Raheel Nawaz

Enriching a biomedical event corpus with meta-knowledge annotation

BackgroundBiomedical papers contain rich information about entities, facts and events of biological relevance. To discover these automatically, we use text mining techniques, which rely on annotated corpora for training. In order to extract protein-protein interactions, genotype-phenotype/gene-disease associations, etc., we rely on event corpora that are annotated with classified, structured representations of important facts and findings contained within text. These provide an important resource for the training of domain-specific information extraction (IE) systems, to facilitate semantic-based searching of documents. Correct interpretation of these events is not possible without additional information, e.g., does an event describe a fact, a hypothesis, an experimental result or an analysis of results? How confident is the author about the validity of her analyses? These and other types of information, which we collectively term meta-knowledge, can be derived from the context of the event.ResultsWe have designed an annotation scheme for meta-knowledge enrichment of biomedical event corpora. The scheme is multi-dimensional, in that each event is annotated for 5 different aspects of meta-knowledge that can be derived from the textual context of the event. Textual clues used to determine the values are also annotated. The scheme is intended to be general enough to allow integration with different types of bio-event annotation, whilst being detailed enough to capture important subtleties in the nature of the meta-knowledge expressed in the text. We report here on both the main features of the annotation scheme, as well as its application to the GENIA event corpus (1000 abstracts with 36,858 events). High levels of inter-annotator agreement have been achieved, falling in the range of 0.84-0.93 Kappa.ConclusionBy augmenting event annotations with meta-knowledge, more sophisticated IE systems can be trained, which allow interpretative information to be specified as part of the search criteria. This can assist in a number of important tasks, e.g., finding new experimental knowledge to facilitate database curation, enabling textual inference to detect entailments and contradictions, etc. To our knowledge, our scheme is unique within the field with regards to the diversity of meta-knowledge aspects annotated for each event.

Event-based text mining for biology and functional genomics

The assessment of genome function requires a mapping between genome-derived entities and biochemical reactions, and the biomedical literature represents a rich source of information about reactions between biological components. However, the increasingly rapid growth in the volume of literature provides both a challenge and an opportunity for researchers to isolate information about reactions of interest in a timely and efficient manner. In response, recent text mining research in the biology domain has been largely focused on the identification and extraction of ‘events’, i.e. categorised, structured representations of relationships between biochemical entities, from the literature. Functional genomics analyses necessarily encompass events as so defined. Automatic event extraction systems facilitate the development of sophisticated semantic search applications, allowing researchers to formulate structured queries over extracted events, so as to specify the exact types of reactions to be retrieved. This article provides an overview of recent research into event extraction. We cover annotated corpora on which systems are trained, systems that achieve state-of-the-art performance and details of the community shared tasks that have been instrumental in increasing the quality, coverage and scalability of recent systems. Finally, several concrete applications of event extraction are covered, together with emerging directions of research.

Negated bio-events: analysis and identification

BackgroundNegation occurs frequently in scientific literature, especially in biomedical literature. It has previously been reported that around 13% of sentences found in biomedical research articles contain negation. Historically, the main motivation for identifying negated events has been to ensure their exclusion from lists of extracted interactions. However, recently, there has been a growing interest in negative results, which has resulted in negation detection being identified as a key challenge in biomedical relation extraction. In this article, we focus on the problem of identifying negated bio-events, given gold standard event annotations.ResultsWe have conducted a detailed analysis of three open access bio-event corpora containing negation information (i.e., GENIA Event, BioInfer and BioNLP’09 ST), and have identified the main types of negated bio-events. We have analysed the key aspects of a machine learning solution to the problem of detecting negated events, including selection of negation cues, feature engineering and the choice of learning algorithm. Combining the best solutions for each aspect of the problem, we propose a novel framework for the identification of negated bio-events. We have evaluated our system on each of the three open access corpora mentioned above. The performance of the system significantly surpasses the best results previously reported on the BioNLP’09 ST corpus, and achieves even better results on the GENIA Event and BioInfer corpora, both of which contain more varied and complex events.ConclusionsRecently, in the field of biomedical text mining, the development and enhancement of event-based systems has received significant interest. The ability to identify negated events is a key performance element for these systems. We have conducted the first detailed study on the analysis and identification of negated bio-events. Our proposed framework can be integrated with state-of-the-art event extraction systems. The resulting systems will be able to extract bio-events with attached polarities from textual documents, which can serve as the foundation for more elaborate systems that are able to detect mutually contradicting bio-events.

