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.
Boland2012 proposed a pattern induction method for extracting dataset references from documents in order to overcome the necessity of such a large training set @cite_1 . Their algorithm starts with either the name of a dataset or with an abbreviation of this name, and then drives patterns of all phrases that contain that name or abbreviation in articles. The patterns are applied to articles in order to extract more dataset names and abbreviations. This process repeats with new abbreviations and names until no more datasets can be detected in articles. It derives patterns of phrases that contain dataset references iteratively by using a bootstrapping approach.
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Objective: To develop methods that automatically map abbreviations to their full forms in biomedical articles. @PARASPLIT Methods: The authors developed two methods of mapping defined and undefined abbreviations (defined abbreviations are paired with their full forms in the articles, whereas undefined ones are not). For defined abbreviations, they developed a set of pattern-matching rules to map an abbreviation to its full form and implemented the rules into a software program, AbbRE (for “abbreviation recognition and extraction”). Using the opinions of domain experts as a reference standard, they evaluated the recall and precision of AbbRE for defined abbreviations in ten biomedical articles randomly selected from the ten most frequently cited medical and biological journals. They also measured the percentage of undefined abbreviations in the same set of articles, and they investigated whether they could map undefined abbreviations to any of four public abbreviation databases (GenBank LocusLink, swissprot, LRABR of the UMLS Specialist Lexicon, and Bioabacus). @PARASPLIT Results: AbbRE had an average 0.70 recall and 0.95 precision for the defined abbreviations. The authors found that an average of 25 percent of abbreviations were defined in biomedical articles and that of a randomly selected subset of undefined abbreviations, 68 percent could be mapped to any of four abbreviation databases. They also found that many abbreviations are ambiguous (i.e., they map to more than one full form in abbreviation databases). @PARASPLIT Conclusion: AbbRE is efficient for mapping defined abbreviations. To couple AbbRE with abbreviation databases for the mapping of undefined abbreviations, not only exhaustive abbreviation databases but also a method to resolve the ambiguity of abbreviations in the databases are needed. Motivation: Biological literature contains many abbreviations with one particular sense in each document. However, most abbreviations do not have a unique sense across the literature. Furthermore, many documents do not contain the long forms of the abbreviations. Resolving an abbreviation in a document consists of retrieving its sense in use. Abbreviation resolution improves accuracy of document retrieval engines and of information extraction systems. Results: We combine an automatic analysis of Medline abstracts and linguistic methods to build a dictionary of abbreviation sense pairs. The dictionary is used for the resolution of abbreviations occurring with their long forms. Ambiguous global abbreviations are resolved using support vector machines that have been trained on the context of each instance of the abbreviation sense pairs, previously extracted for the dictionary set-up. The system disambiguates abbreviations with a precision of 98.9 for a recall of 98.2 (98.5 accuracy). This performance is superior in comparison with previously reported research work. Availability: The abbreviation resolution module is available at http: www.ebi.ac.uk Rebholz software.html Contact: [email protected] The recognition of names and their associated categories within unstructured text traditionally relies on semantic lexicons and gazetteers. The amount of effort required to assemble large lexicons confines the recognition to either a limited domain (e.g., medical imaging), or a small set of pre-defined, broader categories of interest (e.g., persons, countries, organizations, products). This constitutes a serious limitation in an information seeking context. In this case, the categories of potential interest to users are more diverse (universities, agencies, retailers, celebrities), often refined (e.g., SLR digital cameras, programming languages, multinational oil companies), and usually overlapping (e.g., the same entity may be concurrently a brand name, a technology company, and an industry leader). We present a lightly supervised method for acquiring named entities in arbitrary categories. The method applies lightweight lexico-syntactic extraction patterns to the unstructured text of Web documents. The method is a departure from traditional approaches to named entity recognition in that: 1) it does not require any start-up seed names or training; 2) it does not encode any domain knowledge in its extraction patterns; 3) it is only lightly supervised, and data-driven; 4) it does not impose any a-priori restriction on the