods. The connectionist approach based on neura.l networks has been thought not well suited for data mining. One of the major reasons cited is that knowledge generated by neural networks is not explicitly represented in the form of rules suitable for verification or interpretation by humans. This paper examines this issue. With our newly developed algorithms, rules which are similar to, or more concise than those generated by the symbolic methods can be extracted from the neural networks. The data mining process using neural networks with the emphasis on rule extraction is described. ExperimenM results and comparison with previously published works are presented. Distributional approaches to meaning acquisition utilize distributional properties of linguistic entities as the building blocks of semantics. In doing so, they rely fundamentally on a set of assumptions about the nature of language and meaning referred to as the distributional hypothesis. This hypothesis is often stated in terms like “words which are similar in meaning occur in similar contexts” (Rubenstein & Goodenough, 1965); “words with similar meanings will occur with similar neighbors if enough text material is available” (Schutze & Pedersen, 1995); “a representation that captures much of how words are used in natural context will capture much of what we mean by meaning” (Landauer & Dumais, 1997); and “words that occur in the same contexts tend to have similar meanings” (Pantel, 2005), just to quote a few representative examples. The general idea behind the distributional hypothesis seems clear enough: there is a correlation between distributional similarity and meaning similarity, which allows us to utilize the former in order to estimate the latter. However, one can pose two very basic questions concerning the distributional hypothesis. The first is what kind of distributional properties we should look for, and what — if any — the differences are between different kinds of distributional properties. Looking at algorithms for distributional meaning acquisition we can discern two distinct approaches. The first is to build distributional profiles for words based on which other words surround them, as exemplified by Schutze (1992) and the Hyperspace Analogue to Language (HAL) model (Lund, Burgess, & Atchley, 1995). The second is to build distributional profiles based on in which text regions words occur, as exemplified by the Latent Semantic Analysis (LSA) model (Landauer & Dumais, 1997). These approaches are often treated as functionally equivalent when it comes to representing meaning similarities, despite the fact that they are based on different types of distributional raw materials. The second question is in what sense it is meaning that is conveyed by distributional patterns. Proponents of distributional methods often seem comfortable to ascribe meaning to distributional representations without explaining Link analysis typically focuses on a single type of connection, e.g., two journal papers are linked because they are written by the same author. However, often we want to analyze data that has multiple linkages between objects, e.g., two papers may have the same keywords and one may cite the other. The goal of this paper is to show that multilinear algebra provides a tool for multilink analysis. We analyze five years of publication data from journals published by the Society for Industrial and Applied Mathematics. We explore how papers can be grouped in the context of multiple link types using a tensor to represent all the links between them. A PARAFAC decomposition on the resulting tensor yields information similar to the SVD decomposition of a standard adjacency matrix. We show how the PARAFAC decomposition can be used to understand the structure of the document space and define paper-paper similarities based on multiple linkages. Examples are presented where the decomposed tensor data is used to find papers similar to a body of work (e.g., related by topic or similar to a particular author's papers), find related authors using linkages other than explicit co-authorship or citations, distinguish between papers written bymore » different authors with the same name, and predict the journal in which a paper was published.« less Search logs contain examples of frequently occurring patterns of user reformulations of queries. Intuitively, the reformulation "San Francisco" -- "San Francisco 49ers" is semantically similar to "Detroit" -- "Detroit Lions". Likewise, "London" -- "things to do in London" and "New York" -- "New York tourist attractions" can also be considered similar transitions in intent. The reformulation "movies" -- "new movies" and "york" -- "New York", however, are clearly different despite the lexical similarities in the two reformulations. In this paper, we study the distributed representation of queries learnt by deep neural network models, such as the Convolutional Latent Semantic Model, and show that they can be used to represent query reformulations as vectors. These reformulation vectors exhibit favourable properties such as mapping semantically and syntactically similar query changes closer in the embedding space. Our work is motivated by the success of continuous space language models in capturing relationships between words and their meanings using offset vectors. We demonstrate a way to extend the same intuition to represent query reformulations. Furthermore, we show that the distributed representations of queries and reformulations are both useful for modelling session context for query prediction tasks, such as for query auto-completion (QAC) ranking. Our empirical study demonstrates that short-term (session) history context features based on these two representations improves the mean reciprocal rank (MRR) for the QAC ranking task by more than 10 over a supervised ranker baseline. Our results also show that by using features based on both these representations together we achieve a better performance, than either of them individually. A model is presented of the manifestation of the birth and development of a scientific specialty in a collection of journal papers. The proposed model, Cumulative Advantage by Paper with Exemplars (CAPE) is an adaptation of Price's cumulative advantage model (D. Price, [1976]. Two modifications are made: (a) references are cited in groups by paper, and (b) the model accounts for the generation of highly cited exemplar references immediately after the birth of the specialty. This simple growth process mimics many characteristic features of real collections of papers, including the structure of the paper-to-reference matrix, the reference-per-paper distribution, the paper-per-reference distribution, the bibliographic coupling distribution, the cocitation distribution, the bibliographic coupling clustering coefficient distribution, and the temporal distribution of exemplar references. The model yields a great deal of insight into the process that produces the connectedness and clustering of a collection of articles and references. Two examples are presented and successfully modeled: a collection of 131 articles on MEMS RF (microelectromechnical systems radio frequency) switches, and a collection of 901 articles on the subject of complex networks. © 2005 Wiley Periodicals, Inc.