Detecting experimental techniques and selecting relevant documents for protein-protein interactions from biomedical literature

BackgroundThe selection of relevant articles for curation, and linking those articles to experimental techniques confirming the findings became one of the primary subjects of the recent BioCreative III contest. The contest’s Protein-Protein Interaction (PPI) task consisted of two sub-tasks: Article Classification Task (ACT) and Interaction Method Task (IMT). ACT aimed to automatically select relevant documents for PPI curation, whereas the goal of IMT was to recognise the methods used in experiments for identifying the interactions in full-text articles.ResultsWe proposed and compared several classification-based methods for both tasks, employing rich contextual features as well as features extracted from external knowledge sources. For IMT, a new method that classifies pair-wise relations between every text phrase and candidate interaction method obtained promising results with an F1 score of 64.49%, as tested on the task’s development dataset. We also explored ways to combine this new approach and more conventional, multi-label document classification methods. For ACT, our classifiers exploited automatically detected named entities and other linguistic information. The evaluation results on the BioCreative III PPI test datasets showed that our systems were very competitive: one of our IMT methods yielded the best performance among all participants, as measured by F1 score, Matthew’s Correlation Coefficient and AUC iP/R; whereas for ACT, our best classifier was ranked second as measured by AUC iP/R, and also competitive according to other metrics.ConclusionsOur novel approach that converts the multi-class, multi-label classification problem to a binary classification problem showed much promise in IMT. Nevertheless, on the test dataset the best performance was achieved by taking the union of the output of this method and that of a multi-class, multi-label document classifier, which indicates that the two types of systems complement each other in terms of recall. For ACT, our system exploited a rich set of features and also obtained encouraging results. We examined the features with respect to their contributions to the classification results, and concluded that contextual words surrounding named entities, as well as the MeSH headings associated with the documents were among the main contributors to the performance.

Enriching news events with meta-knowledge information

Given the vast amounts of data available in digitised textual form, it is important to provide mechanisms that allow users to extract nuggets of relevant information from the ever growing volumes of potentially important documents. Text mining techniques can help, through their ability to automatically extract relevant event descriptions, which link entities with situations described in the text. However, correct and complete interpretation of these event descriptions is not possible without considering additional contextual information often present within the surrounding text. This information, which we refer to as meta-knowledge, can include (but is not restricted to) the modality, subjectivity, source, polarity and specificity of the event. We have developed a meta-knowledge annotation scheme specifically tailored for news events, which includes six aspects of event interpretation. We have applied this annotation scheme to the ACE 2005 corpus, which contains 599 documents from various written and spoken news sources. We have also identified and annotated the words and phrases evoking the different types of meta-knowledge. Evaluation of the annotated corpus shows high levels of inter-annotator agreement for five meta-knowledge attributes, and moderate level of agreement for the sixth attribute. Detailed analysis of the annotated corpus has revealed further insights into the expression mechanisms of different types of meta-knowledge, their relative frequencies and mutual correlations.

Facilitating the analysis of discourse phenomena in an interoperable NLP platform

The analysis of discourse phenomena is essential in many natural language processing (NLP) applications. The growing diversity of available corpora and NLP tools brings a multitude of representation formats. In order to alleviate the problem of incompatible formats when constructing complex text mining pipelines, the Unstructured Information Management Architecture (UIMA) provides a standard means of communication between tools and resources. U-Compare, a text mining workflow construction platform based on UIMA, further enhances interoperability through a shared system of data types, allowing free combination of compliant components into workflows. Although U-Compare and its type system already support syntactic and semantic analyses, support for the analysis of discourse phenomena was previously lacking. In response, we have extended the U-Compare type system with new discourse-level types. We illustrate processing and visualisation of discourse information in U-Compare by providing several new deserialisation components for corpora containing discourse annotations. The new U-Compare is downloadable from http://nactem.ac.uk/ucompare.