categories of extracted names. We illustrate applications of the method in Web search, and describe experiments on 500 million Web documents and news articles. The location of the author of a social media message is not invariably the same as the location that the author writes about in the message. In applications that mine these messages for information such as tracking news, political events or responding to disasters, it is the geographic content of the message rather than the location of the author that is important. To this end, we present a method to geo-parse the short, informal messages known as microtext. Our preliminary investigation has shown that many microtext messages contain place references that are abbreviated, misspelled, or highly localized. These references are missed by standard geo-parsers. Our geo-parser is built to find such references. It uses Natural Language Processing methods to identify references to streets and addresses, buildings and urban spaces, and toponyms, and place acronyms and abbreviations. It combines heuristics, open-source Named Entity Recognition software, and machine learning techniques. Our primary data consisted of Twitter messages sent immediately following the February 2011 earthquake in Christchurch, New Zealand. The algorithm identified location in the data sample, Twitter messages, giving an F statistic of 0.85 for streets, 0.86 for buildings, 0.96 for toponyms, and 0.88 for place abbreviations, with a combined average F of 0.90 for identifying places. The same data run through a geo-parsing standard, Yahoo! Placemaker, yielded an F statistic of zero for streets and buildings (because Placemaker is designed to find neither streets nor buildings), and an F of 0.67 for toponyms. Abbreviations and acronyms are widely used in the biomedical literature and many of them represent important biomedical concepts. Because many abbreviations are ambiguous (e.g., CAT denotes both chloramphenicol acetyl transferase and computed axial tomography, depending on the context), recognizing the full form associated with each abbreviation is in most cases equivalent to identifying the meaning of the abbreviation. This, in turn, allows us to perform more accurate natural language processing, information extraction, and retrieval. In this study, we have developed supervised approaches to identifying the full forms of ambiguous abbreviations within the context they appear. We first automatically assigned multiple possible full forms for each abbreviation; we then treated the in-context full-form prediction for each specific abbreviation occurrence as a case of word-sense disambiguation. We generated automatically a dictionary of all possible full forms for each abbreviation. We applied supervised machine-learning algorithms for disambiguation. Because some of the links between abbreviations and their corresponding full forms are explicitly given in the text and can be recovered automatically, we can use these explicit links to automatically provide training data for disambiguating the abbreviations that are not linked to a full form within a text. We evaluated our methods on over 150 thousand abstracts and obtain for coverage and precision results of 82p and 92p, respectively, when performed as tenfold cross-validation, and 79p and 80p, respectively, when evaluated against an external set of abstracts in which the abbreviations are not defined. Dimensionality reduction techniques are used for representing higher dimensional data by a more parsimonious and meaningful lower dimensional structure. In this paper we will study two such approaches, namely Carroll’s Parametric Mapping (abbreviated PARAMAP) (Shepard and Carroll, 1966) and Tenenbaum’s Isometric Mapping (abbreviated Isomap) (Tenenbaum, de Silva, and Langford, 2000). The former relies on iterative minimization of a cost function while the latter applies classical MDS after a preprocessing step involving the use of a shortest path algorithm to define approximate geodesic distances. We will develop a measure of congruence based on preservation of local structure between the input data and the mapped low dimensional embedding, and compare the different approaches on various sets of data, including points located on the surface of a sphere, some data called the "Swiss Roll data", and truncated spheres. Terminologies that account for variation in language use by linking synonyms and abbreviations to their corresponding concept are important enablers of high-quality information extraction from medical texts. Due to the use of specialized sub-languages in the medical domain, manual construction of semantic resources that accurately reflect language use is both costly and challenging, often resulting in low coverage. Although models of distributional semantics applied to large corpora provide a potential means of supporting development of such resources, their ability to isolate synonymy from other semantic relations is limited. Their application in the clinical domain has also only recently begun to be explored. Combining distributional models and applying them to different types of corpora may lead to