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 82% and 92%, respectively, when performed as tenfold cross-validation, and 79% and 80%, respectively, when evaluated against an external set of abstracts in which the abbreviations are not defined.

Biomedical abbreviations and acronyms are widely used in biomedical literature. Since many abbreviations represent important content in biomedical literature, information retrieval and extraction benefits from identifying the meanings of biomedical abbreviations. Since many abbreviations are ambiguous, it would be important to map abbreviations to their full forms, which ultimately represent the meanings of the abbreviations. In this study, we present a novel unsupervised method that applies MEDLINE records as a knowledge source for disambiguating abbreviations in full-text biomedical journal articles. We first automatically generated from MEDLINE records a knowledge source or dictionary of abbreviation-full pairs. We then trained on MEDLINE records and predicted the full forms of abbreviations in full-text journal articles by applying supervised machine-learning algorithms in an unsupervised fashion. We report up to 92% prediction precision and up to 91% coverage.

Information on molecular networks, such as networks of interacting proteins, comes from diverse sources that contain remarkable differences in distribution and quantity of errors. Here, we introduce a probabilistic model useful for predicting protein interactions from heterogeneous data sources. The model describes stochastic generation of protein-protein interaction networks with real-world properties, as well as generation of two heterogeneous sources of protein-interaction information: research results automatically extracted from the literature and yeast two-hybrid experiments. Based on the domain composition of proteins, we use the model to predict protein interactions for pairs of proteins for which no experimental data are available. We further explore the prediction limits, given experimental data that cover only part of the underlying protein networks. This approach can be extended naturally to include other types of biological data sources.

Web pages (and resources, in general) can be characterized according to their geographical locality. For example, a web page with general information about wildflowers could be considered a global page, likely to be of interest to a geographically broad audience. In contrast, a web page with listings on houses for sale in a specific city could be regarded as a local page, likely to be of interest only to an audience in a relatively narrow region. Similarly, some search engine queries (implicitly) target global pages, while other queries are after local pages. For example, the best results for query [wildflowers] are probably global pages about wildflowers such as the one discussed above. However, local pages that are relevant to, say, San Francisco are likely to be good matches for a query [houses for sale] that was issued by a San Francisco resident or by somebody moving to that city. Unfortunately, search engines do not analyze the geographical locality of queries and users, and hence often produce sub-optimal results. Thus query [wildflowers] might return pages that discuss wildflowers in specific U.S. states (and not general information about wildflowers), while query [houses for sale] might return pages with real estate listings for locations other than that of interest to the person who issued the query. Deciding whether an unseen query should produce mostly local or global pages---without placing this burden on the search engine users---is an important and challenging problem, because queries are often ambiguous or underspecify the information they are after. In this paper, we address this problem by first defining how to categorize queries according to their (often implicit) geographical locality. We then introduce several alternatives for automatically and efficiently categorizing queries in our scheme, using a variety of state-of-the-art machine learning tools. We report a thorough evaluation of our classifiers using a large sample of queries from a real web search engine, and conclude by discussing how our query categorization approach can help improve query result quality.

Knowledge on interactions between molecules in living cells is indispensable for theoretical analysis and practical applications in modern genomics and molecular biology. Building such networks relies on the assumption that the correct molecular interactions are known or can be identified by reading a few research articles. However, this assumption does not necessarily hold, as truth is rather an emerging property based on many potentially conflicting facts. This paper explores the processes of knowledge generation and publishing in the molecular biology literature using modelling and analysis of real molecular interaction data. The data analysed in this article were automatically extracted from 50000 research articles in molecular biology using a computer system called GeneWays containing a natural language processing module. The paper indicates that truthfulness of statements is associated in the minds of scientists with the relative importance (connectedness) of substances under study, revealing a potential selection bias in the reporting of research results. Aiming at understanding the statistical properties of the life cycle of biological facts reported in research articles, we formulate a stochastic model describing generation and propagation of knowledge about molecular interactions through scientific publications. We hope that in the future such a model can be useful for automatically producing consensus views of molecular interaction data.