Enhancing search: events and their discourse context

Event-based search systems have become of increasing interest. This paper provides an overview of recent advances in event-based text mining, with an emphasis on biomedical text. We focus particularly on the enrichment of events with information relating to their interpretation according to surrounding textual and discourse contexts. We describe our annotation scheme used to capture this information at the event level, report on the corpora that have so far been enriched according to this scheme and provide details of our experiments to recognise this information automatically.

News search using discourse analytics

The vast numbers of digitised documents containing historical data constitute a rich research data repository. However, computational methods and tools available to explore this data are still limited in functionality. Research on historical archives is still largely carried out manually. Text mining technologies offer novel methods to analyse digital content to identify various types of semantic information in these documents and to extract them as semantic metadata. Methods range from the automatic identification of named entities (e.g., people, places, organisations, etc.) to more sophisticated methods to extract information about events (e.g., births, deaths, arrests, etc.), allowing users to greatly increase the specificity of their search. We have created an extended model of event interpretation to allow searches to be refined based on various discourse facets, including isolating definite information about events from more speculative details, distinguishing positive and negative opinions and categorising events according to information source. We present ISHER as an example of a multifaceted, semantically oriented system for searching news articles from the New York Times, dating back to 1987. We explain how our extended event interpretation model can enhance search capabilities in systems such as ISHER, including the identification of contrasting and contradictory information in news articles.

Potentially guided bidirectionalized RRT* for fast optimal path planning in cluttered environments

Abstract Rapidly-exploring Random Tree star (RRT*) has recently gained immense popularity in the motion planning community as it provides a probabilistically complete and asymptotically optimal solution without requiring the complete information of the obstacle space. In spite of all of its advantages, RRT* converges to optimal solution very slowly. Hence to improve the convergence rate, its bidirectional variants were introduced, the Bi-directional RRT* (B-RRT*) and Intelligent Bi-directional RRT* (IB-RRT*). However, as both variants perform pure exploration, they tend to suffer in highly cluttered environments. In order to overcome these limitations we introduce a new concept of potentially guided bidirectional trees in our proposed Potentially Guided Intelligent Bi-directional RRT* (PIB-RRT*) and Potentially Guided Bi-directional RRT* (PB-RRT*). The proposed algorithms greatly improve the convergence rate and have a more efficient memory utilization. Theoretical and experimental evaluation of the proposed algorithms have been made and compared to the latest state of the art motion planning algorithms under different challenging environmental conditions and have proven their remarkable improvement in efficiency and convergence rate.

HRS-CE: A hybrid framework to integrate content embeddings in recommender systems for cold start items

Abstract Recommender systems (RSs) provide the personalized recommendations to users for specific items in a wide range of applications such as e-commerce, media recommendations and social networking applications. Collaborative Filtering (CF) and Content Based (CB) Filtering are two methods which have been employed in implementing the recommender systems. CF suffers from Cold Start (CS) problem where no rating records (Complete Cold Start CSS) or very few records (Incomplete Cold Start ICS) are available for newly coming users and items. The performance of CB methods relies on good feature extraction methods so that the item descriptions can be used to measure items similarity as well as for user profiling. This paper addresses the CS problem by providing a novel way of integrating content embeddings in CF. The proposed algorithm (HRS-CE) generates the user profiles that depict the type of content in which a particular user is interested. The word embedding model (Word2Vec) is used to produce distributed representation of items descriptions. The higher representation for an item description, obtained using content embeddings, are combined with similarity techniques to perform rating predictions. The proposed method is evaluated on two public benchmark datasets (MovieLens 100k and MovieLens 20M). The results demonstrate that the proposed model outperforms the state of the art recommender system models for CS items.