enhanced performance on the tasks of automatically extracting synonyms and abbreviation-expansion pairs. A combination of two distributional models – Random Indexing and Random Permutation – employed in conjunction with a single corpus outperforms using either of the models in isolation. Furthermore, combining semantic spaces induced from different types of corpora – a corpus of clinical text and a corpus of medical journal articles – further improves results, outperforming a combination of semantic spaces induced from a single source, as well as a single semantic space induced from the conjoint corpus. A combination strategy that simply sums the cosine similarity scores of candidate terms is generally the most profitable out of the ones explored. Finally, applying simple post-processing filtering rules yields substantial performance gains on the tasks of extracting abbreviation-expansion pairs, but not synonyms. The best results, measured as recall in a list of ten candidate terms, for the three tasks are: 0.39 for abbreviations to long forms, 0.33 for long forms to abbreviations, and 0.47 for synonyms. This study demonstrates that ensembles of semantic spaces can yield improved performance on the tasks of automatically extracting synonyms and abbreviation-expansion pairs. This notion, which merits further exploration, allows different distributional models – with different model parameters – and different types of corpora to be combined, potentially allowing enhanced performance to be obtained on a wide range of natural language processing tasks. We present a weakly supervised approach for learning hashtags, hashtag patterns, and phrases associated with five emotions: AFFECTION, ANGER RAGE, FEAR ANXIETY, JOY, and SADNESS DISAPPOINTMENT. Starting with seed hashtags to label an initial set of tweets, we train emotion classifiers and use them to learn new emotion hashtags and hashtag patterns. This process then repeats in a bootstrapping framework. Emotion phrases are also extracted from the learned hashtags and used to create phrase-based emotion classifiers. We show that the learned set of emotion indicators yields a substantial improvement in F-scores, ranging from + 5 to + 18 over baseline classifiers. We show quite good face clustering is possible for a dataset of inaccurately and ambiguously labelled face images. Our dataset is 44,773 face images, obtained by applying a face finder to approximately half a million captioned news images. This dataset is more realistic than usual face recognition datasets, because it contains faces captured "in the wild" in a variety of configurations with respect to the camera, taking a variety of expressions, and under illumination of widely varying color. Each face image is associated with a set of names, automatically extracted from the associated caption. Many, but not all such sets contain the correct name. We cluster face images in appropriate discriminant coordinates. We use a clustering procedure to break ambiguities in labelling and identify incorrectly labelled faces. A merging procedure then identifies variants of names that refer to the same individual. The resulting representation can be used to label faces in news images or to organize news pictures by individuals present. An alternative view of our procedure is as a process that cleans up noisy supervised data. We demonstrate how to use entropy measures to evaluate such procedures. The wealth of interaction information provided in biomedical articles motivated the implementation of text mining approaches to automatically extract biomedical relations. This paper presents an unsupervised method based on pattern clustering and sentence parsing to deal with biomedical relation extraction. Pattern clustering algorithm is based on Polynomial Kernel method, which identifies interaction words from unlabeled data; these interaction words are then used in relation extraction between entity pairs. Dependency parsing and phrase structure parsing are combined for relation extraction. Based on the semi-supervised KNN algorithm, we extend the proposed unsupervised approach to a semi-supervised approach by combining pattern clustering, dependency parsing and phrase structure parsing rules. We evaluated the approaches on two different tasks: (1) Protein–protein interactions extraction, and (2) Gene–suicide association extraction. The evaluation of task (1) on the benchmark dataset (AImed corpus) showed that our proposed unsupervised approach outperformed three supervised methods. The three supervised methods are rule based, SVM based, and Kernel based separately. The proposed semi-supervised approach is superior to the existing semi-supervised methods. The evaluation on gene–suicide association extraction on a smaller dataset from Genetic Association Database and a larger dataset from publicly available PubMed showed that the proposed unsupervised and semi-supervised methods achieved much higher F-scores than co-occurrence based method. We present a model for estimating the probability that a pair of author names (sharing last name and first initial), appearing on two different Medline articles, refer