Today, full-texts of scientific articles are often stored in different locations than the used datasets. Dataset registries aim at a closer integration by making datasets citable but authors typically refer to datasets using inconsistent abbreviations and heterogeneous metadata (e.g. title, publication year). It is thus hard to reproduce research results, to access datasets for further analysis, and to determine the impact of a dataset. Manually detecting references to datasets in scientific articles is time-consuming and requires expert knowledge in the underlying research domain.We propose and evaluate a semi-automatic three-step approach for finding explicit references to datasets in social sciences articles.We first extract pre-defined special features from dataset titles in the da|ra registry, then detect references to datasets using the extracted features, and finally match the references found with corresponding dataset titles. The approach does not require a corpus of articles (avoiding the cold start problem) and performs well on a test corpus. We achieved an F-measure of 0.84 for detecting references in full-texts and an F-measure of 0.83 for finding correct matches of detected references in the da|ra dataset registry.
The problem that we aim to solve involves the two subtasks of 1. identifying dataset references in an article, and then 2. finding at least one correct match for each of these identified references. Literature citation mining is the process of determining the number of citations that a specific article receives. It constructs a literature citation network, which can be used for detecting the impact of an article @cite_11 . Citation mining can usually be handled by three subtasks. First, literature references should be extracted from the bibliography section of a document, and afterwards, metadata extraction should be applied on the references extracted in the first phase. Finally, each reference should be linked to the cited article by using the metadata extracted in the second step @cite_11 .
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In this paper, we define and study a novel text mining problem, which we refer to as Comparative Text Mining (CTM). Given a set of comparable text collections, the task of comparative text mining is to discover any latent common themes across all collections as well as summarize the similarity and differences of these collections along each common theme. This general problem subsumes many interesting applications, including business intelligence and opinion summarization. We propose a generative probabilistic mixture model for comparative text mining. The model simultaneously performs cross-collection clustering and within-collection clustering, and can be applied to an arbitrary set of comparable text collections. The model can be estimated efficiently using the Expectation-Maximization (EM) algorithm. We evaluate the model on two different text data sets (i.e., a news article data set and a laptop review data set), and compare it with a baseline clustering method also based on a mixture model. Experiment results show that the model is quite effective in discovering the latent common themes across collections and performs significantly better than our baseline mixture model. Text mining and information retrieval techniques have been developed to assist us with analyzing, organizing and retrieving documents with the help of computers. In many cases, it is desirable that the authors of such documents remain anonymous: Search logs can reveal sensitive details about a user, critical articles or messages about a company or government might have severe or fatal consequences for a critic, and negative feedback in customer surveys might negatively impact business relations if they are identified. Simply removing personally identifying information from a document is, however, insufficient to protect the writer's identity: Given some reference texts of suspect authors, so-called authorship attribution methods can reidentfy the author from the text itself. One of the most prominent models to represent documents in many common text mining and information retrieval tasks is the vector space model where each document is represented as a vector, typically containing its term frequencies or related quantities. We therefore propose an automated text anonymization approach that produces synthetic term frequency vectors for the input documents that can be used in lieu of the original vectors. We evaluate our method on an exemplary text classification task and demonstrate that it only has a low impact on its accuracy. In contrast, we show that our method strongly affects authorship attribution techniques to the level that they become infeasible with a much stronger decline in accuracy. Other than previous authorship obfuscation methods, our approach is the first that fulfills differential privacy and hence comes with a provable plausible deniability guarantee. Across academia and industry, text mining has become a popular strategy for keeping up with the rapid growth of the scientific literature. Text mining of the scientific literature has mostly been carried out on collections of abstracts, due to their availability. Here we present an analysis of 15 million English scientific full-text articles published during the period 1823–2016. We describe the development in article length and publication sub-topics during these nearly 250 years. We showcase the potential of text mining by extracting published protein–protein, disease–gene, and protein subcellular associations using a named entity recognition system, and quantitatively report on their accuracy using gold standard benchmark data sets. We subsequently compare the findings to corresponding results obtained on 16.5 million abstracts included in MEDLINE and show that text mining of full-text articles consistently outperforms using abstracts only. We approach the problem of academic literature search by considering an unpublished manuscript as a query to a search system. We use the text of previous literature as well as the citation graph that connects it to find