In textual information extraction and other sequence labeling tasks it is now common to use recurrent neural networks (such as LSTM) to form rich embedded representations of long-term input co-occurrence patterns. Representation of output co-occurrence patterns is typically limited to a hand-designed graphical model, such as a linear-chain CRF representing short-term Markov dependencies among successive labels. This paper presents a method that learns embedded representations of latent output structure in sequence data. Our model takes the form of a finite-state machine with a large number of latent states per label (a latent variable CRF), where the state-transition matrix is factorized---effectively forming an embedded representation of state-transitions capable of enforcing long-term label dependencies, while supporting exact Viterbi inference over output labels. We demonstrate accuracy improvements and interpretable latent structure in a synthetic but complex task based on CoNLL named entity recognition.
The ability of neural networks to efficiently represent local context features sometimes allows them to make surprisingly good independent decisions for each structured output variable @cite_9 . However, these independent classifiers are often insufficient for structured prediction tasks where there are strong dependencies between the output labels @cite_9 @cite_8 . A natural solution is to use these neural feature representations to parameterize the factors of a conditional random field @cite_12 for joint inference over output variables @cite_9 @cite_10 @cite_8 . However, most previous work restricts the linear-chain CRF states to be the labels themselves---learning no additional output structure.
@cite_9 @cite_10 @cite_12 @cite_8
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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. 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. 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. 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 . 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. 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. 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] 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 ... The popular h-index used to measure scientific output can be described in terms of a pool of evaluated objects (the papers), a quality function on the evaluated objects (the number of citations received by each paper) and a sentencing line crossing the origin, whose intersection with the graph of the quality function yields the index value (in the h-index this is a line with slope 1). Based on this abstraction, we present a new index, the c-index, in which the evaluated objects are the citations received by an author, a group of authors, a journal, etc., the quality function of a citation is the collaboration distance between the authors of the cited and the citing papers, and the sentencing line can take slopes between 0 and ∞. As a result, the new index counts only those citations which are significant enough, where significance is proportional to collaboration distance. Several advantages of the new c-index with respect to previous proposals are discussed. Conditional random fields (CRF) are widely used for predicting output variables that have some internal structure. Most of the CRF research has been done on structured classification where the outputs are discrete. In this study we propose a CRF probabilistic model for structured regression that uses multiple non-structured predictors as its features. We construct features as squared prediction errors and show that this results in a Gaussian predictor. Learning becomes a convex optimization problem leading to a global solution for a set of parameters. Inference can be conveniently conducted through matrix computation. Experimental results on the remote sensing problem of estimating Aerosol Optical Depth (AOD) provide strong evidence that the proposed CRF model successfully exploits the inherent spatio-temporal properties of AOD data. The experiments revealed that CRF are more accurate than the baseline neural network and domain-based predictors. 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. 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. Preface 1. Introduction 2. Some context for Context Analysis: a view of the origins of structural studies of face-to-face interaction 3. Some functions of gaze direction in two-person conversation 4. Movement co-ordination in social interaction 5. Some functions of the face in a kissing round 6. A description of some human greetings 7. Spatial organisation in social encounters: the F-formation system 8. Behavioural foundations for the process of frame-attunement in face-to-face interaction List of films cited References Index. Background The h-index has already been used by major citation databases to evaluate the academic performance of individual scientists. Although effective and simple, the h-index suffers from some drawbacks that limit its use in accurately and fairly comparing the scientific output of different researchers. These drawbacks include information loss and low resolution: the former refers to the fact that in addition to h2 citations for papers in the h-core, excess citations are completely ignored, whereas the latter means that it is common for a group of researchers to have an identical h-index. Methodology Principal Findings To solve these problems, I here propose the e-index, where e2 represents the ignored excess citations, in addition to the h2 citations for h-core papers. Citation information can be completely depicted by using the h-index together with the e-index, which are independent of each other. Some other h-type indices, such as a and R, are h-dependent, have information redundancy with h, and therefore, when used together with h, mask the real differences in excess citations of different researchers. Conclusions Significance Although simple, the e-index is a necessary h-index complement, especially for evaluating highly cited scientists or for precisely comparing the scientific output of a group of scientists having an identical h-index. NNScore is a neural-network-based scoring function designed to aid the computational identification of small-molecule ligands. While the test cases included in the original NNScore article demonstrated the utility of the program, the application examples were limited. The purpose of the current work is to further confirm that neural-network scoring functions are effective, even when compared to the scoring functions of state-of-the-art docking programs, such as AutoDock, the most commonly cited program, and AutoDock Vina, thought to be two orders of magnitude faster. Aside from providing additional validation of the original NNScore function, we here present a second neural-network scoring function, NNScore 2.0. NNScore 2.0 considers many more binding characteristics when predicting affinity than does the original NNScore. The network output of NNScore 2.0 also differs from that of NNScore 1.0; rather than a binary classification of ligand potency, NNScore 2.0 provides a single estimate of the pKd. To fac... Abstract We study the behavior at infinity of the tail of the stationary solution of a multidimensional linear auto-regressive process with random coefficients. We exhibit an extended class of multiplicative coefficients satisfying a condition of irreducibility and proximality that yield to a heavy tail behavior. To cite this article: B. de , C. R. Acad. Sci. Paris, Ser. I 339 (2004). Supervised deep learning has been successfully applied to many recognition problems. Although it can approximate a complex many-to-one function well when a large amount of training data is provided, it is still challenging to model complex structured output representations that effectively perform probabilistic inference and make diverse predictions. In this work, we develop a deep conditional generative model for structured output prediction using Gaussian latent variables. The model is trained efficiently in the framework of stochastic gradient variational Bayes, and allows for fast prediction using stochastic feed-forward inference. In addition, we provide novel strategies to build robust structured prediction algorithms, such as input noise-injection and multi-scale prediction objective at training. In experiments, we demonstrate the effectiveness of our proposed algorithm in comparison to the deterministic deep neural network counterparts in generating diverse but realistic structured output predictions using stochastic inference. Furthermore, the proposed training methods are complimentary, which leads to strong pixel-level object segmentation and semantic labeling performance on Caltech-UCSD Birds 200 and the subset of Labeled Faces in the Wild dataset. Identifying expansion forms for acronyms is beneficial to many natural language processing and information retrieval tasks. In this work, we study the problem of finding expansions in texts for given acronym queries by modeling the problem as a sequence labeling task. However, it is challenging for traditional sequence labeling models like Conditional Random Fields (CRF) due to the complexity of the input sentences and the substructure of the categories. In this paper, we propose a Latent-state Neural Conditional Random Fields model (LNCRF) to deal with the challenges. On one hand, we extend CRF by coupling it with nonlinear hidden layers to learn multi-granularity hierarchical representations of the input data under the framework of Conditional Random Fields. On the other hand, we introduce latent variables to capture the fine granular information from the intrinsic substructures within the structured output labels implicitly. The experimental results on real data show that our model achieves the best performance against the state-of-the-art baselines.