to the same individual. The model uses a simple yet powerful similarity profile between a pair of articles, based on title, journal name, coauthor names, medical subject headings (MeSH), language, affiliation, and name attributes (prevalence in the literature, middle initial, and suffix). The similarity profile distribution is computed from reference sets consisting of pairs of articles containing almost exclusively author matches versus nonmatches, generated in an unbiased manner. Although the match set is generated automatically and might contain a small proportion of nonmatches, the model is quite robust against contamination with nonmatches. We have created a free, public service (“Author-ity”: ) that takes as input an author's name given on a specific article, and gives as output a list of all articles with that (last name, first initial) ranked by decreasing similarity, with match probability indicated. © 2005 Wiley Periodicals, Inc. Due to name abbreviations, identical names, name misspellings, and pseudonyms in publications or bibliographies (citations), an author may have multiple names and multiple authors may share the same name. Such name ambiguity affects the performance of document retrieval, Web search, database integration, and may cause improper attribution to authors. We investigate two supervised learning approaches to disambiguate authors in the citations. One approach uses the naive Bayes probability model, a generative model; the other uses support vector machines (SVMs) [V. Vapnik (1995)] and the vector space representation of citations, a discriminative model. Both approaches utilize three types of citation attributes: coauthor names, the title of the paper, and the title of the journal or proceeding. We illustrate these two approaches on two types of data, one collected from the Web, mainly publication lists from homepages, the other collected from the DBLP citation databases. The usual approach to named-entity detection is to learn extraction rules that rely on linguistic, syntactic, or document format patterns that are consistent across a set of documents. However, when there is no consistency among documents, it may be more effective to learn document-specific extraction rules.This paper presents a knowledge-based approach to learning rules for named-entity extraction. Document-specific extraction rules are created using a generate-and-test paradigm and a database of known named-entities. Experimental results show that this approach is effective on Web documents that are difficult for the usual methods. Twitter is a popular platform for sharing activities, plans, and opinions. Through tweets, users often reveal their location information and short term visiting plans. In this paper, we are interested in extracting fine-grained locations mentioned in tweets with temporal awareness. More specifically, we like to extract each point-of-interest (POI) mention in a tweet and predict whether the user has visited, is currently at, or will soon visit this POI. Our proposed solution, named PETAR, consists of two main components: a POI inventory and a time-aware POI tagger. The POI inventory is built by exploiting the crowd wisdom of Foursquare community. It contains not only the formal names of POIs but also the informal abbreviations. The POI tagger, based on Conditional Random Field (CRF) model, is designed to simultaneously identify the POIs and resolve their associated temporal awareness. In our experiments, we investigated four types of features (i.e., lexical, grammatical, geographical, and BILOU schema features) for time-aware POI extraction. With the four types of features, PETAR achieves promising extraction accuracy and outperforms all baseline methods. In this paper, we address the tasks of recognition and interpretation of affect communicated through text messaging. The evolving nature of language in online conversations is a main issue in affect sensing from this media type, since sentence parsing might fail while syntactical structure analysis. The developed Affect Analysis Model was designed to handle not only correctly written text, but also informal messages written in abbreviated or expressive manner. The proposed rule-based approach processes each sentence in sequential stages, including symbolic cue processing, detection and transformation of abbreviations, sentence parsing, and word phrase sentence-level analyses. In a study based on 160 sentences, the system result agrees with at least two out of three human annotators in 70 of the cases. In order to reflect the detected affective information and social behaviour, an avatar was created. In this paper we address the problem of dataset extraction from research articles. With the growing digital data repositories and the demand of data centric research in data mining community, finding appropriate dataset for a research problem has become an essential step in scientific research. But given the wide variety of data usage in scientific research it is very difficult to figure out which datasets are most useful for a particular research topic. To alleviate this problem, an automated dataset