relevant related material. We evaluate our technique with manual and automatic evaluation methods, and find an order of magnitude improvement in mean average precision as compared to a text similarity baseline. Some large scale topical digital libraries, such as CiteSeer, harvest online academic documents by crawling open-access archives, university and author homepages, and authors' self-submissions. While these approaches have so far built reasonable size libraries, they can suffer from having only a portion of the documents from specific publishing venues. We propose to use alternative online resources and techniques that maximally exploit other resources to build the complete document collection of any given publication venue. We investigate the feasibility of using publication metadata to guide the crawler towards authors' homepages to harvest what is missing from a digital library collection. We collect a real-world dataset from two Computer Science publishing venues, involving a total of 593 unique authors over a time frame of 1998 to 2004. We then identify the missing papers that are not indexed by CiteSeer. Using a fully automatic heuristic-based system that has the capability of locating authors' homepages and then using focused crawling to download the desired papers, we demonstrate that it is practical to harvest using a focused crawler academic papers that are missing from our digital library. Our harvester achieves a performance with an average recall level of 0.82 overall and 0.75 for those missing documents. Evaluation of the crawler's performance based on the harvest rate shows definite advantages over other crawling approaches and consistently outperforms a defined baseline crawler on a number of measures The exploration and analysis of scientific literature collections is an important task for effective knowledge management. Past interest in such document sets has spurred the development of numerous visualization approaches for their interactive analysis. They either focus on the textual content of publications, or on document metadata including authors and citations. Previously presented approaches for citation analysis aim primarily at the visualization of the structure of citation networks and their exploration. We extend the state-of-the-art by presenting an approach for the interactive visual analysis of the contents of scientific documents, and combine it with a new and flexible technique to analyze their citations. This technique facilitates user-steered aggregation of citations which are linked to the content of the citing publications using a highly interactive visualization approach. Through enriching the approach with additional interactive views of other important aspects of the data, we support the exploration of the dataset over time and enable users to analyze citation patterns, spot trends, and track long-term developments. We demonstrate the strengths of our approach through a use case and discuss it based on expert user feedback. A challenging problem in open information extraction and text mining is the learning of the selectional restrictions of semantic relations. We propose a minimally supervised bootstrapping algorithm that uses a single seed and a recursive lexico-syntactic pattern to learn the arguments and the supertypes of a diverse set of semantic relations from the Web. We evaluate the performance of our algorithm on multiple semantic relations expressed using "verb", "noun", and "verb prep" lexico-syntactic patterns. Human-based evaluation shows that the accuracy of the harvested information is about 90 . We also compare our results with existing knowledge base to outline the similarities and differences of the granularity and diversity of the harvested knowledge. Citations play an essential role in navigating academic literature and following chains of evidence in research. With the growing availability of large digital archives of scientific papers, the automated extraction and analysis of citations is becoming increasingly relevant. However, existing approaches to citation extraction still fall short of the high accuracy required to build more sophisticated and reliable tools for citation analysis and corpus navigation. In this paper, we present techniques for high accuracy extraction of citations and references from academic papers. By collecting multiple sources of evidence about entities from documents, and integrating citation extraction, reference segmentation, and citation-reference matching, we are able to significantly improve performance in subtasks including citation identification, author named entity recognition, and citation-reference matching. Applying our algorithm to previously-unseen documents, we demonstrate high F-measure performance of 0.980 for citation extraction, 0.983 for author named entity recognition, and 0.948 for citation-reference matching. In this paper, we present the results of a user study on exploratory search activities in a social science digital library. We conducted a user study with 32 participants with a social sciences background—16 postdoctoral researchers and 16 students—who were asked to solve a task on searching related work to a given topic. The exploratory search task was performed in a 10-min time slot. The use of certain search activities is measured and compared to gaze data recorded with an eye tracking device. We use a novel tree graph representation to visualise the users’ search patterns and introduce a way to combine multiple search session trees. The tree graph representation is capable of creating one single tree for multiple users and identifying common search patterns. In addition, the information behaviour of students and postdoctoral researchers is being compared. The results show that search activities on the stratagem level are frequently utilised by both user groups. The most heavily used search activities were keyword search, followed by browsing through references and citations, and author searching. The eye tracking results showed an intense examination of documents metadata, especially on the level of citations and references. When comparing the group