KnowLife: A Versatile Approach for Constructing a Large Knowledge Graph for Biomedical Sciences

BACKGROUND: Biomedical knowledge bases (KB’s) have become important assets in life sciences. Prior work on KB construction has three major limitations. First, most biomedical KBs are manually built and curated, and cannot keep up with the rate at which new findings are published. Second, for automatic information extraction (IE), the text genre of choice has been scientific publications, neglecting sources like health portals and online communities. Third, most prior work on IE has focused on the molecular level or chemogenomics only, like protein-protein interactions or gene-drug relationships, or solely address highly specific topics such as drug effects. RESULTS: We address these three limitations by a versatile and scalable approach to automatic KB construction. Using a small number of seed facts for distant supervision of pattern-based extraction, we harvest a huge number of facts in an automated manner without requiring any explicit training. We extend previous techniques for pattern-based IE with confidence statistics, and we combine this recall-oriented stage with logical reasoning for consistency constraint checking to achieve high precision. To our knowledge, this is the first method that uses consistency checking for biomedical relations. Our approach can be easily extended to incorporate additional relations and constraints. We ran extensive experiments not only for scientific publications, but also for encyclopedic health portals and online communities, creating different KB’s based on different configurations. We assess the size and quality of each KB, in terms of number of facts and precision. The best configured KB, KnowLife, contains more than 500,000 facts at a precision of 93% for 13 relations covering genes, organs, diseases, symptoms, treatments, as well as environmental and lifestyle risk factors. CONCLUSION: KnowLife is a large knowledge base for health and life sciences, automatically constructed from different Web sources. As a unique feature, KnowLife is harvested from different text genres such as scientific publications, health portals, and online communities. Thus, it has the potential to serve as one-stop portal for a wide range of relations and use cases. To showcase the breadth and usefulness, we make the KnowLife KB accessible through the health portal (http://knowlife.mpi-inf.mpg.de). ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-015-0549-5) contains supplementary material, which is available to authorized users

Proceedings of the Workshop Semantic Content Acquisition and Representation (SCAR) 2007

This is the proceedings of the Workshop on Semantic Content Acquisition and Representation, held in conjunction with NODALIDA 2007, on May 24 2007 in Tartu, Estonia.</p

Designing Statistical Language Learners: Experiments on Noun Compounds

The goal of this thesis is to advance the exploration of the statistical language learning design space. In pursuit of that goal, the thesis makes two main theoretical contributions: (i) it identifies a new class of designs by specifying an architecture for natural language analysis in which probabilities are given to semantic forms rather than to more superficial linguistic elements; and (ii) it explores the development of a mathematical theory to predict the expected accuracy of statistical language learning systems in terms of the volume of data used to train them. The theoretical work is illustrated by applying statistical language learning designs to the analysis of noun compounds. Both syntactic and semantic analysis of noun compounds are attempted using the proposed architecture. Empirical comparisons demonstrate that the proposed syntactic model is significantly better than those previously suggested, approaching the performance of human judges on the same task, and that the proposed semantic model, the first statistical approach to this problem, exhibits significantly better accuracy than the baseline strategy. These results suggest that the new class of designs identified is a promising one. The experiments also serve to highlight the need for a widely applicable theory of data requirements.Comment: PhD thesis (Macquarie University, Sydney; December 1995), LaTeX source, xii+214 page

Human-Level Performance on Word Analogy Questions by Latent Relational Analysis

This paper introduces Latent Relational Analysis (LRA), a method for measuring relational similarity. LRA has potential applications in many areas, including information extraction, word sense disambiguation, machine translation, and information retrieval. Relational similarity is correspondence between relations, in contrast with attributional similarity, which is correspondence between attributes. When two words have a high degree of attributional similarity, we call them synonyms. When two pairs of words have a high degree of relational similarity, we say that their relations are analogous. For example, the word pair mason/stone is analogous to the pair carpenter/wood; the relations between mason and stone are highly similar to the relations between carpenter and wood. Past work on semantic similarity measures has mainly been concerned with attributional similarity. For instance, Latent Semantic Analysis (LSA) can measure the degree of similarity between two words, but not between two relations. Recently the Vector Space Model (VSM) of information retrieval has been adapted to the task of measuring relational similarity, achieving a score of 47% on a collection of 374 college-level multiple-choice word analogy questions. In the VSM approach, the relation between a pair of words is characterized by a vector of frequencies of predefined patterns in a large corpus. LRA extends the VSM approach in three ways: (1) the patterns are derived automatically from the corpus (they are not predefined), (2) the Singular Value Decomposition (SVD) is used to smooth the frequency data (it is also used this way in LSA), and (3) automatically generated synonyms are used to explore reformulations of the word pairs. LRA achieves 56% on the 374 analogy questions, statistically equivalent to the average human score of 57%. On the related problem of classifying noun-modifier relations, LRA achieves similar gains over the VSM, while using a smaller corpus