search engine is a powerful tool. In this work we propose a novel approach to extract dataset names from research articles. We propose a novel way of using "web intelligence" from academic search engines and online dictionaries to mine dataset names from research articles. We also show a comparison between different sources of "web knowledge" by comparing different academic search engines such as Google scholar, Microsoft academic search. The performance of this approach is evaluated using standard information retrieval metric such as precision, recall and F-measure. We get an F-measure of 80 . This accuracy is significant for an unsupervised approach. In a social community, multiple persons may share the same name, phone number or some other identifying attributes. This, along with other phenomena, such as name abbreviation, name misspelling, and human error lead to erroneous aggregation of records of multiple persons under a single reference. Such mistakes affect the performance of document retrieval, web search, database integration, and more importantly, improper attribution of credit (or blame). The task of entity disambiguation partitions the records belonging to multiple persons with the objective that each partition is composed of records of a unique person. Existing solutions to this task use either biographical attributes, or auxiliary features that are collected from external sources, such as Wikipedia. However, for many scenarios, such auxiliary features are not available, or they are costly to obtain. Besides, the attempt of collecting biographical or external data sustains the risk of privacy violation. In this work, we propose a method for solving entity disambiguation task from timestamped link information obtained from a collaboration network. Our method is non-intrusive of privacy as it uses only the graph topology of an anonymized network. Experimental results on two real-life academic collaboration networks show that the proposed method has satisfactory performance. The pervasiveness of mobile devices and location based services is leading to an increasing volume of mobility data.This side eect provides the opportunity for innovative methods that analyse the behaviors of movements. In this paper we propose WhereNext, which is a method aimed at predicting with a certain level of accuracy the next location of a moving object. The prediction uses previously extracted movement patterns named Trajectory Patterns, which are a concise representation of behaviors of moving objects as sequences of regions frequently visited with a typical travel time. A decision tree, named T-pattern Tree, is built and evaluated with a formal training and test process. The tree is learned from the Trajectory Patterns that hold a certain area and it may be used as a predictor of the next location of a new trajectory finding the best matching path in the tree. Three dierent best matching methods to classify a new moving object are proposed and their impact on the quality of prediction is studied extensively. Using Trajectory Patterns as predictive rules has the following implications: (I) the learning depends on the movement of all available objects in a certain area instead of on the individual history of an object; (II) the prediction tree intrinsically contains the spatio-temporal properties that have emerged from the data and this allows us to define matching methods that striclty depend on the properties of such movements. In addition, we propose a set of other measures, that evaluate a priori the predictive power of a set of Trajectory Patterns. This measures were tuned on a real life case study. Finally, an exhaustive set of experiments and results on the real dataset are presented. Computing the semantic similarity between terms (or short text expressions) that have the same meaning but which are not lexicographically similar is a key challenge in many computer related fields. The problem is that traditional approaches to semantic similarity measurement are not suitable for all situations, for example, many of them often fail to deal with terms not covered by synonym dictionaries or are not able to cope with acronyms, abbreviations, buzzwords, brand names, proper nouns, and so on. In this paper, we present and evaluate a collection of emerging techniques developed to avoid this problem. These techniques use some kinds of web intelligence to determine the degree of similarity between text expressions. These techniques implement a variety of paradigms including the study of co-occurrence, text snippet comparison, frequent pattern finding, or search log analysis. The goal is to substitute the traditional techniques where necessary. We implemented a web server for acronym and abbreviation lookup, containing a collection of acronyms and their expansions gathered from a large number of web pages by a heuristic extraction process. Several different extraction algorithms were evaluated and compared. The corpus resulting from the best algorithm is comparable to a high-quality hand-crafted site, but has the potential to be much more inclusive as data from more web pages are processed.