of students and postdoctoral researchers, we found significant differences regarding gaze data on the area of the journal name of the seed document. In general, we found a tendency of the postdoctoral researchers to examine the metadata records more intensively with regard to dwell time and the number of fixations. By creating combined session trees and deriving subtrees from those, we were able to identify common patterns like economic (explorative) and exhaustive (navigational) behaviour. Our results show that participants utilised multiple search strategies starting from the seed document, which means that they examined different paths to find related publications. This paper reports on a novel technique for literature indexing and searching in a mechanized library system. The notion of relevance is taken as the key concept in the theory of information retrieval and a comparative concept of relevance is explicated in terms of the theory of probability. The resulting technique called “Probabilistic Indexing,” allows a computing machine, given a request for information, to make a statistical inference and derive a number (called the “relevance number”) for each document, which is a measure of the probability that the document will satisfy the given request. The result of a search is an ordered list of those documents which satisfy the request ranked according to their probable relevance. The paper goes on to show that whereas in a conventional library system the cross-referencing (“see” and “see also”) is based solely on the “semantical closeness” between index terms, statistical measures of closeness between index terms can be defined and computed. Thus, given an arbitrary request consisting of one (or many) index term(s), a machine can elaborate on it to increase the probability of selecting relevant documents that would not otherwise have been selected. Finally, the paper suggests an interpretation of the whole library problem as one where the request is considered as a clue on the basis of which the library system makes a concatenated statistical inference in order to provide as an output an ordered list of those documents which most probably satisfy the information needs of the user. This article proposes a process to retrieve the URL of a document for which metadata records exist in a digital library catalog but a pointer to the full text of the document is not available. The process uses results from queries submitted to Web search engines for finding the URL of the corresponding full text or any related material. We present a comprehensive study of this process in different situations by investigating different query strategies applied to three general purpose search engines (Google, Yahoo!, MSN) and two specialized ones (Scholar and CiteSeer), considering five user scenarios. Specifically, we have conducted experiments with metadata records taken from the Brazilian Digital Library of Computing (BDBComp) and The DBLP Computer Science Bibliography (DBLP). We found that Scholar was the most effective search engine for this task in all considered scenarios and that simple strategies for combining and re-ranking results from Scholar and Google significantly improve the retrieval quality. Moreover, we study the influence of the number of query results on the effectiveness of finding missing information as well as the coverage of the proposed scenarios. This paper addresses several key issues in the ArnetMiner system, which aims at extracting and mining academic social networks. Specifically, the system focuses on: 1) Extracting researcher profiles automatically from the Web; 2) Integrating the publication data into the network from existing digital libraries; 3) Modeling the entire academic network; and 4) Providing search services for the academic network. So far, 448,470 researcher profiles have been extracted using a unified tagging approach. We integrate publications from online Web databases and propose a probabilistic framework to deal with the name ambiguity problem. Furthermore, we propose a unified modeling approach to simultaneously model topical aspects of papers, authors, and publication venues. Search services such as expertise search and people association search have been provided based on the modeling results. In this paper, we describe the architecture and main features of the system. We also present the empirical evaluation of the proposed methods. Given a large-scale linked document collection, such as a collection of blog posts or a research literature archive, there are two fundamental problems that have generated a lot of interest in the research community. One is to identify a set of high-level topics covered by the documents in the collection; the other is to uncover and analyze the social network of the authors of the documents. So far these problems have been viewed as separate problems and considered independently from each other. In this paper we argue that these two problems are in fact inter-dependent and should be addressed together. We develop a Bayesian hierarchical approach that performs topic modeling and author community discovery in one unified framework. The effectiveness of our model is demonstrated on two blog data sets in different domains and one research paper citation data from CiteSeer. Scientists continue to find challenges in the ever increasing amount of information that has been produced on a world wide scale, during the last decades. When writing a paper, an author searches for the most relevant citations that started or were the foundation of a particular topic, which would very likely explain the thinking or algorithms that are employed. The search is usually done using specific keywords submitted to literature search engines such as Google Scholar and CiteSeer. However, finding relevant citations is distinctive from producing articles that are only topically similar to an author's proposal. In this paper, we address the problem of citation recommendation using a singular value decomposition approach. The models are trained and evaluated on the Citeseer digital library. The results of our experiments show that the