Knowledge-based methods for automatic extraction of domain-specific ontologies

Semantic web technology aims at developing methodologies for representing large amount of knowledge in web accessible form. The semantics of knowledge should be easy to interpret and understand by computer programs, so that sharing and utilizing knowledge across the Web would be possible. Domain specific ontologies form the basis for knowledge representation in the semantic web. Research on automated development of ontologies from texts has become increasingly important because manual construction of ontologies is labor intensive and costly, and, at the same time, large amount of texts for individual domains is already available in electronic form. However, automatic extraction of domain specific ontologies is challenging due to the unstructured nature of texts and inherent semantic ambiguities in natural language. Moreover, the large size of texts to be processed renders full-fledged natural language processing methods infeasible. In this dissertation, we develop a set of knowledge-based techniques for automatic extraction of ontological components (concepts, taxonomic and non-taxonomic relations) from domain texts. The proposed methods combine information retrieval metrics, lexical knowledge-base(like WordNet), machine learning techniques, heuristics, and statistical approaches to meet the challenge of the task. These methods are domain-independent and automatic approaches. For extraction of concepts, the proposed WNSCA+{PE, POP} method utilizes the lexical knowledge base WordNet to improve precision and recall over the traditional information retrieval metrics. A WordNet-based approach, the compound term heuristic, and a supervised learning approach are developed for taxonomy extraction. We also developed a weighted word-sense disambiguation method for use with the WordNet-based approach. An unsupervised approach using log-likelihood ratios is proposed for extracting non-taxonomic relations. Further more, a supervised approach is investigated to learn the semantic constraints for identifying relations from prepositional phrases. The proposed methods are validated by experiments with the Electronic Voting and the Tender Offers, Mergers, and Acquisitions domain corpus. Experimental results and comparisons with some existing approaches clearly indicate the superiority of our methods. In summary, a good combination of information retrieval, lexical knowledge base, statistics and machine learning methods in this study has led to the techniques efficient and effective for extracting ontological components automatically

Slot Filling

Slot filling (SF) is the task of automatically extracting facts about particular entities from unstructured text, and populating a knowledge base (KB) with these facts. These structured KBs enable applications such as structured web queries and question answering. SF is typically framed as a query-oriented setting of the related task of relation extraction. Throughout this thesis, we reflect on how SF is a task with many distinct problems. We demonstrate that recall is a major limiter on SF system performance. We contribute an analysis of typical SF recall loss, and find a substantial amount of loss occurs early in the SF pipeline. We confirm that accurate NER and coreference resolution are required for high-recall SF. We measure upper bounds using a naïve graph-based semi-supervised bootstrapping technique, and find that only 39% of results are reachable using a typical feature space. We expect that this graph-based technique will be directly useful for extraction, and this leads us to frame SF as a label propagation task. We focus on a detailed graph representation of the task which reflects the behaviour and assumptions we want to model based on our analysis, including modifying the label propagation process to model multiple types of label interaction. Analysing the graph, we find that a large number of errors occur in very close proximity to training data, and identify that this is of major concern for propagation. While there are some conflicts caused by a lack of sufficient disambiguating context—we explore adding additional contextual features to address this—many of these conflicts are caused by subtle annotation problems. We find that lack of a standard for how explicit expressions of relations must be in text makes consistent annotation difficult. Using a strict definition of explicitness results in 20% of correct annotations being removed from a standard dataset. We contribute several annotation-driven analyses of this problem, exploring the definition of slots and the effect of the lack of a concrete definition of explicitness: annotation schema do not detail how explicit expressions of relations need to be, and there is large scope for disagreement between annotators. Additionally, applications may require relatively strict or relaxed evidence for extractions, but this is not considered in annotation tasks. We demonstrate that annotators frequently disagree on instances, dependent on differences in annotator world knowledge and thresholds on making probabilistic inference. SF is fundamental to enabling many knowledge-based applications, and this work motivates modelling and evaluating SF to better target these tasks

Augmented trading:From news articles to stock price predictions using semantics

This thesis tries to answer the question how to predict the reaction of the stock market to news articles using the latest suitable developments in Natural Language Processing. This is done using text classiffication where a new article is matched to a category of articles which have a certain influence on the stock price. The thesis first discusses why analysis of news articles is a feasible approach to predicting the stock market and why analysis of past prices should not be build upon. From related work in this domain two main design choices are extracted; what to take as features for news articles and how to couple them with the changes in stock price. This thesis then suggests which different features are possible to extract from articles resulting in a template for features which can deal with negation, favorability, abstracts from companies and uses domain knowledge and synonyms for generalization. To couple the features to changes in stock price a survey is given of several text classiffication techniques from which it is concluded that Support Vector Machines are very suitable for the domain of stock prices and extensive features. The system has been tested with a unique data set of news articles for which results are reported that are signifficantly better than random. The results improve even more when only headlines of news articles are taken into account. Because the system is only tested with closing prices it cannot concluded that it will work in practice but this can be easily tested if stock prices during the days are available. The main suggestions for feature work are to test the system with this data and to improve the filling of the template so it can also be used in other areas of favorability analysis or maybe even to extract interesting information out of texts

D6.1: Technologies and Tools for Lexical Acquisition

This report describes the technologies and tools to be used for Lexical Acquisition in PANACEA. It includes descriptions of existing technologies and tools which can be built on and improved within PANACEA, as well as of new technologies and tools to be developed and integrated in PANACEA platform. The report also specifies the Lexical Resources to be produced. Four main areas of lexical acquisition are included: Subcategorization frames (SCFs), Selectional Preferences (SPs), Lexical-semantic Classes (LCs), for both nouns and verbs, and Multi-Word Expressions (MWEs)