OBJECTIVE: The authors present a system that scans electronic records from cardiac surgery and uses inference rules to identify and classify abnormal events (e.g., hypertension) that may occur during critical surgical points (e.g., start of bypass). This vital information is used as the content of automatically generated briefings designed by MAGIC, a multimedia system that they are developing to brief intensive care unit clinicians on patient status after cardiac surgery. By recognizing patterns in the patient record, inferences concisely summarize detailed patient data. DESIGN: The authors present the development of inference rules that identify important information about patient status and describe their implementation and an experiment they carried out to validate their correctness. The data for a set of 24 patients were analyzed independently by the system and by 46 physicians. MEASUREMENTS: The authors measured accuracy, specificity, and sensitivity by comparing system inferences against physician judgments, in cases where all three physicians agreed and against the majority opinion in all cases. RESULTS: For laboratory inferences, evaluation shows that the system has an average accuracy of 98 percent (full agreement) and 96 percent (majority model). An analysis of interrater agreement, however, showed that physicians do not agree on abnormal hemodynamic events and could not serve as a gold standard for evaluating hemodynamic events. Analysis of discrepancies reveals possibilities for system improvement and causes of physician disagreement. CONCLUSIONS: This evaluation shows that the laboratory inferences of the system have high accuracy. The lack of agreement among physicians highlights the need for an objective quality-assurance tool for hemodynamic inferences. The system provides such a tool by implementing inferencing procedures established in the literature.

We investigate four hierarchical clustering methods (single-link, complete-link, groupwise-average, and single-pass) and two linguistically motivated text features (noun phrase heads and proper names) in the context of document clustering. A statistical model for combining similarity information from multiple sources is described and applied to DARPA's Topic Detection and Tracking phase 2 (TDT2) data. This model, based on log-linear regression, alleviates the need for extensive search in order to determine optimal weights for combining input features. Through an extensive series of experiments with more than 40,000 documents from multiple news sources and modalities, we establish that both the choice of clustering algorithm and the introduction of the additional features have an impact on clustering performance. We apply our optimal combination of features to the TDT2 test data, obtaining partitions of the documents that compare favorably with the results obtained by participants in the official TDT2 competition.

We present a corpus-based study of the sequential ordering among premodifiers in noun phrases. This information is important for the fluency of generated text in practical applications. We propose and evaluate three approaches to identify sequential order among premodifiers: direct evidence, transitive closure, and clustering. Our implemented system can make over 94% of such ordering decisions correctly, as evaluated on a large, previously unseen test corpus.

We identify and validate from a large corpus constraints from conjunctions on the positive or negative semantic orientation of the conjoined adjectives. A log-linear regression model uses these constraints to predict whether conjoined adjectives are of same or different orientations, achieving 82% accuracy in this task when each conjunction is considered independently. Combining the constraints across many adjectives, a clustering algorithm separates the adjectives into groups of different orientations, and finally, adjectives are labeled positive or negative. Evaluations on real data and simulation experiments indicate high levels of performance: classification precision is more than 90% for adjectives that occur in a modest number of conjunctions in the corpus.

We present a corpus-based study of methods that have been proposed in the linguistics literature for selecting the semantically unmarked term out of a pair of antonymous adjectives. Solutions to this problem are applicable to the more general task of selecting the positive term from the pair. Using automatically collected data, the accuracy and applicability of each method is quantified, and a statistical analysis of the significance of the results is performed. We show that some simple methods are indeed good indicators for the answer to the problem while other proposed methods fail to perform better than would be attributable to chance. In addition, one of the simplest methods, text frequency, dominates all others. We also apply two generic statistical learning methods for combining the indications of the individual methods, and compare their performance to the simple methods. The most sophisticated complex learning method offers a small, but statistically significant, improvement over the original tests.

Large-scale natural language generation requires the integration of vast amounts of knowledge: lexical, grammatical, and conceptual. A robust generator must be able to operate well even when pieces of knowledge are missing. It must also be robust against incomplete or inaccurate inputs. To attack these problems, we have built a hybrid generator, in which gaps in symbolic knowledge are filled by statistical methods. We describe algorithms and show experimental results. We also discuss how the hybrid generation model can be used to simplify current generators and enhance their portability, even when perfect knowledge is in principle obtainable.

In this paper we present a method to group adjectives according to their meaning, as a first step towards the automatic identification of adjectival scales. We discuss the properties of adjectival scales and of groups of semantically related adjectives and how they imply sources of linguistic knowledge in text corpora. We describe how our system exploits this linguistic knowledge to compute a measure of similarity between two adjectives, using statistical techniques and without having access to any semantic information about the adjectives. We also show how a clustering algorithm can use these similarities to produce the groups of adjectives, and we present results produced by our system for a sample set of adjectives. We conclude by presenting evaluation methods for the task at hand, and analyzing the significance of the results obtained.