proposed approach achieves significant success when compared with collaborative filtering methods on the citation recommendation task. Objective: The amount of new discoveries (as published in the scientific literature) in the biomedical area is growing at an exponential rate. This growth makes it very difficult to filter the most relevant results, and thus the extraction of the core information becomes very expensive. Therefore, there is a growing interest in text processing approaches that can deliver selected information from scientific publications, which can limit the amount of human intervention normally needed to gather those results. Materials and methods: This paper presents and evaluates an approach aimed at automating the process of extracting functional relations (e.g. interactions between genes and proteins) from scientific literature in the biomedical domain. The approach, using a novel dependency-based parser, is based on a complete syntactic analysis of the corpus. Results: We have implemented a state-of-the-art text mining system for biomedical literature, based on a deep-linguistic, full-parsing approach. The results are validated on two different corpora: the manually annotated genomics information access (GENIA) corpus and the automatically annotated arabidopsis thaliana circadian rhythms (ATCR) corpus. Conclusion: We show how a deep-linguistic approach (contrary to common belief) can be used in a real world text mining application, offering high-precision relation extraction, while at the same time retaining a sufficient recall. This paper addresses the problem of making text mining results more comprehensible to humanities scholars, journalists, intelligence analysts, and other researchers, in order to support the analysis of text collections. Our system, FeatureLens1, visualizes a text collection at several levels of granularity and enables users to explore interesting text patterns. The current implementation focuses on frequent itemsets of n-grams, as they capture the repetition of exact or similar expressions in the collection. Users can find meaningful co-occurrences of text patterns by visualizing them within and across documents in the collection. This also permits users to identify the temporal evolution of usage such as increasing, decreasing or sudden appearance of text patterns. The interface could be used to explore other text features as well. Initial studies suggest that FeatureLens helped a literary scholar and 8 users generate new hypotheses and interesting insights using 2 text collections. Traditional text mining techniques transform free text into flat bags of words representation, which does not preserve sufficient semantics for the purpose of knowledge discovery. In this paper, we present a two-step procedure to mine generalized associations of semantic relations conveyed by the textual content of Web documents. First, RDF (resource description framework) metadata representing semantic relations are extracted from raw text using a myriad of natural language processing techniques. The relation extraction process also creates a term taxonomy in the form of a sense hierarchy inferred from WordNet. Then, a novel generalized association pattern mining algorithm (GP-Close) is applied to discover the underlying relation association patterns on RDF metadata. For pruning the large number of redundant overgeneralized patterns in relation pattern search space, the GP-Close algorithm adopts the notion of generalization closure for systematic overgeneralization reduction. The efficacy of our approach is demonstrated through empirical experiments conducted on an online database of terrorist activities To reveal information hiding in link space of bibliographical networks, link analysis has been studied from different perspectives in recent years. In this paper, we address a novel problem namely citation prediction, that is: given information about authors, topics, target publication venues as well as time of certain research paper, finding and predicting the citation relationship between a query paper and a set of previous papers. Considering the gigantic size of relevant papers, the loosely connected citation network structure as well as the highly skewed citation relation distribution, citation prediction is more challenging than other link prediction problems which have been studied before. By building a meta-path based prediction model on a topic discriminative search space, we here propose a two-phase citation probability learning approach, in order to predict citation relationship effectively and efficiently. Experiments are performed on real-world dataset with comprehensive measurements, which demonstrate that our framework has substantial advantages over commonly used link prediction approaches in predicting citation relations in bibliographical networks. We propose a new unsupervised learning technique for extracting information from large text collections. We model documents as if they were generated by a two-stage stochastic process. Each author is represented by a probability distribution over topics, and each topic is represented as a probability distribution over words for that topic. The words in a multi-author paper are assumed to be the result of a mixture of each authors' topic mixture. The topic-word and author-topic distributions are learned from data in an unsupervised manner using a Markov chain Monte Carlo algorithm. We apply the methodology to a large corpus of 160,000 abstracts and 85,000 authors from the well-known CiteSeer digital library, and learn a model with 300 topics. We discuss in detail the interpretation of the results discovered by the system including specific topic and author models, ranking of authors by topic and topics by author, significant trends in the computer science literature between 1990 and 2002, parsing of abstracts by topics and authors and detection of unusual papers by specific authors. An online query interface to the model is also discussed that allows interactive exploration of author-topic models for corpora such as CiteSeer. 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.